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The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract

Background Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown. Results To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity. Conclusions This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2216-7) contains supplementary material, which is available to authorized users.

Background
The gastrointestinal (GI) tract of vertebrates is colonised by a complex microbial community dominated by bacteria referred to as the gut microbiota. By having a profound influence on vertebrate physiology, metabolism, and immune functions, the gut microbiota plays important roles in the health of the host [1,2]. These associations open avenues for the development of therapies that aim to restore the ecosystem, but their implementation requires a mechanistic understanding about the ecological principles that shape and regulate microbial communities [3,4]. In contrast to microbial symbiosis in invertebrates, little is known about the basic principles that underlie symbiotic interactions in vertebrates and how they evolve [5].
Lactobacillus reuteri, a Gram-positive bacterial species that colonises the gut of a variety of vertebrate species, has been used as a model to determine the ecology and evolution of vertebrate gut symbionts [5]. The ecological strategies of L. reuteri are fundamentally different in humans and animals [6]. In rodents, pigs, chickens and horses, lactobacilli form large populations in proximal regions of the GI tract, and they adhere directly to the stratified squamous epithelium present at these sites [7][8][9]. In mice and rats, adherence occurs in the forestomach [10,11], and this process appears to be important with regards to the ecological fitness of the bacteria [5]. The epithelial associations formed can be considered biofilms as the bacteria are arranged in multiple layers and are encased in a polysaccharide matrix [9,12,13]. In contrast, stratified squamous epithelia are absent in the human gut, and epithelial cell layers rich in lactobacilli equivalent to those found in the above-mentioned animals have not been described [6]. Rather, a more transient colonisation of the human GI tract by L. reuteri is likely to be mediated by mucus-binding adhesins (as discussed below), resulting in a relatively low prevalence in the human population even although this species is still considered to be autochthonous in humans [5,6].
Using a combination of population genetics and comparative genomics, we have recently demonstrated that L. reuteri is composed of host-specific clades with lineagespecific genomic differences that reflect the niche characteristics in the GI tract of the respective hosts. Host adaptation of this species is supported by genetic clustering of strains originating from common or related hosts. Amplified-fragment length polymorphism (AFLP) and multi-locus sequence analysis (MLSA) with more than 100 L. reuteri strains isolated from humans, pigs, rats, mice, chickens and turkeys revealed that considerable genetic heterogeneity exists within the L. reuteri population, with distinct phylogenetic clades that reflect host origin of the strains [14]. Experiments in Lactobacillusfree mice to measure the ecological fitness of strains originating from different hosts supported host adaptation, as only rodent strains colonised mice efficiently [15]. Furthermore the ability of L. reuteri to form epithelial biofilms in the mouse forestomach of mono-associated mice was strictly dependent on the strain's host origin [12].
Genome comparisons of L. reuteri strains originating from different hosts identified lineage-specific genomic content that reflects the niche differences in the GI tract of rodents and humans. The ecological significance of a subset of rodent-specific L. reuteri 100-23 genes was demonstrated in the context of the murine gut [12]. This mutational analysis revealed that genes encoding proteins involved in epithelial adherence, specialised protein transport, cell aggregation, environmental sensing and cell lysis contributed to biofilm formation and colonisation. In particular, the inactivation of a serine-rich repeat protein (SRRP) surface adhesin with a devoted transport system (the SecA2-SecY2 pathway) completely abrogated colonisation of the mouse forestomach, indicating that initial adhesion represented the most significant step in biofilm formation, likely conferring host specificity [12]. Similarly, host-strain specific adhesins have been recently reported in other L. reuteri strains as playing a key role in the interaction of the bacteria with their host. These include the mucus-binding proteins, CmbA from L. reuteri human strains [16,17] and MUB from L. reuteri ATCC 53608, a strain isolated from pig [18][19][20][21].
Comparative genomics of L. reuteri strains also revealed distinct levels of genetic heterogeneity in different phylogenetic lineages. While human L. reuteri strains from the lineage II, F275 (JCM1112 T /DSM20015 T ), ATCC PTA-6475 (MM4-1a), and ATCC PTA-4659 (MM2-3) possess a closed pan-genome with >99.5 % average nucleotide identity (ANI), strains from rodents possessed a larger pan-genome with a variable gene content and an ANI of around 96-97 %, and the majority of the rodent-specific genes detected by comparative genomic hybridisation (CGH) were not conserved among rodent strains [15].
The work described above has established L. reuteri as an excellent model to elucidate mechanisms for host-microbial symbiosis in vertebrates. However, the mechanisms by which L. reuteri strains specifically colonise the porcine GI tract and the evolutionary processes that resulted in host-specific phylogenetic clusters have not been elucidated. Such knowledge is relevant as L. reuteri is one of the most dominant species in the porcine GI tract [22] and pig-derived strains of L. reuteri are used as probiotics to improve pig health and well-being [23][24][25]. Previous MLSA indicated that porcine isolates fall within two distinct phylogenetic groups, clades IV and V, that are to a large degree host-specific, suggesting adaptation and specialisation towards the porcine host [14]. Here we performed a pan-genome analysis of six L. reuteri strains isolated from pigs (four from clade IV and two from clade V) with the goal to gain insight into the molecular basis for colonization of the porcine gut, identify genes marking host-specific adaptations, and determine differences between the two L. reuteri lineages present in pigs. Further comparison with the genomes from human and rodent L. reuteri strains was carried out providing novel insights into the genomic events in L. reuteri that occurred during specialisation to the porcine host.

Results and discussion
Complete genome sequence of the pig L. reuteri strain ATCC 53608 The L. reuteri ATCC 53608 genome was sequenced by 454 pyrosequencing and previously published as a draft assembly [26]. According to previous phylogenetic analyses, the ATCC 53608 strain falls into the pig-specific MLST cluster IV [14] (Table 1). Here the genome was completed and fully assembled as described in Methods to create a model reference backbone for genome comparisons of L. reuteri strains from pig.

Genome organisation
The genome of L. reuteri ATCC 53608 consists of three circular molecules ( Fig. 1 and Table 2), a chromosome of 1943635 bp and two plasmids of 138515 bp (pI) and 9093 bp (pII), respectively. The two plasmids were confirmed to be closed circular molecules by PCR with primer pairs B40/B41 (pI) and sc10-for/sc10-rev (pII) that flanked each single gap. The chromosome has an average GC content of 38.96 % compared with 38.17 % for the small and 35.84 % for the large plasmid. The Oriloc software [27] in combination with the R software package [28] was used to identify the putative oriC and ter regions based on the cumulated 3 rd codon position skews. In the case of the chromosome, the positive peak for the combined skew is located immediately upstream of the dnaA gene and we predict the origin of replication to be located in the AT rich (69.9 % A + T) intergenic region between the rpmH (LRATCC53608_1967) and dnaA (LRATCC53608_0001) genes. Allowing for one mismatch, we detected 10 DnaA boxes (TTRTCCACA) in this stretch of the genome, which were equally distributed between the forward and the reverse strands and we therefore designated the first base pair of dnaA as position 1 of the chromosome. The negative peak of the combined skew, indicating the putative terminus region, is located in LRATCC53608_1036 (position 1008794-1010011). A total of 1880 CDSs were identified on the chromosome, 75.6 % of which were encoded on the leading strand of chromosome replication. This strong leading strand coding preference is a typical value observed in many other Grampositive organisms. Plasmid pI is a megaplasmid which carries a RepA/ParA type replicative system and-like the chromosome-displays strong 3 rd codon position skews. This plasmid carries a total of 160 CDSs, 98.8 % of which are encoded on the leading strand of replication. Besides an incomplete prophage, the plasmid also carries genes encoding enzymes for purine and pyrimidine metabolism (deoxyguanosine kinase, nucleoside deoxyribosyltransferase, thymidine kinase), a nicotinamide mononucleotide transporter, a dnaE and tRNA genes (tRNA-Thr, -Met, -Gly, -Asn, -Trp and -Arg). Though none of these can explain the stable maintenance of this megaplasmid, resulting in a considerable burden on the cell's metabolism, as they are all additional copies of genes that are also present on the chromosome. A toxin-antitoxin system encoded on this plasmid (LRATCC53608_pI137-_pI138) is the most likely explanation for its stability. Plasmid pI also encodes a large number of hypothetical proteins. Plasmid pII carries six CDSs and is potentially mobilisable by means of a predicted relaxase/mobilase. A putative replication protein shares low sequence similarity with replication proteins from other lactobacilli. Interestingly, the completed genome sequence confirmed plasmid isolation data that strain ATCC 53608 lacks the 10251 bp plasmid pLUL631 [EMBL:HF570055] which is present in parental strain 1063 [29] (Additional file 1: Figure S1A) and which encodes resistance to both erythromycin (ermB) and streptogramin A (satG).

Predicted primary metabolism
Based on the genome annotation, L. reuteri ATCC 53608 has very limited amino acid synthesis capabilities. This strain should be able to synthesise serine and glycine de novo from pyruvate using serine dehydratase (EC 4.3.1.17), which catalyses pyruvateserine interconversion. The α and β chains of this  protein are encoded by sdaAA and sdaAB (LRATCC53608_0899 and _0898), respectively. Serine could subsequently be converted to glycine by serine hydroxymethyltransferase encoded by glyA. L. reuteri cannot carry out de novo synthesis of the aspartate family of amino acids as it does not carry a gene for pyruvate carboxylase, however it should be able to synthesise lysine and asparagine from aspartate. The strain also lacks the gene for glutamate synthase but can interconvert glutamate and glutamine and carries a proBAC operon enabling the synthesis of proline from glutamate. Most pathways for vitamin biosynthesis are incomplete (biotin, cobalamine, pantothenate, pyridoxal phosphate, nicotinate and thiamine). Complete pathways were only found for the biosynthesis of folate and possibly riboflavin. L. reuteri ATCC 53608 cannot synthesise lipoic acid, but appears able to produce coenzyme A from pantothenate and NAD + and NADP + from nicotinamide mononucleotide, for whose uptake the genome encodes two transport proteins (LRATCC53608_0249 and LRATCC53608_pI116). Purine and pyrimidine biosynthetic pathways are present in L. reuteri ATCC 53608 and the formation of deoxyribonucleotides is not hampered by oxygen, as the strain possesses an oxygenrequiring class Ib enzyme encoded by nrdE2 and nrdF1 (LRATCC53608_1673 and _1674, respectively) and the necessary auxiliary proteins NrdH and NrdI (LRATCC53608_1672 and LRATCC53608_0276), in addition to oxygen-sensitive class III ribonucleotide reductases encoded by nrdD and nrdG (LRATCC53608_0711 and _0712, respectively). The genes encoding these different ribonucleotide reductases appear organised in two operons (nrdDG and nrdHE2F1), the first gene of which is preceded by one or two NrdR boxes, respectively, that according to the RegPrecise database [30] are typical for Lactobacillaceae, indicating that these genes are regulated by the negative transcriptional regulator NrdR (LRATCC53608_0784).

Horizontal gene transfer (HGT): pseudogenes, alien genes, IS elements and bacteriophages
The genome of L. reuteri ATCC 53608 contains 140 pseudogenes in total, representing around 6.8 % of the total gene number, thus significantly higher than the 1-5 % average figure reported for other bacterial genomes [31]. The Colombo SIGI-HMM software [32] predicts 1.5 % of the total gene content of strain ATCC 53608 to originate from HGT ( Fig. 1). The genome of ATCC 53608 was found to be moderately repetitive, containing 15 different insertion sequence (IS) elements from seven IS element families, particularly of the IS30 family (Additional file 2) contributing a total of 126 genes (including 37 pseudogenes) or 6.2 % of all genes encoded in the genome of L. reuteri ATCC 53608. Using the IS element sequences we tried to identify the insertion sites and in many cases were able to create target site sequence logos using WebLogo 3 [33] on the basis of the direct repeats flanking the IS elements (Additional file 1: Figure S2). The PHAST software [34] identified three extended regions of bacteriophage origin in the genome of L. reuteri ATCC 53608. The first is located on the chromosome (position 650477-661412) and the latter two are located in close vicinity to each other on plasmid I (positions 1-36485 and 43193-57464) ( Fig. 1).
Assembly and chromosomal features of four additional pig strains of L. reuteri We selected four additional L. reuteri strains isolated from pigs for genome sequencing, choosing strains from both pigspecific MLST clades IV (strains lp167-67 and pg-3b) and V (strains 20-2 and 3c6) [14] ( Table 1, which includes their different geographical locations). Based on MLST analysis of seven housekeeping genes, type V strains are located phylogenetically close to, although distinct from, L. reuteri strains of human/avian origin type VI, whereas those from type IV fall between human and rodent isolates of types II and III, respectively [14]. High coverage Illumina data were obtained for these four L. reuteri strains and draft assemblies were generated as described in Methods. Here we assigned taxon data to each separate contig and plotted % GC against the % coverage. During the assembly process, a very low proportion of the reads was assigned to a few contaminating contigs of eukaryotic origin; additionally, in one of the assemblies (namely 20-2), it was possible to discern a related Lactobacillus sequence at a very low coverage, which gave rise to many short contigs that were removed from the final assembly. The length of the final assembly and representation of expected genes is presented in Table 3. Each of the assemblies possessed ≤201 contigs of >100 bp at high coverage with a median contig length of 7676, 5185, 6647 and 5386 bp for pg-3b, 3c6, 20-2 and lp167-67, respectively. The chromosomes of the completed and draft assembly strains showed syntenic conservation as aligned by Mauve [35] and by MUMmer v3.0 [36] with relatively few regions of difference observed (Fig. 2). Each draft genome was compared to the ATCC 53608 genome by measuring the % ANI-lp167-67 (99.6 %), pg-3b (99.2 %), 3c6 (95.2 %) and 20-2 (95.1 %). All their ANI values were >95 %, confirming their identities as members of the same species [37], viz. L. reuteri. The slightly lower ANI values of just over 95 % for strains 3c6 and 20-2 reflected their presence in a separate phylogenetic clade to the others.
The pig L. reuteri pan-genome The complete ATCC 53608 genome was used as a model reference backbone to compare the assemblies of the additional four draft genomes of L. reuteri from pigs (lp167-67, pg-3b, 20-2 and 3c6). In addition, the recently completed genome of another pig L. reuteri strain, I5007 (isolated from the colonic mucosa of a weaning piglet in China) [38], was included in genome comparisons. The combination of these six strains was referred to as the pig L. reuteri pan-genome.

Analysis of the pig chromosomal core and accessory genomes
The backbone genetic information is defined as the genetic information common to all strains tested, which is also referred to as the 'core genome' and in this case represents genes present in all of the above L. reuteri strains isolated from pig. The core set from these six genomes contained 1364 orthologous gene clusters as determined by OrthoMCL analysis [39] and 1210 gene clusters, comprising 1652 "unique" genes that occurred at least once in individual genomes-the difference between the latter two values being due to the presence of at least two gene copies in some genomes. Another 799 gene clusters were shared by at least two genomes, giving a total of 3373 orthologous gene clusters in the current pig strain pan-genome ( Fig. 3 and Additional file 1: Figure S3A). Very short predicted genes (<150 bp) were excluded from the analysis. Genes variable among pig strains make up the accessory genome. These regions were parsed from the pig isolates at the DNA level using the Panseq program [40]. A successive round of bioinformatic purification of DNA sequence from the output of the Panseq pipeline was carried out using MUMmer [36] to further refine the data. The accessory regions were annotated separately and viewed functionally as a pie chart (Fig. 4). Compared to the functions of the whole genomes, these regions are rich in genes encoding cell wall-associated proteins, capsule/exopolysaccharide (EPS) biosynthetic enzymes, phage-related functions, mobile elements and DNA metabolic enzymes, whilst being low in essential metabolism genes. This is similar to the situation with rodent strains of L. reuteri where MLST Strain Fig. 2 Genome conservation in the six pig strains of L. reuteri. From top to bottom, the Mauve-alignment backbone of the draft genome sequences is shown as follows: I5007, ATCC 53608, lp167-67, pg-3b, 20-2 and 3c6. Blocks of sequence conservation are denoted by burgundy lines, whilst blocks as calculated by Mauve are shown in alternating colours many cell surface proteins, proteins involved in surface polysaccharide biosynthesis and prophages fall within the accessory genome [15]. The six genome sequences from porcine origin were examined further for the presence of clustered regularly interspaced short palindromic repeats (CRISPRs) against the CRISPRdb database [41] using the CRISPRFinder tool [42] and any such sequences compared using the CRISPRcompar website [43]. However, although questionable CRISPRs were identified for all genomes, no confirmed CRISPRs were uncovered by this analysis. Questionable CRISPRs include small CRISPRs of two to three direct repeats and structures where the repeats are not 100 % identical. In the ATCC 53608 finished genome, questionable CRISPRs were located at 893116-893231 bp and comprised a set of two virtually identical direct repeats. An almost identical situation occurs at 868686-868801 bp in strain I5007. However, no CRISPR-associated (cas) gene hits were uncovered upstream or downstream of that region in either ATCC 53608 or I5007, which is located directly downstream from the accessory secretion system, a genetic region likely acquired by HGT.

Analysis of plasmids in porcine L. reuteri strains
The putative plasmid DNA sequences of the four pig draft genomes were aligned to plasmid sequences of pI and pII from L. reuteri ATCC 53608, the sequence of plasmid pLUL631 from parental strain 1063 and the six plasmid sequences from strain I5007 and compared. This method was used to extract potential plasmid sequences as contigs from the total assembly of the four strains. Without exception, all of the contigs extracted from each of the strains were present within the respective accessory regions that had been identified previously in comparison to strain ATCC 53608. Efforts to compare the gene annotations from the L. reuteri ATCC 53608 plasmids to those of the newly identified sequences were unsuccessful, in line with the lack of DNA sequence alignment, and supporting the findings that the plasmid DNA is heterogeneous and relatively unrelated in each of these strains. Further comparisons of the plasmids of ATCC 53608 with those from the other L. reuteri pig strains did not indicate large conservation amongst the plasmids of this species. Rather the plasmids appear isolate-dependent, which correlates with the results of plasmid isolation from these strains (Additional file 1: Figure S1B).
Comparative genomics of L. reuteri genomes from different host origin In order to gain insights into the subset of genes involved in adaptation to the porcine gut, we performed a Fig. 3 Pan-genome of the six pig L. reuteri strains. Each genome is represented by a coloured oval. The number in the centre represents the core gene set shared among the six pig strain genomes expressed as orthologous gene clusters per genome. The numbers of genes unique to each genome are indicated by the outer values. In addition, 799 orthologous gene clusters were shared by at least two genomes, contributing to a current pig strain pan-genome of 3373 orthologous gene clusters. Short genes (<150 bp) were excluded from the analysis genomes was used in the analysis, whereby JCM1112 T and DSM20016 T were considered as a single genome (that of JCM1112 T ) since these two strains are derived from the same isolate (F275). The core set of these 19 genomes contained 851 orthologous gene clusters by OrthoMCL [39] analysis, while there were 1890 gene clusters, comprising 3479 "unique" genes that occurred at least once in individual genomesthe difference between the latter two values again being due to the presence of at least two gene copies in some genomes. Another 2484 gene clusters were shared by at least two genomes, giving a total L. reuteri pan-genome of 5225 orthologous gene clusters (Additional file 1: Figures S3B and S4). A circular comparison of the genomes of the six strains isolated from pig with genomes from a selection of seven other L. reuteri strains from human and rodent is shown in Additional file 1: Figure S5. Homologous genes were calculated using L. reuteri ATCC 53608 as the reference strain by reciprocal best match analysis requiring a 40 % match by FASTA searches over 80 % of the target protein length. This required the target protein to be predicted almost in entirety using current gene prediction software Prodigal [44] and Glim-mer3 [45]. With this method, unpredicted proteins, either due to unusual base composition or to fragmentation at the contig level, would lead to a negative result. Using protein sequences derived from the genomic data, three additional analyses (see Methods) using the Joint Genome Institute's Integrated Microbial Genomes (IMG/ER) Phylogenetic Profiler tool [46], reciprocal FASTA with the annotation software Artemis [47,48], and OrthoMCL [39] all indicated that there were no genes conserved in all six pig-derived genomes that were absent in the genomes of L. reuteri strains from other hosts. Therefore our analyses showed that there are no pigspecific genes.
Previous MLSA revealed that pig isolates fall into two distinct clades [14]. A phylogeny based on the core genes of 20 strains of L. reuteri (Fig. 5) confirmed the phylogenetic clusters and their membership. Clade IV contains strains I5007, ATCC 53608, lp167-67 and pg-3b, and is more closely related to the rodent cluster III, while clade V, which is more closely related to human/poultry strains of clade VI, contains strains 20-2 and 3c6. As reported previously [14], the geographical origin of the strains was not related to the phylogenetic clades since L. reuteri strain I5007 was isolated in China [38] but found as a close relative of ATCC 53608 (parental strain designated 1063), isolated in Sweden [49]. These findings indicate that the co-evolution of L. reuteri with pigs has resulted in the formation of two vastly distinct phylogenetic clusters, which suggests that evolution of these two populations, although driven by the porcine host (thus the confinement of the clusters to pig isolates), was subjected to different selective pressures that led to their separation. The distinct evolutionary trajectories could also have resulted in the absence of common genes that reflect host adaptation among porcine strains. The relatedness of pig clade IV with rodent clade III strains, and of pig clade V with human/poultry clade VI strains may reflect their evolution from ancestral strains of rodent and human origin, respectively, following contact with pig populations.
To gain insight into this diversification process, we identified genes that were specific to the two individual clades, and conserved among the strains. This analysis revealed 10 lineage IV-specific genes encoding proteins >60 amino acids. Among these genes was one (LRATCC53608_0212) encoding a surface protein of 1166 amino acids in length that contained five mucus-binding (MucBP) domains (Table 4). In addition, cluster IV strains contained three linked genes (LRATCC53608_0113-_0115) encoding a TetR family transcriptional regulator, a conserved hypothetical protein with a DHS-like NAD/FAD-  binding domain and an NAD-dependent protein deacetylase of the SIR2 family whose functions are as yet unknown. The two clade IV-specific esterase-lipases (LRATCC53608_0604 and _0605) could be involved in the utilization of lipids in the pig's diet but on closer examination appeared to be two parts of the same pseudogene. An interesting feature of the clade-IV-specific genes was that they had very high levels of homology (>99 % aa identity) among the four different strains, which supports that they are highly conserved among porcine isolates of this clade. Of the 22 genes encoding proteins >60 amino acids that were specific to pig cluster V (Table 4), several represented mobile genetic elements, including transposons and phage-related sequences. However, four lineagespecific surface proteins were detected, three of which contained a SEC10/PgrA surface exclusion domain, found in Gram-positive adhesins such as SpyAD from Group A Streptococci and implicated in cell adhesion [50]. Two of these SEC10/PgrA proteins (homologues of LR202_01429 and _02163) also contained a Rib/alpha-like repeat from the Rib adhesin of Group B Streptococci [51]. Two genes encoding glycosyltransferases (predicted to be involved in biosynthesis of surface carbohydrates or protein glycosylation) were also identified. In addition, a putative copper oxidase and a magnesium-transporting ATPase were detected, suggesting interactions of this L. reuteri lineage with metal ions. Several hypothetical proteins were found with high homology among the two strains. Interestingly, one of these proteins (LR202_00788) showed 97 % aa identity to a protein from Lactobacillus amylovorus, which is indicative of HGT from another dominant member of the pig microbiota [22], suggesting an important function in the pig gut.
Previous pan-genome analysis of L. reuteri rodent and human strains revealed that the pdu-cbi-cob-hem cluster was conserved within human strains, and the cluster was absent in most rodent strains [5,15]. This cluster codes for cobalamin (vitamin B12) biosynthesis, glycerol utilization, propanediol fermentation and production of the antimicrobial compound reuterin [5,52]. The genetic region encompassing the reuterin and vitamin B12 biosynthetic pathways is located at 293889-338218 bp on porcine reference isolate L. reuteri ATCC 53608. As in rodent strains, it appears that this pdu-cbi-cob-hem genomic island is present only in a subset of porcine strains, confirming previous findings [5,15]. Out of the four strains from clade IV, only ATCC 53608 and lp167-67 possess this genomic island, while it is present in both clade V strains 20-2 and 3c6 studied ─ although this island is not conserved in other members of pig clade V [5,15]. Thus it appears that the possession of the reuterin genomic island does not correlate directly with the relationship of the genetic backbone. As with the rat isolate 100-23, there is evidence that the cluster has been deleted from the genome of pig isolate I5007 through the action of mobile elements.

Molecular determinants of host recognition
In order to gain further insight into the molecular determinants of host-strain specificity, we focused on the genomic analysis of the major cell surface components that have been implicated in the interaction of L. reuteri strains with the host in vivo.
Here, a total of 41 surface protein-encoding genes and three conserved pseudogenes were predicted from the completed genome of strain ATCC 53608 (Additional file 3). Potential homologues were identified in the other pig strains from the annotation and sequence read data from the draft assemblies by alignment to ATCC 53608 using Bowtie 2 [55] and checked separately by Burrows-Wheeler Aligner software, BWA [56]. Using BEDTools [57], the percentage of each protein coding sequence covered was determined in the four pig strain draft genomes and results are displayed in a heatmap (Additional file 1: Figure S6) with the characteristics of the proteins. Many of these surface proteins are predicted to be involved in epithelial adhesion and biofilm formation. MUB was found only in strain ATCC 53608 but a few other MucBP (Pfam PF06458) domain-containing proteins were identified, some as conserved pseudogenes, and two were found to be pig clade IV-specific (homologues of LRATCC53608_0212 and LRATCC53608_0767-_0769). Other putative surface proteins found only in ATCC 53608 were LRATCC53608_0656, _0662 and _0644 although the significance of these is unknown. Several proteins with one or more lysin motif (LysM/CBM50), a domain involved in peptidoglycan binding [58], were present in all five pig strains analysed, including homologues of LRATCC53608_1570, which are identical to Lr_71416 from rodent strain 100-23. LysM-containing proteins Lr_71416 and Lr_70152 are putative aggregation promoting factor proteins that have been implicated in biofilm formation and colonisation of strain 100-23 in mice [12], suggesting a similar role in the pig host. In the heatmap of Additional file 1: Figure S6, there is therefore a clear difference between the two representatives of clade IV, pg-3b and lp167-67, and the two representatives of clade V, 20-2 and 3c6, with respect to the presence or absence of certain surface proteins. On the other hand, the other member of clade IV that was used as the reference strain, ATCC 53608, possessed additional surface proteins not found in strains pg-3b and lp167-67.
One interesting putative surface protein, not included in the above analysis because of its lack of a consensus secretion signal, was the DUF1542 repeat-containing protein encoded by LRATCC53608_1774 and its homologues in pig clade IV and in three sourdough strains (Additional file 4). Although a putative pseudogene in these strains, it may still be translated as a protein ranging in size from about 880-2400 aa and exported by a non-classical secretion pathway (with a SecretomeP NNscore >0.5; [59]). DUF1542 repeats are found in many Gram-positive cell surface adhesins, such as MabA, a modulator of adhesion and biofilm formation, from Lactobacillus rhamnosus GG [60]. Homologues of this protein were not found in the two pig clade V strains and were also absent in all human strains but functional counterparts with a typical secretion signal were present in all rodent strains and one sourdough strain (Additional file 4). The significance of this DUF1542 repeat-containing surface protein in L. reuteri is as yet unknown but it appears to be conserved phylogenetically as either putative pseudogenes or functional genes in different host-derived strains.

The accessory SecA2-SecY2 secretion system
In streptococci and staphylococci, the accessory SecA2-SecY2 system facilitates the selective export of glycosylated serine-rich repeat proteins (SRRPs) that often function as adhesins such as GspB, Fap1 and SraP [61][62][63]. This auxiliary protein secretion system is present in a limited number of Gram-positive bacteria and mycobacteria and other members of the Class Bacilli [64]; its sparse distribution among different species of lactobacilli implies that this system was horizontally acquired by only a few Lactobacillus lineages. In the L. reuteri rodent strain 100-23, an SRRP (Lr_70902) was identified as the only protein secreted by SecA2-SecY2 and shown to be essential for the formation of biofilm in germ-free mice [12]. The gene content within the accessory Sec cluster is conserved in L. reuteri ATCC 53608 when compared with that of rat strain 100-23 (Additional file 1: Figure S7). Furthermore, the SecA2-SecY2 cluster is also conserved in the other five pig strains (Fig. 6). It is of note that on the phylogenetic tree of Fig. 6, the SecA2-SecY2 clusters of ATCC 53608 and of I5007 fell between those of clade V strains 20-2 and 3c6 and the other clade IV strains pg-3b and lp167-67, with which ATCC 53608 and I5007 share the most backbone genetic material. This may indicate that the SecA2-SecY2 region of ATCC 53608 has undergone HGT from clade IV or that some amount of Fig. 6 Phylogeny and BLAST comparisons of SecA2-SecY2 regions from the six pig strains of L. reuteri. For the four draft genomes of lp167-67, pg-3b, 20-2 and 3c6, the differently coloured gene bars represent separate contigs that were brought together after alignment to the completed reference ATCC 53608 genome using MUMmer. Genome comparisons are shown as BLAST matches, with the darker bars being of higher match. The phylogenetic tree was generated from the sequences only of the SecA2-SecY2 regions introgression is underway. HGT of the SecA2-SecY2 cluster in L. reuteri pig strains is supported by the presence of mobile genetic elements within the cluster of ATCC 53608 (LRATCC53608_0918-0921), a low GC content and by results from the analysis with Alien_ hunter [65,66] confirming that this region is likely to have been acquired by HGT, although it cannot be excluded that the presence of mobile elements is a prelude to deletion or modification of the cluster. By analogy to the 100-23 SRRP and to SRRPs from other bacteria, the SRRP homologue in ATCC 53608 (LRATCC53608_0906) and the other pig strains is likely to be secreted through this accessory pathway and indeed, this protein is found in extracellular extracts of ATCC 53608 (D. Latousakis and D. Kavanaugh, IFR, Norwich, UK, personal communication). LRATCC53608_0906, like Lr_70902 from 100-23, is unusually serine rich (25.2 and 36.1 % serine, respectively) and contains 11 of the predominant 10-amino acid repeat SLSNSVSMSE, compared with 91 such repeats in Lr_70902. However, each SRRP from the pig and rodent strains differs with respect to the number and sequences of their serine-rich repeats (Additional file 5). Comparing these repeat sequences, the SRRPs from clade IV strains ATCC 53608, lp167-67 and I5007 are more similar, while that from the other clade IV strain, pg-3b, is more like the SRRP from clade V strain 20-2. The serine residues of the SRRPs are likely to be glycosylated by glycosyltransferases associated with the SecA2-SecY2 cluster (LRATCC53608_0913 and LRATCC53608_0914).
No other functional large surface proteins are linked to the SecA2-SecY2 cluster in these pig strains, except for two LPXTG-containing pseudogenes that flank the cluster at either end (e.g. in strain ATCC 53608, LRATCC53608_ 0902-_0904 and LRATCC53608_0916-_0917). LRATCC 53608_0902-_0904 is a MucBP-containing LPXTG pseudogene whereas LRATCC53608_0916-_0917 is an SRRP pseudogene that possibly arose from gene duplication of the functional SRRP, LRATCC53608_0906. In the completed genome of strain I5007 the SRRP itself is a pseudogene (LRI_0846-_0848) but not annotated as such (Fig. 6). Interestingly, this strain possesses a homologue (LRI_1680) of the CmbA (Lar_0958) mucusbinding protein that is found in many human isolates of L. reuteri [16,17] but is absent in other pig strains. Also of interest, the MucBP-LPXTG pseudogenes from the pig strains have intact homologues in rodent and sourdough isolates of L. reuteri, suggesting their loss of function during evolution in the pig host (Additional file 6). The SRRPs showed high sequence conservation among pig strains, particularly in the N-terminal putative binding region (87-96 % aa identity; Additional file 5). Homology between the N-terminal domains of SRRPs from pig and rodent strains was lower (~50 % aa identity), suggesting that they may share a common structure but bind to different target ligands in their respective hosts. As expected, the pseudo-SRRPs showed more sequence diversity and were only about 30-40 % identical at the amino acid level to their respective functional counterparts (Additional file 7). Conservation of the SRRPs and SecA2-SecY2 cluster in all six L. reuteri strains from pig MLSA lineages IV and V (this work) and in most strains from rodents (MLSA lineages I and III) but not in isolates from human and poultry hosts (MLSA lineages II and VI) may explain host-specific differences in L. reuteri biofilm formation [12].
The EPS cluster L. reuteri strains can produce EPS in several forms depending on the strain -levan (a β-2,6-linked fructan polymer) catalysed by the enzyme levansucrase (Lev, also known as fructosyltransferase, Ftf ), inulin (β-2,1-linked fructooligosaccharides, FOSs, of varying chain length) catalysed by the enzyme inulosucrase (Inu) [13,67,68] and reuteran (a complex, branched 1-4, 1-6-α-D-glucan polymer) catalysed by glucosyltransferases (Gtf 's) GtfA or GtfO [69][70][71]. Ftf and Inu share 86 % aa similarity and are therefore difficult to distinguish at the sequence level. Some L. reuteri strains possess both types of enzyme but others have only one. Mutation of the single ftf gene in rodent strain 100-23 resulted in loss of EPS production and although the ftf mutant was able to colonise the murine GI tract of Lactobacillus-free mice in the absence of competition, colonisation was impaired in competition with the wild type, indicating a role in host interaction [72]. Genomic analyses of L. reuteri ATCC 53608 and the other five pig strains identified Ftf/Inu homologues in all six strains with approximately 80 % similarity at the protein level to that from rat strain 100-23 (LRATCC53608_1011, LRI_0973, LRLP167_01956, LR202_00872, LR3C6_01749 and LRPG3B_01561), suggesting that the ftf/inu gene was acquired by HGT early in the evolution of the species and subsequently diversified at accelerated rates. Homologues of Ftf/Inu are also present in human isolates of L. reuteri, ATCC 55730 [SD2112] and CF48-3a1. Recently, a cluster of more than 25 genes, including several encoding Gtf's, that may contribute to EPS synthesis and is similarly organised compared to EPSrelated genes described in other Lactobacillus strains, including L. rhamnosus GG [73], was reported in the L. reuteri human strain ATCC 55730 [SD2112] [74]. Although the start of this operon was similar in the human strain ATCC PTA-6475 [MM4-1a], the presence of an insertional element in strain ATCC PTA-6475 [MM4-1a] after the first 12 genes indicated that genomic rearrangements and gene loss had occurred [74]. Regions relating to these putative EPS gene clusters were found in the accessory genomes of the six pig strains (Fig. 7). Despite the close phylogenetic relationships between strains of the ATCC 53608 clade, the predicted EPS gene clusters showed poor conservation, with only the EpsA, C and D encoding genes strictly conserved, suggesting large-scale EPS gene cluster differences at the isolate level between these strains. This is in accordance with the EPS cluster in rodent L. reuteri strains, where the two EPS gene clusters show high variability [15]. Like the rodent strains, all six pig strains also possessed a second cluster of genes unlinked to the putative EPS cluster in Fig. 7-LRATCC53608_0648-_ 0660, LRI_0601-_0628, LR3C6_00497-_00506, LR202_ 01632-_01617, LRLP167_00566-_00570 and LRPG3B_ 01609-_01605four of which included a second EpsCencoding gene and were therefore capable of producing other extracellular polysaccharides.
The glucansucrase/reuteransucrase GtfA responsible for reuteran biosynthesis was originally described in probiotic strain 121 [69] and an NCBI BLASTp analysis revealed the presence of homologues in sourdough strains TMW1.106 and TMW1.656 with 93 % aa identity to GtfA. The homologous GtfO [71] from human probiotic strains CF48-3a1 and ATCC 55730 [SD2112] are 68 % identical to GtfA. Other L. reuteri homologues Gtf180 and GtfML1 with 78-79 % aa identity to GtfA have been described in probiotic strain 180 and mouse strain ML1, synthesising α-1,6-linked dextran and α-1,3-linked mutan, respectively [71]. Interestingly, no homologues with significant (>40 %) aa identity to the above-mentioned four Gtf's over the entire protein length were found in pig isolates ATCC 53608, 3c6 and 20-2. However, homologues from the other pig strains I5007, pg-3b and lp167-67 (LRI_0915, LRPG3B_00275 and LRLP167_01392, respectively) had 95-99 % aa identity to Gtf180, suggesting that these three clade IV strains most likely synthesise an α-1,6-linked dextran-type polymer. Like the ftf and inu genes, the gtf180 homologues are unlinked to the putative EPS clusters displayed in Fig. 7, indicating that the latter are involved in the biosynthesis of other types of EPS. Thus, the ability of different strains to produce distinct types of EPS in the extracellular matrix in the host's GIT may be a contributing factor in determining host specificity.

Conclusions
This comparative genomics study provides novel insights into the ecology and evolution of the species L. reuteri A B C D E F Fig. 7 Predicted EPS gene clusters in the six L. reuteri pig strains. a, pg-3b, b, lp167-67, c, 3c6, d, 20-2, e, ATCC 53608 and f, I5007. Colour scheme: yellow, Gtf; green, other protein involved in polysaccharide biosynthesis; blue, membrane protein; orange, hypothetical protein; pink, transposase/ mobile element protein; brown, pseudogene; red, RNA polymerase σ subunit with the porcine host. Together with previous phylogenetic analyses based on a small set of housekeeping genes, the genomic analysis highlights two divergent clades within L. reuteri pig strains that can be differentiated from other L. reuteri lineages. Although no genes were identified that were conserved among all pig isolates and specific to this host, we identified genes specific for and conserved among strains from the two pig phylogenetic lineages IV and V, with high rates of homology among strains. The two populations of porcine L. reuteri appear to have evolved separately, through a process driven by distinct selective pressures, e.g. different pig host genotypes or environmental factors such as dietary components, which resulted in the absence of common pigspecific genes among these two populations. However, from the phylogenetic analysis, the closeness of rodent clade III with pig clade IV strains, and of human clade VI with pig clade V strains could reflect an evolution of ancestral strains following contact of rodents and humans, respectively, with pig populations. The identification of several surface proteins, some with mucus-binding MucBP domains or other repeated domains found associated with adhesins, as being pig clade-specific might contribute to host-specificity, and ultimately to the clustering of strains away from other L. reuteri lineages. Clearly, these genes provide a basis for future functional studies on the ecology of L. reuteri in the pig GIT.

Strains
The origins of the L. reuteri strains used in this study are listed in Table 1.
Genome sequencing, assembly and annotation Complete genome sequence of the pig L. reuteri strain ATCC 53608 For the initial draft assembly [26] L. reuteri DNA had been used to generate in excess of 365 Mbp of sequence from a combination of shotgun and 3-kbp paired-end libraries (220 Mbp and 145 Mbp, respectively) on the 454 GS FLX sequencer (Roche) using the Titanium Chemistry. Reads passing the default filter settings had been assembled using gsAssembly V2.3 software (Roche) and had generated 13 scaffolds containing 99 large contigs (>500 bp) and spanning 1.96 Mbp of sequence. Standard PCR followed by primer walk sequencing on the resulting products was used to close the gaps located in scaffolds. Multiplex PCR was employed to identify adjoining contigs and respective primer pairs for which no linkage had been established previously and upon re-amplification under standard conditions the resulting products were analysed by primer walk sequencing. The sequence assembly was carried out using the Phred/Phrap [75] software in conjunction with the Staden package [76] and the expected error rate is around 1/500000 bp.

Bioinformatics analyses of ATCC 53608 genome
The finished L. reuteri ATCC 53608 sequence was annotated using the GenDB 2.4 annotation tool [77]. Proteincoding ORF sequences (CDS) were determined using Prodigal [44]. tRNA genes were identified with tRNAscan-SE [78]. An automatic functional annotation was computed in GenDB (CeBiTec) based on different analyses, and in addition, results from an automated RAST (Rapid Annotation using Subsystem Technology) [79] annotation were imported into the GenDB environment. The combined information available was employed for the manual annotation of each predicted gene. Pseudogenes were identified through a comparison of predicted gene products with respective proteins in the non-redundant peptide sequence database. Similarity searches [80] were performed against different databases, including the nonredundant and the Refseq protein [81] databases provided by National Centre for Biotechnology Information (NCBI), SWISS-PROT and TrEMBL [82], KEGG [83], Pfam [84] and TIGRFAM [85]. Additionally, SignalP [86,87], PRED-LIPO [88,89], LipoP [90][91][92], an additional lipoprotein pattern search [93] and TMHMM [94,95] were applied to detect potential secretion signals, lipoproteins and transmembrane helical domains, respectively. Predicted ORF sequences were manually reviewed and alterations were made on the basis of the presence of potential ribosomal binding sites, sequence alignments and available literature data. Putative carbohydrate-active enzymes were identified with the methods used for the daily updates of the CAZy database [96,97].
Sequencing of four draft genomes of L. reuteri strains isolated from pigs DNA was extracted using the method of [14], purified further after treatment with DNase-free RNase to remove RNA and supplied to The Genome Analysis Centre (TGAC) for Illumina sequencing using the GAII platform. Paired-end sequencing was carried out using approximately 500-600 bp insert libraries. Between 45.6-50.7 × 10 6 reads were collected for each sample, respectively, corresponding to a depth of coverage of approximately × 1800. Three alternative assemblies were created, set 1 was carried out using the Abyss assembler at TGAC, set 2 was created by Genostar, Montbonnot, France and set 3, from SequenceAnalysis.co.uk, Norwich, UK, corresponded to the second assembly with contaminating contigs of low coverage removed. Sequences from the Illumina marker phage, PhiX174, were detected in the draft assemblies and excluded from the final assembly. Annotation was built from a set of three inputs, a Genostar-based annotation platform, input from the RAST annotation program [79], Prokka rapid annotation [98] and with additional annotation from SequenceAnalysis.co.uk. Gene numbers were created for each strain with an included qualifier to link the gene numbering for conserved genes to that of L. reuteri ATCC 53608.
Bioinformatics analyses of completed and draft L. reuteri genomes Calculating the % average nucleotide identity (ANI) The completed genome of strain ATCC 53608 was compared individually with each of the draft genomes of strains lp167-67, pg-3b, 3c6 and 20-2. ANIs were calculated using JSpecies [99].
Determining the two sets of pig clade-specific genes Genes specific to the porcine phylogenetic lineages IV and V were identified using the Phylogenetic Profiler tool (which is based on pre-computed similarities between genes) implemented in the Integrated Microbial Genomes (IMG/ER) system of the Joint Genome Institute [46]. All 20 available completed and draft genomes of L. reuteri were included in the analysis, and genes were identified that had homologues in all strains from lineage IV or V, respectively, but not in strains from all other lineages, using a minimum percent identify of 50 % and a maximum E-value of 1e-5 (with the exclusion of pseudogenes).
In addition to the above analysis, a full reciprocal FASTA analysis was carried out and examined in the genome browser Artemis [47,48]. A cut-off of 30 % identity over 80 % of the protein length was used. As a third alternative analysis to the above, all of the orthologous gene clusters were computed with OrthoMCL [39] default parameters and examined separately using the MySQL [100] database method and the GET_HOMOLOGUES programme [101].


s2fieldsofstudy: Biology Medicine

text:
The nutritional composition and anti-obesity effects of an herbal mixed extract containing Allium fistulosum and Viola mandshurica in high-fat-diet-induced obese mice

Background In traditional oriental medicine, A. fistulosum and V. mandshurica are considered to be effective in promoting blood circulation. Therefore, in this study, we investigated whether a solution containing both A. fistulosum and V. mandshurica (AFE + VME) extracts has synergistic effects on the treatment of hyperlipidemia and obesity. Methods Anti-obesity effects of an herbal extract containing Allium fistulosum and Viola mandshurica (AFE + VME) were investigated in high-fat diet (HFD)-induced obese mice. AFE + VME was orally administrated to mice with the HFD at a dose of 200 mg/kg/day for 8 weeks. We observed the effects of mixed extract on body weight, fat mass, serum lipid levels, and mRNA expression levels of lipid metabolism-related genes in the adipose tissue of mice. Results The nutritional analysis revealed that this mixed extract is high in carbohydrate (72.2 g/100 g) and protein (11.5 g/100 g); low in fat (1.7 g/100 g); rich in vitamins E (4.8 mg/100 g), B1 (14.8 mg/100 g), B2 (1.0 mg/100 g), niacin (7.9 mg/100 g), and folic acid (1.57 mg/100 g); and rich in minerals such as calcium (600 mg/100 g), iron (106.1 mg/100 g), and zinc (5.8 mg/100 g). The oral administration of AFE + VME in obese mice reduced body weight, tissue weight, adipocyte size, and lipid accumulation in the liver compared with HFD control mice. AFE + VME also decreased serum triglyceride, total cholesterol, and leptin concentrations. Furthermore, AFE + VME markedly increased the mRNA expression of peroxisome proliferator-activated receptor-γ (PPAR-γ), uncoupling protein-2 (UCP-2), and adiponectin and decreased leptin expression in the epididymal white adipose tissue. Our results suggest that the extract containing A. fistulosum and V. mandshurica improved lipid metabolism via the up-regulation of PPAR-γ, UCP-2, and adiponectin expression and the down-regulation of leptin in HFD-induced obese mice. Conclusions Therefore, the extract containing Allium fistulosum and Viola mandshurica may be a potentially effective therapy for obesity and its related metabolic disorders such as hyperlipidemia and insulin resistance.

Background
Allium fistulosum (commonly known as welsh onion or scallions), a perennial plant in the Alliaceae family, is used as a major flavoring agent in Chinese, Japanese, and Korean cuisine. A. fistulosum also has been traditionally used to treat common colds, headache, abdominal pain, and cardiovascular disease [1]. Several studies have indicated that A. fistulosum has anti-platelet, antioxidative, anti-hypertensive, and anti-hyperlipidemic properties [2][3][4]. Viola mandshurica (Commonly known as violet), a perennial herb in the Violaceae family, is a traditional herbal medicine with expectorant, diuretic, and anti-inflammatory effects [5]. It also has been reported that V. mandshurica has anti-oxidative and anti-diabetic effects [6]. In traditional oriental medicine, A. fistulosum and V. mandshurica also are considered to be effective in promoting blood circulation [7,8].
Obesity is a serious public health issue and plays a critical role in the pathogenesis of hypertension, dyslipidemia, diabetes mellitus, stroke, osteoarthritis, coronary heart disease, certain types of cancer (e.g., colon, breast, gall bladder), and impaired fertility [9]. Due to the potentially hazardous side effects of the anti-obesity drugs such as orlistat and sibutramine that are currently on the market, a wide variety of natural products to treat obesity are under exploration. These products, which include crude extracts and isolated compounds from plants, may be safe and effective alternative strategies for treating obesity in the future [10]. A previous study from our group showed that A. fistulosum extract suppressed the increase in body weight, fat mass, and lipid levels in high-fat-diet (HFD)-induced obese mice via the downregulation of obesity-related lipogenic genes [11]. Another study from our group showed that V. mandshurica extract and its primary constituent, esculetin, inhibited adipocyte differentiation in 3 T3-L1 cells, and suppressed body weight, lipogenesis, and epididymal fat accumulation via the activation of AMP-activated protein kinase in HFD-induced obese mice [12]. These observations indicate that A. fistulosum and V. mandshurica extracts may be a good candidate for the control of obesity and hyperlipidemia [11,12]. The combination of various herbal extracts may synergistically increase or decrease the activity or toxicity of drugs [13]. Therefore, in this study, we investigated whether a solution containing both A. fistulosum and V. mandshurica (AFE + VME) extracts has synergistic effects on the treatment of hyperlipidemia and obesity in HFD-induced obese mice.

Extract preparation
A. fistulosum and V. mandshurica were purchased from Jeongdo Medicinal Herb Co. (Guri, Korea) and authenticated based on their microscopic and macroscopic characteristics by the Classification and Identification Committee of the Korea Institute of Oriental Medicine (KIOM). A mixed extract (200 g) was prepared with a 1:1 ratio of A. fistulosum (100 g) and V. mandshurica (100 g). The mixing ratio of extract was based on the dosage ratios from previous in vitro and in vivo studies. The A. fistulosum (200 g), V. mandshurica (200 g), and mixed herbs (200 g) were boiled in distilled water at 100°C for 2 h. The extracts then were filtered, lyophilized, and subsequently stored at −20°C. The yield of the dried extracts from A. fistulosum and V. manshurica was 11.25 % (w/w) and 15 % (w/w), respectively. The yield of the mixed extract was 11. 25 % (w/w).

Nutritional content
One hundred grams sample of the mixed extract (AFE + VME) containing A. fistulosum and V. mandshurica was analyzed for nutritional components by the Jeonnam Biofood Technology Center (Jeonnam, Korea). The extract was analyzed for carbohydrate, protein, fat, cholesterol, vitamins, and minerals. All tests performed were in compliance with the standards recommended by the Association of Analytical Communities/ Association of Official Agricultural Chemist (AOAC) and American Association of Cereal Chemists (AACC). The cholesterol and vitamin levels were measured using highperformance liquid chromatography (HPLC 1200 series, Alltech, USA) and the mineral contents were assessed using inductively coupled plasma optical emission spectrometry (ICP-MS XSERIES2, Thermo, USA).

Animals and diets
Eight-week-old male C57BL/6 J mice were purchased from The Jackson Laboratory (Bar Harbor, ME, USA) and housed in an air-conditioned room at a temperature of 21 ± 2°C and humidity of 50 ± 5 % under a 12:12 light:dark cycle. The mice were fed a commercial diet and water ad libitum for 1 week. Mice then were fed a high-fat diet (Rodent Diet D12492, Research Diet, New Brunswick, NJ, USA) consisting of 60 % fat, 20 % protein, and 20 % carbohydrate, to induce obesity. Normal control mice were provided a commercial standard diet (AIN-76A, Research Diet, New Brunswick, NJ, USA) consisting of 11.5 % fat, 20.8 % protein, and 67.7 % carbohydrate. Diets were purchased from Orient Bio Inc. (Seongnam, Korea).
The mice were randomly divided into five groups and each of the five groups included 5 mice. The mice were respectively fed a normal diet (ND), a high-fat diet (HFD), a high-fat diet plus A. fistulosum extract (AFE), a high-fat diet plus V. mandshurica extract (VME), and a high-fat diet plus a 1:1 ratio mixed extract of A. fistulosum and V. mandshurica (AFE + VME) for 8 weeks. AFE, VME, and the mixed extract were dissolved in normal saline and administrated orally to the mice (200 mg/kg/day). The normal and HFD-control mice were treated with vehicle (normal saline) only. Body weight and food intake were monitored once per week. Obesity is generally defined as being 20 % or more over ideal body weight. After one week of feeding, the body weight of the HFD group was approximately 20 % higher than the normal control group. All animal procedures were performed according to the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health and was approved by the Institutional Animal Care and Use Committee of Daejeon University in Daejeon, Korea (Approval No. DJUARB2013-022). Food efficiency ratio was calculated as follows: Food efficiency ratio (%) = [Body weight gain (g/day) / food intake (g/day)] × 100.

Serum assays
At the end of the experimental period, the mice were anesthetized with ether following an overnight fast. Blood was drawn from the abdominal aorta into a BD Microtainer Blood collection tube (BD, Plymouth, UK). Whole blood samples were centrifuged at 2000 × g for 15 min at 4°C, and the separated serum was stored at −70°C until analysis. The serum biochemical concentrations of total cholesterol, HDL cholesterol, LDL cholesterol, triglycerides, glucose, creatinine, aspartate aminotransferase (AST), and alanine aminotransferase (ALT) were determined using an automatic analyzer (Express Plus, Chiron Diagnostics, East Walpole, MA, USA) with reagents (Bio-Clinical System, Gyeonggi-do, Korea). Serum leptin levels were measured by immunoassay (ELISA) using commercially available kits (Linco Research, Charles, MO, USA). The absorbance was measured using a microplate spectrophotometer (BioRad, Hercules, CA, USA).

Weight and histology analysis of liver and adipose tissues
After collecting the blood, the liver and white adipose tissues (subcutaneous and epididymal fats) were removed from the mice and weighed immediately. For adipocyte staining, the liver and visceral adipose tissue were fixed in 10 % neutral formalin solution for 1 day, and embedded in paraffin. All tissues were cut with a thickness of 6 μm, and stained with hematoxylin and eosin. To quantify adipocyte size, the stained sections were analyzed using light microscopy (Olympus BX51, Olympus Optical Co., Tokyo, Japan) and an image analysis program (Image-Pro Plus 5.0, Media Cybernetics, Silver Spring, MD, USA).

Real-time quantitative RT-PCR
The adipose tissue was homogenized and total RNA from epididymal adipose tissue was isolated with TRI reagent (Sigma, St. Louis, MO, USA) and digested with DNase I (Life Technologies, Grand Island, NY, USA) to remove chromosomal DNA. Five μg of total RNA were reverse transcribed into cDNA with the First Strand Table 1 The primer and probe sequences used in the real-time RT-PCR analysis Genes Probe and primer Sequence GeneBank accession number

Statistical analysis
The data were analyzed by a one-way analysis of variance (ANOVA) followed by Tukey's range tests using statistical software Origin v.8.6. All data are presented as the mean ± standard error (SE). Significant differences were accepted when the p-value was less than 0.05.

Nutritional analysis
The nutritional composition of the mixed extract (AFE + VME) is shown in

Body weight, fat mass, and food efficiency ratio
The final body weight and body weight gain were significantly lower in mice fed with AFE, VME, or the combination diet (AFE + VME) compared with the HFD control mice, and the largest effect was observed among mice on the combination diet ( Fig. 1a and Table 3). Food intake did not differ significantly among the groups ( Table 3). The food efficiency ratio was significantly lower in the mice fed AFE, VME, or the combination diet (AFE + VME) compared with the HFD mice ( Table 3). The weight of the liver, epididymal fat, and subcutaneous fat was higher in the HFD group compared with the ND group. These tissue weights were significantly decreased in mice fed the AFE, VME, or the combination diet, and the largest effect was observed among mice fed the combination diet (Fig. 1b-d).

Serum biochemical analysis
The AFE, VME, and AFE + VME diets significantly inhibited the HFD-induced increase in serum triglycerides and total cholesterol levels ( Fig. 2), and the combination diet (AFE + VME) was most effective in reducing serum triglyceride, leptin, and total cholesterol levels.
The AFE and VME reduced serum leptin levels, but not significant. Serum glucose, LDL cholesterol, and HDL cholesterol levels did not differ among the groups. To evaluate potential toxicity of the mixed extract, we measured serum markers of liver and kidney injuries. AST and ALT were significantly lower in the AFE, VME, and AFE + VME groups, and these levels were similar between the AFE + VME and ND groups ( Fig. 3a-b). Serum creatinine level was significantly lower in the AFE + VME group compared with the HFD group, and this level was similar to that in the ND group (Fig. 3c). Therefore, the combination of extracts decreased the toxicity on the liver and kidney of the mice.

Histological examination of liver and adipose tissue
The adipocyte size in the epididymal white adipose tissue was larger in the HFD group compared with the ND group. The adipocyte size was significantly smaller in the AFE, VME, and AFE + VME groups, and the adipocyte size in the AFE + VME group was similar to that in the ND group (Fig. 4a). Fat accumulation in the liver also was lower in the AFE, VME, and AFE + VME (Fig. 4b).
Gene expression in epididymal white adipose tissue The mRNA expression levels of UCP-2, adiponectin, and PPAR-γ were significantly higher in the AFE + VME group compared with the HFD group (Fig. 5a-c). The mRNA levels of leptin were significantly higher in the HFD group compared with the ND group, and were lower in the combination group (AFE + VME) (Fig. 5d). The AFE and VME increased mRNA levels of leptin, but not significant.

Discussion
The mixed extract of A. fistulosum and V. mandshurica was rich in vitamins (E, B 1 , B 2 , niacin, and folic acid) and essential minerals (calcium, iron, and zinc). Vitamins and minerals play crucial roles in obesity and obesity-related diseases. Vitamin E has been shown to regulate the expression of adipocytokines such as leptin and adiponectin and decrease oxidative stress in an HFD-induced obese rat [14]. Vitamin B 1 (thiamine) has been shown to prevent obesity through the alleviation of body weight gain, adipocyte hypertrophy, and liver steatosis [15]. Folic acid supplementation in mice has been shown to have a protective effect against HFD-induced body mass, hepatic oxidative stress, and liver injury [16]. Niacin treatment has been shown to increase adiponectin levels and attenuate obesity-induced adipose tissue inflammation as well as obesity in HFD-fed mice [17]. The mixed extract of A. fistulosum and V. mandshurica also included high levels of iron (884 % of the RDA). HFD-induced obesity leads to reduced iron storage, and a grape seed and skin extract has been shown to prevent dyslipidemia by increasing anti-oxidant capacity and modulating iron deficiency [18]. These results therefore suggest that the mixed extract of A. fistulosum and V. mandshurica, which is rich in vitamins and essential We investigated the effect of AFE, VME, and the mixed extract of A. fistulosum and V. mandshurica (AFE + VME) in HFD-induced obese mice and found that AFE + VME effectively ameliorated obesity by synergistically reducing body weight, fat mass, and serum triglyceride and cholesterol levels. In addition, the mixed extract increased the mRNA levels of PPAR-γ, UCP-2, and adiponectin and decreased leptin expression in the epididymal white adipose tissue. UCP-2 is involved in the regulation of thermogenesis, energy expenditure, and obesity [19]. The adipocytes secrete various bioactive proteins called adipocytokines, such as leptin and adiponectin, into the blood circulation. Leptin, the gene product of the obesity gene, is directly associated with the regulation of adipose tissue mass and body weight in humans and rodents [20]. Adiponectin plays a major role in the modulation of glucose and lipid metabolism in insulin-sensitive tissues in both humans and animals [21]. PPAR-γ is a major ligand-activated transcription factor for regulating the various adipocyte genes and adipocyte differentiation [21]. Thiazolidinedione (TZD), a specific synthetic ligand activator of PPAR-γ, improves glucose tolerance, insulin sensitivity, and lipid metabolism in type 2 diabetes mellitus and obesity [22,23]. The administration of TZDs has been shown to increase the expression and plasma concentration of adiponectin via the activation of the adiponectin promoter in diabetic patients and animals with insulin resistance [24]. Our results suggest that the mixed extract of A. fistulosum and V. mandshurica improved lipid metabolism via the up-regulation of PPAR-γ, UCP-2, and adiponectin expression and down-regulation of leptin in adipose tissue.
Previous phytochemical studies have revealed that the extract of A. fistulosum contains ferulic acid and quercetin [25] and the extract of V. mandshurica contains esculetin [26]. These phenolic compounds were shown to effectively inhibit adipocyte differentiation and reduce body weight, fat accumulation, and oxidation as well as inflammation in HFD-induced obese mice [27][28][29]. Although the anti-obesity effects of these constituents has not been demonstrated in this work, these results suggest that these phenolic compounds may synergistically contribute to the antiobesity and hypolipidemic effects of the mixed extract of A. fistulosum and V. mandshurica.

Conclusion
The oral administration of the mixed extract of A. fistulosum and V. mandshurica (AFE + VME) significantly reduced body weight, fat mass, and adipocyte size, and improved serum triglyceride, total cholesterol, and leptin levels in high-fat-diet-induced obese mice. The mixed extract also decreased the serum levels of AST and ALT, which are markers of liver injury. The anti-obesity and hypolipidemic effects of AFE + VME were associated with the up-regulation of the mRNA expression of PPAR-γ, UCP-2, and adiponectin and the down-regulation of leptin in high-fat-diet-induced obese mice. Therefore, AFE + VME may be a potentially effective therapy for obesity and its related metabolic disorders.
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Optical Clearing in Dense Connective Tissues to Visualize Cellular Connectivity In Situ

Visualizing the three-dimensional morphology and spatial patterning of cells embedded deep within dense connective tissues of the musculoskeletal system has been possible only by utilizing destructive techniques. Here we utilize fructose-based clearing solutions to image cell connectivity and deep tissue-scale patterning in situ by standard confocal microscopy. Optical clearing takes advantage of refractive index matching of tissue and the embedding medium to visualize light transmission through a broad range of bovine and whole mount murine tissues, including cartilage, bone, and ligament, of the head and hindlimb. Using non-destructive methods, we show for the first time intercellular chondrocyte connections throughout the bulk of cartilage, and we reveal in situ patterns of osteocyte processes and the lacunar-canalicular system deep within mineralized cortical bone. Optical clearing of connective tissues is expected to find broad application for the study of cell responses in normal physiology and disease pathology.

Introduction
With the advent of confocal and multi-photon microscopy, the ability to characterize cellular morphology deep within tissues has prompted the further refinement of clearing methodologies that aim to better match the index of refraction of tissues and the fluid in which they are immersed. This is typically accomplished by equilibrating specimens in aqueous or organic reagents that have indexes of refraction close to that of biological tissue [1,2] or through the removal of light-scattering lipids [3,4]. Advances in optical clearing have predominantly centered around the fields of embryology and neurology [1][2][3][4][5][6]. Recently these techniques have been adapted for studies investigating adult tissues beyond the brain, including large intestine [7], lung [8], heart [9], skin [10], spinal cord and peripheral nerve [4,11], as well as tissue engineered constructs [12]. However, the use of optical clearing for the visualization of cellular morphology, spatial patterning, or connectivity within the musculoskeletal system has not been reported.
The tissues of the musculoskeletal system are predominantly composed of dense extracellular matrix (ECM) networks and mineral (in the case of bone), which limit penetration of light and increase scattering in microscopy studies. Consequently, non-destructive investigations into cell-cell and cell-ECM interactions have been limited to the surface of these tissues, and yet recent studies suggest that cells deeply embedded within musculoskeletal tissues profoundly influence normal physiology and the pathogenesis of numerous diseases, for example osteoarthritis [13] and osteoporosis [14]. Visualization and study of sub-surface or deep cells that have different phenotypes and morphology than those near the surface has historically required mechanical sectioning, which can introduce artifacts and is destructive to the native tissue. Without the ability to non-destructively probe and image the 3D morphology of musculoskeletal cells in situ, we are not yet able to address many elementary unresolved issues, including a) the extent that chondrocytes communicate with adjacent cells, b) patterns of cellular connections across tissue interfaces (e.g. entheses and myotendinous junctions) that may facilitate mechanical/chemical crosstalk, c) how baseline cell distributions within tissues influence normal physiology, and d) how deviations from the norm define specific disease states and the progression toward regeneration and repair.
We explored the possibility that optical clearing of dense connective tissues could reveal unique microstructural and cellular characteristics that are not easily observed or quantified using standard microscopy or histomorphometry techniques. The main objective of this study was to determine the effect of optical clearing on cellular morphology within bovine connective tissues, including cartilage, bone, meniscus, and ligament, and whole mount murine tissues of the head and hindlimb. We reveal the utility of SeeDB [1], a fructose-based clearing agent that requires minimal processing during both tissue harvest and image analysis, for characterizing the 3D distribution of cells in connective tissue rich specimens, a representative biological example that highlights our ability visualize cellular structures within tissues in situ. SeeDB is a simple water-based optical clearing agent that takes advantage of saturated fructose solutions having a refractive index close to that of fixed tissue (n = 1.49) and permits imaging to depths greater than 2,000 μm using conventional confocal microscopy in brain tissue [1]. The combination of optical clearing and membrane-localized fluorophores enabled us to probe deep within musculoskeletal tissues in situ to confirm the presence of intercellular connections between adjacent chondrocytes and resolve the intricate dendritic processes that osteocytes use for intercellular communication while embedded within mineralized cortical bone.

Materials and Methods
Animal care and tissue harvest Multiple tissues from bovine and murine sources were used in optical clearing experiments. Musculoskeletal tissues were harvested from juvenile bovine knee (stifle) joints obtained from a local United States Department of Agriculture (USDA) regulated abattoir (Dutch Valley Foods, Holland, IL) within 24 hours of slaughter. As these joints were classified as non-edible food items, no additional regulatory compliance was necessary. Joints (n 3) were opened under aseptic conditions to expose the tibial and femoral condyles and the trochlear groove. Osteochondral (cartilage-bone) plugs were removed from the load-bearing region of the medial condyle using a 5 mm diameter coring reamer [15]. Joint tissue sections were likewise harvested from the medial meniscus, synovium, and anterior cruciate ligament, and separately from the quadriceps muscle and tendon. Tissues were immediately fixed in 4% paraformaldehyde (PFA) diluted in phosphate buffered saline (PBS) for 1-2 days at 4°C with gentle rocking then rinsed at least 2× 1 hour with PBS at room temperature with gentle rocking. Tissues were trimmed to specimens 2.5-3 mm thick before beginning the clearing process (see below).
Young adult mice heterozygous for either Pax3-Cre:R26ZsGreen [16,17] or mT/mG [18] were utilized for bulk tissue optical clearing (derived from animals obtained from The Jackson Laboratory). All murine experiments were approved by the Purdue Animal Care and Use Committee (PACUC; protocols 1305000861 and 1209000723). The PACUC ensures that all animal programs, procedures, and facilities at Purdue University adhere to the policies, recommendations, guidelines, and regulations of the USDA and the United States Public Health Service (USPHS) in accordance with the Animal Welfare Act and Purdue's Animal Welfare Assurance. Mice were euthanized via CO 2 inhalation, which was confirmed by cervical dislocation. Like bovine tissues, murine organ and multi-tissue systems were immediately harvested and fixed in 4% PFA for 1-2 days at 4°C, and then rinsed with PBS. Subsequent fluorescent labeling and clearing of fixed samples were carried out immediately or after storage at 4°C for no more than 7 days.

Optical Clearing
Tissues were cleared following Ke et al., 2013 [1]. Fructose solutions of varying concentrations (20%, 40%, 60%, 80%, 100% and 115% wt/vol) were generated by dissolving D-(-)-fructose (JT Baker, Center Valley, PA) in milliQ water with 0.5% α-thioglycerol (Sigma-Aldrich St. Louis, MO) to prevent browning. Tissues were equilibrated to increasing concentrations of fructose by incubating in each formulation for at least 24 hours under gentle rocking at room temperature. Unclearing, or reversal to PBS, was performed by equilibrating samples in fructose solutions of decreasing concentrations under the same conditions for clearing.

Imaging
Using a stereo dissecting microscope (Leica M80, Wetzlar Germany), light transmission was visualized through the bulk bovine and murine tissues. Images were acquired with front and back lighting to visualize bovine tissues placed on a printed grid pattern (spacing = 2.1 mm).
The comparison of signal penetration was carried out on a Nikon A1Rsi inverted confocal microscope using a 20× multi-immersion objective (Plan Fluor, NA = 0.75, working distance ≈ 300 mm) with four available excitation laser wavelengths (405, 488, 555, 633 nm). Specimens were imaged with a 3× optical zoom and 2× frame average. For control samples, water was the immersion medium and cleared samples utilized oil with a refractive index of 1.515. Imaging parameters: field of view = 211.9 × 211.9 mm 2 ; matrix = 512 × 512 pixels 2 , Δz = 1.0 μm.
A Leica TCS LSI-III Confocal was used to image the cleared head of an mT/mG mouse in which all tissues remained intact except for the overlying skin. The sample was placed in a standard tissue culture dish with minimal amount of clearing solution. The area to be imaged was faced upwards toward the objective lens and no further dissection was required as the samples were non-invasively imaged. An initial lambda scan was performed to determine the optimal emission spectra to set the spectral prism. Tissues were excited with 561 nm laser set at 100% on AOFT for maximum penetration and scanned with a frame average of 3 or 4×. Airy unit sizes were varied to achieve the best image quality and deeper penetration into sample required a larger confocal pinhole size.

Image Processing
Confocal stacks were rendered in 3D using FIJI (NIH). Figures were assembled by taking 2D slices from stacks or snapshots of 3D rendered image volumes and arranged using Adobe Photoshop and Illustrator.

Results
To determine the utility of optical clearing for musculoskeletal tissues, we first tested the extent that clearing enhanced light transmission at the macroscopic level. When 2.5 mm-thick slices of cartilage (top row) and ligament (bottom row) were equilibrated in concentrated fructose solutions, the specimens became noticeably more transparent as evidenced by the ability to resolve grid patterns placed behind the specimen (Fig. 1). While the transmission of light was greater in the meniscus after clearing, the grid could not be visualized (middle row, Fig. 1). Transmission of light through synovium and tendon, and to a lesser extent muscle, was also observed (S1 Fig.).
We next utilized confocal microscopy to determine how SeeDB-based clearing affected specimen visualization at the cellular level. A current bottleneck in the adaptation of clearing techniques for whole-mount labeling of specific tissue components is the slow diffusion of high molecular weight primary and secondary antibodies (MW ≈ 150 kDa for unconjugated IgG). Therefore, to maximize signal penetration, we specifically chose fluorescently-labeled probes of low MW. Starting at the specimen surface, representative volume elements 100 μm thick were acquired at 20× using standard confocal microscopy before and after clearing. Control specimens were placed in PBS and imaged using water immersion (n = 1.33). After clearing, specimens were suspended in the 115% fructose solution (n = 1.49) and imaged using oil immersion (n = 1.518). Due to the inherent differences in imaging with water versus oil immersion, it was not feasible to keep all imaging parameters consistent. Nevertheless, the same laser power, pixel dwell time, and x, y and z-dimensions were used. To emphasize the enhancement of signal intensity due to optical clearing, images were left unprocessed (i.e. no bleach correction or image filtering) except for using FIJI to equilibrate intensity histograms of the stacks taken before and after clearing, based on the fifth z-slice from the tissue surface.
Chondrocytes within articular cartilage were labeled using DiI-SP (MW = 1.1 kDa), a lipophilic membrane probe. In control specimens, signal intensity was greatly diminished 50 μm into the sample ( Fig. 2A-D), whereas after clearing, chondrocytes could be visualized through the entire 100 μm representative volume element ( Fig. 2A'-D'). Meniscus, ligament and cartilage were stained with AlexaFluor 488-conjugated wheat germ agglutinin (WGA; MW = 38 kDa), a lectin that binds to glycoproteins, to visualize ECM organization [19] Fig.). Autofluorescence in the 488 channel became more prominent after clearing (Fig. 2I'); however, it was mainly restricted to the surface. These data indicate that the imaging of cells and ECM within musculoskeletal tissues can be enhanced at least two-fold by simple equilibration in fructose solutions without any additional acquisition or post-processing enhancements.
The representative volume element containing DiI-SP-stained chondrocytes in 2C' was taken from a larger 307 μm-thick z-stack. When bleach corrected, interactions between DiI-SP labeled chondrocytes could be clearly resolved through the full depth, as we were limited by the working distance of our objectives. At 60 μm and 270 μm away from the articular surface, neighboring chondrocytes could be seen making putative connections ( Fig. 3 and S1-S4 Movies).
When intact murine heads and hindlimbs were cleared, structures normally hidden by dense connective tissues (i.e. calvaria and ligaments/fascia) could be visualized at the macroscopic scale (Fig. 4A). To also assess if the resolution of fluorescent structures was enhanced, tissues from Pax3-Cre:R26ZsGreen mice were used. In this mouse line, all descendants of Pax3-expressing cells are GFP+ including skeletal muscle, neural crest and a small subset of endothelial cells [20]. While some structures became clearer in the concentrated fructose solution, for example large nerves in the head (arrowhead, top row, Fig. 4A) and musculature as seen  Fig. 4A), the strong fluorescent signal, combined with widefield microscopy, interfered with visualization of fine structures in these bulk tissues.
In contrast, we were able to visualize the morphology of cleared bone at multiple scales utilizing tissues from the mT/mG mouse line, in which all cells express membrane-localized tdTomato [18]. Using a Leica LSI system, a large-scale true point scanning spectral confocal, we were able to scan the overview of a cleared mouse head and in to the finer details without changing objectives zoom. The skin was removed from the intact head and then scanned with out any further dissection. Clearing with SeeDB, in combination with the unique design of the microscope, allowed visualization of the vasculature within the skull and the interface of the skull and meninges (Fig. 5A). To image deeper with greater confocal zoom the pinhole was opened wider to three airy units, enabling the higher resolution of structure in this undissected mouse head, highlighting the vasculature (Fig. 5B) and osteocyte distribution (arrowheads, Fig. 5C).
One of the limitations of the Leica LSI is that the upright objective utilizes air immersion, preventing the use of higher power objectives. Therefore, to better visualize osteocytes in situ, we isolated an intact femur from the mT/mG mouse line and compared cell morphology in uncleared and cleared specimens. After clearing, the fine cytoplasmic processes of osteocytes in the distal epiphysis of the femur could be imaged to 40 μm below the bone surface. In cleared samples, osteocyte dendritic processes were plainly visible extending from the osteocyte cell body, through the pericellular space to the lacunar wall, and continuing through the fine intercellular canaliculi coursing through the mineralized bone tissue. The morphologic details of phalloidin (green) and Hoescht 34580 (blue) to label F-actin and cell nuclei respectively. As with cartilage and meniscus, substantial increases in total depth imaged was observed after clearing (I'-L'), particularly evident in the 3D rendering (K'). Specimens were imaged using a Nikon A1R microscope, with a PlanFluor 20× multi-immersion objective, NA = 0.75, 3× optical zoom and 2× frame average. For control samples, water was the immersion medium and cleared samples utilized oil with a refractive index of 1.515. Image dimensions: 512 × 512 pixels 2 , Δz = 1.0 μm. Stacks were rendered in 3D using FIJI. Bars in A, D, E, H, I and L = 50 μm.
doi:10.1371/journal.pone.0116662.g002 Figure 3. High resolution imaging of cartilage reveals evidence of connectivity between individual chondrocytes. Interactions between individual chondrocytes within bovine articular cartilage can be resolved throughout the entire 307 μm-thick z-stack (arrowheads). The same z-stack shown in Fig. 2C'was bleached corrected and rendered in 3D using FIJI. The top of the volume was imaged just below the articular surface and goes deeper into the cartilage as z increases. Cartilage was stained with DiI, cleared with SeeDB and imaged using a Nikon A1R microscope, with a PlanFluor 20× multi-immersion objective, NA = 0.75, 3× confocal zoom. The depth of the image stack was limited by the working distance of the objective. Tick marks on isolated cell volumes = 10 μm. See also S1-S4Movies. osteocytes in uncleared bone were difficult to discern (Fig. 6). Apart from bleach correction and brightness/contrast adjustment, these images were not subject to any additional postprocessing.

Discussion
A number of optical clearing methods that facilitate the imaging of cellular morphology deep within tissues have been developed; however the majority are not without limitations: CLARITY requires specialized equipment [3]; ClearT is based on formamide, a highly corrosive teratogen [2]; 3DISCO is not compatible with lipid based dyes or investigations of membrane-bound molecules of interest [4]; Scale and BABB induce significant changes in specimen volume [5,6]; and no clearing agents yet permit deep imaging of live, viable cells in native tissue. SeeDB relies upon basic reagents, does not influence specimen size or integrity and clearing of tissues takes less than a week, whereas other methods such as CLARITY and Scale can require a minimum of 2 weeks. The initial study by Ke et al. described how SeeDB enhances light transmission in embryonic tissue and adult brain, quantifying the advantage of SeeDB over Scale and BABB in maintaining specimen fluorescence and geometry [1]. Herein, we show the expanded utility of this simple agent by demonstrating that tissues of the  . Visualization of osteocyte processes within intact bone. The distal epiphysis of a femur from an mTmG mouse was imaged after equilibration in either PBS or SeeDB. Z-projections of the cleared bone, encompassing 10 μm, revealed distinct cytoplasmic extensions at both 9 and 29 μm below the surface of the bone (arrowheads) whereas only faint outlines could be discerned in the control after equivalent image processing. The femur was kept intact (i.e. without sectioning or fracturing) and imaged through the periosteum using a Zeiss 710 confocal microscope with a 25× multi-immersion lens, NA = 0.8, 3× confocal zoom. Images were bleach corrected using FIJI, and then z-projections were made without any additional post-processing. Bar = 20 μm.  musculoskeletal system can be cleared using SeeDB to reveal interactions between cells embedded within a dense, and even mineralized, ECM.
Certain types of optical clearing methodologies have been previously reported for tendon [21], bone [22] and skin [23]; however, the aim of these studies was to enhance in vivo imaging and phototherapy through these cleared tissues rather than characterize the cells or ECM within them [24]. The agents utilized in this area of research tend to alter tissue architecture through dehydration and/or disruption of collagen fiber architecture [21,24], limiting the function of these techniques for describing cell morphology in situ.
Within articular cartilage, chondrocytes show a gradient in morphology that starts with flattened disc-shaped (superficial zone) cells near the load-bearing surface, becoming more ovoid deeper within the bulk (middle zone) of the tissue [25]. Chondrocytes are enveloped by a pericellular matrix composed of type VI collagen and perlecan, and further surrounded with an interstitial ECM dominated by type II collagen fibrils and aggregates of hyaluronic acid and aggrecan. It has been traditionally thought that individual chondrocytes are isolated from direct contact with adjacent cells by these extensive ECM networks. Recently, researchers utilizing confocal microscopy to describe the 3D morphology of chondrocytes and the pericellular matrix proximal to the surface of the imaged tissue [25,26] observed pronounced cytoplasmic extensions atypical of the homeostatic chondrocyte, which were correlated with osteoarthritis [27][28][29]. Additional reports on healthy cartilage have revealed apparent connectivity between adjacent cells based on cytoskeletal stains [30]. These previous confocal-based investigations of mapping the 3D distribution of chondrocytes have been limited to depths of less that 100 μm due to loss of signal in these dense tissues [28,31], and attempts to characterize cellular morphology within the bulk of the tissue have necessitated mechanical sectioning, which can introduce artifacts. Our demonstration that SeeDB can enable visualization of chondrocytes at least 300 μm within intact tissues provides evidence of cell connectivity that may extend beyond the immediate pericellular space. Moreover, the novelty and utility of deep microscopy of chondrocytes is strengthened by our results from the membrane-specific DiI stain, confirming interactions between cells not only at the surface, but also at depths greater than 250 μm, far removed from any surface artifact (Fig. 3).
Of the cells associated with bone, osteocytes have proven to be the most difficult to image in situ due to their isolation within a dense type I collagen-hydroxyapatite matrix [32]. What is known about osteocyte morphology has come from studies that relied upon significant specimen processing such as decalcifying, dehydration, and/or cryosectioning to visualize cells below the surface [33] or estimated osteocyte shape using fluorescent probes to fill the lacunar space [34,35]. Van Hoeve et al. visualized osteocytes within 60 μm-thick z-stacks; however, it was necessary for the images to be deconvolved to resolve any osteocyte processes [36]. After PFA fixation and clearing with SeeDB, osteocyte processes could be easily discerned 10-40 μm below the surface of intact cortical bone without extensive image processing (Fig. 6). Importantly, these high quality renderings of osteocyte processes were obtained using a mouse line in which tdTomato was localized to the plasma membrane, which were previously not apparent when imaging cryosections from the same mouse line [18,37,38]. By utilizing mouse lines engineered to have more intense fluorescence (e.g. ubiquitously expressed ZsGreen1 [17]) in combination with multiphoton microscopy, significant potential for enhanced depth penetration and resolution exists.
The 3D arrangement of cells within ligaments, tendons and menisci has received even less attention than that of cartilage and bone; however, that is not indicative of the importance of the role of these tissues within the musculoskeletal system. Ligaments and tendons are critical components that maintain the integrity of the articulated bony scaffold (via bone-ligament-bone linkages) and facilitate movement by transmitting muscle-generated force to bone. These tissues are primarily composed of aligned type I collagen fibrils embedded within a glycosaminoglycanand proteoglycan-rich matrix, and have a very low cell density compared with most tissues. The unique arrangement of tendon cells within a 1D array, extending processes into the surrounding collagenous ECM was discovered through initial 3D investigations, but these studies were limited to serial sectioning with subsequent reconstruction [39] or imaging of 20 μm-thick cryosections [40]. Clearing of intact ligaments and tendons with SeeDB has the potential to reveal gradients in cell-cell interactions and morphology extending from the surface further into the bulk.
The menisci compensate for the geometric mismatch between opposing bones in certain joints, and facilitate the dissipation of energy and transfer of mechanical force across the joint space during loading and movement. Confocal microscopy of adult rabbit meniscus showed a graduation of cell morphology: stellate with long vimentin-rich processes at the surface to more rounded and fibrocartilagenous at the interface with articular cartilage [41]. While the stains employed within this study did not enable us to discern cells within the meniscus, the enhanced clearing afforded by SeeDB combined with the appropriate cytoskeletal antibodies will provide the opportunity to describe intercellular interactions across the meniscus.
This study purposefully utilized small molecular weight fluorescent probes and endogenously expressed fluorophores to efficiently test the utility of clearing ECM-rich tissues. While staining with antibodies enables the identification of specific molecules of interest, the larger molecular weight introduces long incubation times (10 days-6 weeks) to stain structures deep within the tissue of interest and requires high concentrations of antibodies [3,42]. We are currently working on optimizing staining conditions to visualize the distribution of specific ECM.
Our data demonstrate how optical clearing can enhance the study of cellular morphology in ECM-rich tissues. Adaptation of optical clearing methods such as SeeDB will further the knowledge of intercellular interactions and tissue structure within the intact musculoskeletal system, critical to the understanding of recapitulation strategies of regenerative medicine and tissue engineering. We anticipate that optical clearing of connective tissues will find application in a broad range of applications in physiology and pathology. Chondrocytes stained with phalloidin (green) and Hoescht 34580 could barely be visualized 50 μm deep, whereas after clearing the actin filaments and nuclei could be seen throughout the entire 212 μm × 212 μm × 100 μm representative volume element. Specimens were imaged using a Nikon A1R microscope, with a PlanFluor 20× multi-immersion objective, NA = 0.75, 3× optical zoom and 2× frame average. For control samples, water was the immersion medium and cleared samples utilized oil with a refractive index of 1.515. Image dimensions: 512 × 512 pixels 2 , Δz = 1.0 μm. Stacks were rendered in 3D using FIJI. Bars in A, D, E, H, I and L = 50 μm. (TIF) S1 Movie. 3D rendering of bovine cartilage stained with DiI from Fig. 3. The image stack was acquired using a Nikon A1R microscope, with a PlanFluor 20× multi-immersion objective (oil n = 1.515), NA = 0.75, 3× confocal zoom and 2× frame average. Image dimensions = 212 × 212 μm2, 512 × 512 pixels 2 , Δz = 1.0 μm, 307 slices. The image stack rendered in 3D using FIJI.