bat guano , an excrement of the cave - dwelling bats forms the basis of the ecology inside the cave by acting as a food source for detritivorous microbes . it contains high content of organic carbon , nitrogen , phosphate , and potassium , . bacteria present in bat guano were reported to be involved in nitrification process and were also known as potential chitinase producer . a clone library based study in bat guano samples has revealed the presence of group 1.1a and 1.1b crenarchaeota , an efficient ammonia oxidizer , . analyzing bat guano is also important since they often harbor various pathogens which can be thread for speleologists , and tourists . although the microbial communities in diverse cave ecosystems have been studied , little is known about the microbial communities of bat guano heaps ,   and there has been no studies using high throughput sequencing technology . meghalaya is known to possess the largest and most diverse karst caves in the world . pnahkyndeng cave located in ri - bhoi district of meghalaya , india is a home of various bats and offering an ideal environment for studying the bat guano microbiota without any anthropological influence . samples were collected on february 2014 from the bat guano of pnahkyndeng cave ( 255722.70n , 915543.10e ) , nongpoh , ri - bhoi district , india . ten composite guano samples were collected from different places of the cave floor and the soil community dna was extracted separately using the fast dna spin kit for soils ( mp biomedical , solon , oh , usa ) . the freshly extracted dna was purified twice using 0.5% low melting point agarose gel and mixed to prepare a composite sample . final dna concentrations were quantified by the using a microplate reader ( bmg labtech , jena , germany ) . the v4 region of the 16s rrna gene was amplified using f515/r806 primer combination ( 5-gtgccagcmgccgcggtaa-3 ; 5-ggactachvgggtwtctaat-3 ) . amplicon was extracted from 2% agarose gels and purified using the qia quick gel extraction kit ( qiagen , valencia , ca , usa ) according to the manufacturer 's instructions . quality filtering on raw sequences was performed according to base quality score distributions , average base content per read and gc distribution in the reads . singletons , the unique otu that did not cluster with other sequences , were removed as it might be a result of sequencing errors and can result in spurious otus . chimeras were also removed using uchime and pre - processed consensus v4 sequences were grouped into operational taxonomic units ( otus ) using the clustering program uclust at a similarity threshold of 0.97 , . all the pre - processed reads were used to identify the otus using qiime program for constructing a representative sequence for each otus . the representative sequence was finally aligned to the greengenes core set reference databases using pynast program , . , 403,529 reads were classified at the phylum , 282,350 at the order , 188,406 at the family and 2926 sequences were classified at the species levels . classified otus belonged to 18 different phyla dominated by chloroflexi , crenarchaeota , actinobacteria , bacteroidetes , proteobacteria , and planctomycetes ( fig .  1 ) . analysis of bacterial communities revealed the two most dominant bacteria 's  chloroflexi ( 29.97% ) and actinobacteria ( 22.55% ) , which are known to be a common inhabitant of cave microflora . other identified phyla include crenarchaeota ( 16.96% ) , planctomycetes ( 12.41% ) and proteobacteria ( 12.03% ) . chloroflexi was divided into 11 classes  thermomicrobia , planctomycetia , gitt - gs-136 , ktedonobacteria , anaerolineae , tk10 , tk17 , s085 , chloroflexi , ellin6529 , and gitt - gs-136 . the most dominant otu within this phyla was denovo 317 , classified under the class thermomicrobia ( 40.52% ) followed by denovo 710 under the thermomicrobia ( 7.61% ) , denovo 235 under the genus thermogemmatisporaceae ( 7.18% ) and denovo 3 under the genus gemmataceae ( 2.98% ) . the dominant otu within this phyla was denovo 74 under the genus mycobacterium ( 29.39% ) followed by denovo 993 ( 8.27% ) and denovo 372 ( 5.27% ) classified under the genus acidimicrobiales and actinomycetales , respectively . only five otus were classified up to the species level ( mycobacterium llatzerense and mycobacterium celatum ) . a third dominant phylum in this sample was identified as planctomycetes comprising of 91 otus and 46,063 reads . seventeen archeal otus were classified under the order nrp - j , methanomicrobiales and methanosarcinales . four of them were identified at the genus level ( methanosarcina , haloquadratum , methanosaeta and methanocorpusculum ) . the phylogenetic tree based on the genus level relationships is provided as supplementary fig .  1 . previous study on archaeal communities present in bat guano identified many ammonia oxidizing bacteria but it was limited with a few number of clones . our analysis provides in - depth and high throughput identification of the bacterial communities present in bat guano . in the present study , we identified 18 bacterial phyla and most of the bacterial genus identified was known to be involved in nitrogen cycling as seen in previous study . a significant portion of otus still remains unclassified which indicates the possibility for the presence of novel species in pnahkyndeng cave . further studies like whole metagenome sequencing or functional metagenomics can illustrate the detailed information of this bacterial community .