Vigna unguiculata (L.) Walp.] is a crop with significant agronomic and nutritional value. In Togo, the crop is very appreciated by local people. It is the third food habit in Togo after maize and rice. However, several accessions of cowpea cultivated in Togo are now prone to extinction, creating a risk of genetic erosion. It is therefore urgent to assess the genetic diversity of accessions in order to set up a good conservation program. To achieve this, genetic diversity and phylogenetic relationships among 70 accessions of cowpea collected in the five (5) administrative regions of Togo were assessed using Simple Sequence Repeat (SSR) molecular markers. The twenty-eight SSR primers used in this study generated a total of 164 alleles with an average of 5.82 alleles per locus. Polymorphic Information Content (PIC) values ranged from 0.20 to 0.89 with an average value of 0.58. Population structure analysis using model-based revealed that the cowpea germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 98% of genetic variation existed among accessions within regions. The fixation index (Fst) value, which was 0.069 was low, indicating relatively low population differentiation. The phylogenetic analysis grouped the 70 accessions into two main groups that can be further divided into four groups independent of their origins. This study provides a foundation for a Togolese cowpea germplasm conservation program and can serve for the selection of parental material for further studies aimed at the genetic improvement of local germplasm.Cowpea [ Vigna unguiculata (L.) Walp.] is an important food legume in developing countries of the tropics and subtropics, especially in Sub-Saharan Africa, Asia, and Central and South America [Cowpea [ America , 2, and  America , 4. Its  America . Cowpea  America . It is r America . Besides America , 9. All  America . It also America . Besides America , 12, 13.Of late, the increase in world population and problems related to climatic variability has led to high demand of food. Unfortunately, in Togo for instance, many cowpea landraces are abandoned due to the farmer’s preference for variety presenting a relatively short development cycle, a higher productivity, a good market value and a good taste , 15. TheGenetic diversity is the extent to which heritable material differs within a group of plants as a result of evolution, including domestication and plant breeding. Assessing the genetic diversity of cowpea germplasm is a prerequisite for effective breeding and germplasm conservation. Genetic studies of cowpea diversity have been carried out in several countries using DNA molecular markers such as random amplified polymorphic DNA (RAPD) , 17, ampTogo is a west-African country covering about 56,600 square kilometers and stretching from its 51 kilometers coastline in the Gulf of Guinea northward for about 515 kilometers between Ghana to the west and Benin to the east to its boundary with Burkina Faso in the north. The country is divided in five administrative regions namely Maritime, Plateaux, Centrale, Kara and Savanes and is under a general tropical climate with average temperatures ranging from 23°C on the coast to about 30°C in the northernmost regions. In the three northernmost regions, there is a single wet season occurring between May and November. In the south, there are two seasons of rain (the first between April and July and the second between September and November), even though the average rainfall is not very high [As a crop cultivated across the whole country, the cowpea accessions were collected in the country’s five administrative region. The collection was done in collaboration with the Togolese Institute of Advices and Technical Supports (ICAT) technicians who are in charge of providing assistance and technical supports to farmers in order to help them maximize their crop production and by using the snowball method. Briefly, for the villages’ selection, firstly the villages producing cowpea and cowpea producer in each region were identified based on informations provided by ICAT technicians. Then in the first selected village of each region cowpea producers were asked to cite the villages known for cowpea production and those that have cultivars that were absent in their own village. The choice of the next village was done following the farmers recommendations after consulting the ICAT agents.Using that method, a total of 70 cowpea accessions were collected from producers of 50 villages in the five regions of Togo between 2014 and 2016 , Table 1The DNA extraction and PCR amplification were done at the Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS) in Senegal. The genomic DNA was extracted from a bulk of fresh leaf material of 21 day-old-plants of each of the 70 cowpea accessions following the mixed alkyl trimethyl ammonium bromide (MATAB) protocol described by Risterucci et al. . The ext2 (0.5 mM), 9 μL of each primer (0.1 μM), 9 μL of IR dye (0.1 μM), 55 μL of Taq Polymerase 1U and 227 μL of ultrapure water. The PCR reaction was carried out in a 96-block thermal cycler (MWG AG biotech). The thermal cycling conditions were as follows: initial denaturation step at 94°C for 4 min followed by 26 cycles of denaturation (94°C) for 60 s, hybridization (50–55°C according to the primers) for 1 min, primer extension (72°C) for 1 min 15 seconds, followed by a final extension at 72°C for 7 min. After PCR, a 0.8% agarose gel was used to control the quality of the amplification products. The PCR plates were then covered with aluminum foil to prevent fluorochrome degradation and placed in a refrigerator for conservation purposes.A total of 28 polymorphic SSR markers were used to screen 70 cowpea DNA samples . Those pThe amplification PCR products were analysed by electrophoresis on a 6.5% polyacrylamide denaturing gel on Licor 4300 sequencer . Before loading the gel, the multiplexed PCR products were denatured at 94° C for 3 min, and then the plate was placed on ice. The amount of denatured DNA loaded in the wells of the deposition rack was 2.5 μL. An infrared camera detected the fluorescence signals emitted by the marked fragments when excited with laser diodes at two different wavelengths (682 and 782 nm). The images were automatically recorded and downloaded for analysis. Allele sizes were estimated by comparing them with different bands of the size marker (ladder produced by CIRAD) .ST) among populations. The statistical parameters such as total number of alleles per locus (Na), number of effective alleles per locus (Ne = Ne = 1/ (Pi*Ln (pi))), observed heterozygosity (Ho = number of heterozygotes/number of genotypes (N)), gene diversity  to fourteen (14), with an average of 5.86 alleles per loci. The lowest number of alleles per locus was detected for the markers SSR6217, SSR6774, SSR6311, SSR6243, SSR6671, and SSR6288. The highest number of alleles was recorded for SSR6800. A total of 18 rare alleles were detected in this study. The number of effective alleles per marker ranged from 1.21 to 6.44, with an average of 3.05 with the markers SSR6571 and the marker SSR6807 having respectively the lowest and the highest number of effective alleles respectively. For the SSR loci, polymorphism information content (PIC) representing a measure of the allelic diversity for a specific locus varied from 0.20 to 0.89 with an average of 0.58. Ten SSR loci  exhibited PIC values higher than 0.70, indicating their usefulness in discriminating genotypes. The observed heterozygosity values ranged from 0.00 to 0.38 with an average of 0.07, and the major allele frequency varied from 16.17% to 89.06% . This stSSR markers used in this study revealed high percentages of polymorphic loci (average of 99.28%). The lowest percentage of polymorphism was observed for cowpea population one, corresponding to the Centrale region, while the percentage of polymorphism observed for each of the other four regions was 100%. The number of alleles detected in each population is not uniform and varied from 102 alleles in the cowpea population from the Centrale region to 127 alleles in the population of the Plateaux region. Among the five population investigated, the mean values of observed alleles (Na) and effective alleles (Ne) were 3.96 and 2.92, respectively. Population 3  recorded the lowest value of Na (3.64), while the highest value (4.54) was recorded from population 5 (from Savane Region). For the effective number of alleles, the lowest value (2.85) was recorded from population 3 (from Maritime Region), while the highest value (3.07) was displayed by population 5. Shannon’s information index ranged from 1 to 1.08 with a mean of 1.03. The observed heterozygosity (Ho) ranged from 0.07  to 0.08 (population 1 and population 2) with an average of 0.07. The expected heterozygosity (He) was moderately high and ranged from 0.53 (Population 2) to 0.55 (Population 1 and Population 3), with an average of 0.54. The unbiased expected heterozygosity ranged from 0.56  to 0.58 (Population 1 and Population 3), with an average of 0.57. According to the results, the five regions displayed almost similar diversity of cowpea. The values for the inbreeding coefficient expressed by the fixation index F ranged from 0.79 (Population 5) to 0.85 (Population 3) with an average of 0.82 at the population level . GeneticThe genetic differentiation indices between populations (Fst) varied from 0.00  to 0.057 between Centrale and Maritime Regions. Differentiation appears to be null or low between accessions from different regions except for Centrale and Maritime Regions, which appears moderate .AMOVA was performed using the matrix of distances for genetic differentiation. The results of AMOVA revealed that the majority of variance occurred within individuals and accounted for98% among individuals within regions of the total variation, whereas 2% and 13% of the variation was attributed to differences between populations. The results indicated that the diversity within regions  was far greater than the diversity between regions , and the low Fst value (0. 069) indicated a low genetic variation among regions. The haploid Nm was very high (8.970) indicating a high gene exchange among populations while the inbreeding coefficient and the overall fixation where respectively 0.830 and 0.835 across the SSR loci. These results demonstrated that genetic differentiation among subpopulations was low and within subpopulations was very high .The accessions studied were clustered into two main groups (I and II) based on Ward’s minimum variance method . There wThe genetic distance among cowpea accessions in this study varied from 0.1432 between Kétséyi soukpélo an accession belonging to the erected-type with small purple grain collected from the Kara Region and Gouarga, an accession belonging to the creeping-type, with white small grain collected from the Savanes Region to 0.9317 between Hèkou hèkou a creeping-type accession with white medium size grain collected from Centrale Region and Kampirigbène a semi-erected type accession with white small grain collected in the Savanes Region .Genetic relationships among the selected accessions were further assessed using principal coordinate analysis (PCoA). The first three principal coordinates explained 10.62%, 17.73%, and 23.85% of the variance. The PCA further supported the grouping of the accessions in four groups .The structure analysis of the population structure based on the ΔK value grouped the seventy accessions into two subpopulations (clusters) . MembersThe expected heterozygosity  inside each cluster was average (respectively 0.53 and 0.54 respectively for cluster 1 and cluster 2) while the fixation index in both clusters was low (respectively 0.08 and 0.15 for cluster 1 and cluster 2). These results indicate a relatively low level of population structure .An efficient evaluation of genetic resources can help reduce redundancies and build a core collection which can be screened to identify traits of interest. Further, a crop improvement and conservation program mainly depend on the presence of a genetic variability and on the characterization of the variability. Molecular markers are powerful tools for elucidating variations and relationships within and between crops germplasm populations. Among the genetic markers, SSRs are successfully applied in various breeding programs to study genetic diversity because of their multi-allelic nature, their level of polymorphism and the ease of their use , 27, 29.This study revealed a number of allele ranging from 2 to 14 allele per locus, which appeared to be relatively low compared to the value of 2 to 15 alleles per locus obtained by Sarr et al.  using 15The estimated average PIC value (0.67) recorded in the current study was similar to the value (0.68) reported by Ogunkanmi et al. , higher The average gene diversity expressed by the expected heterozygosity (He), which is a measure of genetic diversity observed in the present study (0.54), was higher than the value 0.488) reported by Ali et al.  for a Su8 reporteThe dendrogram generated based on Ward’s minimum variance method has divided the 70 accessions in two main groups which is consistent with the results obtained from the population structure analysis. Each group can be further divided in two sub groups. This indicates the existence of a high degree of genetic diversity in the germplasm evaluated in this study. Therefore, these germplasms could serve as a valuable source for the selection of diverse parents for a breeding program aimed at creating new cultivars associating different traits of interest. However, in this study, the grouping of the accessions was not observed according to regional basis. Asare et al.  have alsLike in many sub-Saharan African countries, cowpea accessions grown in Togo are identified by local names given by farmers based on their morphological characteristics such as seed characteristics, plant and pod shape . This noThe population structure analysis based on STRUCTURE software revealed the presence of two subpopulations among the 70 cowpea accessions collected from the five regions of Togo, while Sarr et al.  and XionS5 Table). The observed similarity can be explained by the proximity of Kara Region to the two other regions. In fact, Kara Region is located in-between those two regions. This proximity might favor exchange of seeds between farmers of these regions.In the present study, the genetic variation components confirmed fair genetic diversity among individuals within regions (98%) than among regions (2%). The current study agrees with the findings of Sarr et al. (2020), who also reported a higher percentage variation among individuals within regions (75%). However, the percentage of variation attributed to differences between populations obtained in their study is higher than the 2% obtained in the current study. As already suggested by Sarr et al. , the higThe value of Fst was observed to be 0.069, indicating little differentiation among populations. The fixation index (Fst) obtained in the current study was much lower than the value of 0.114 obtained for the Senegalese germplasm and the value of 0.16 obtained by Fatokun et al.  when stuIn Togo, cowpea is one of the main legume crops. However, the crop is poorly characterized. The current study provides useful information on the variability of SSR markers leading to a better understanding of the population structure and the genetic basis existing. It is the first study to address the genetic characterization of the Togolese germplasm, and it showed that the genetic structure does not depend on regions. The results obtained from this study will serve as basic information by providing options to breeders to develop, through selection and breeding, new and more productive cowpea cultivars that are adapted to changing environments. Furthermore, the collected germplasm could also be used for developing population for QTLs mapping studies in order to identify loci controlling traits with agronomic importance.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file.


The availability of genome data provides a unique window into speciation mechanisms with virtually infinite amounts of information, providing a pathway for a better understanding of major evolutionary questions. The process of speciation is a key aspect of understanding biodiversity. Each species inhabits a specific environment, a niche, that, through the action of natural selection and other evolutionary forces, shapes its unique genomic program–genome sequence, its diversity and expression. Species exist as genetic pools within a specific area or ecological niche, as variations of constantly recombining genetic code, and they diverge when the exchange of information between populations is interrupted. As environments continuously change, some species can change and adapt, while others, lacking genome variation, cannot keep up with the change and become extinct. Genetic diversity is continuously formed by a balance of mutation and drift, contributing to diversity across the genome and creating a backdrop for the action of natural selection, enabling adaptation ,2 , a natural hybrid between the marsh frog P. ridibundus (RR) and the pool frog P. lessonae (LL)  demGenomics is becoming increasingly important for solving the major evolutionary questions about adaptation and speciation. Genetic diversity within a species is valuable, not only due to the existence of combinations of genes and alleles present at a given time in a population, but also because it contributes to ongoing evolutionary processes  (Stange In this Special Issue, we presented examples of different approaches to studying adaptation and speciation using genome-scale data. Genome-scale data allow us to resolve patterns of phylogenetic relationships and species evolution, identify reproductive barriers, and reinforce the speciation process. Transcriptomic data are complementary in the context of variable gene expression driven by environmental variation, which produces expression profiles that make species unique. Genomic approaches that incorporate sequencing and bioinformatics can identify signatures of adaptation, and more contiguous assemblies may allow for better estimates. Finally, technological breakthroughs in genomics allow us to understand and visualize genetic diversity among the chromosomes of endangered species.


The article analyses the spatial and temporal differences in the environmental quality of production, living and ecology of 285 cities in China from 2010 to 2020 by using the entropy method, the Theil index and correlation analysis. The study concludes the following: (1) in terms of overall differences, the overall differences in the “production, living and ecological” environmental quality indices of 285 cities during the study period undergo a process of “narrowing–widening–narrowing”. The differences within the four major zones of the country are higher than those between the four major zones, and the differences within the zones show an increasing trend year by year. (2) In terms of temporal differences, the combined scores of “production, living and ecological” environmental quality of the 285 cities in the study period show a decreasing trend, and the contribution of the PLE subsystem scores are, in descending order, production environmental quality > living environmental quality > ecological environmental quality. (3) In terms of overall ranking, the head effect of the combined production, living and ecological environmental quality (PLE) scores of cities in the study period is significant, and the top 10 cities in terms of combined scores are all small and medium-sized cities with significant regionalization characteristics. (4) In terms of spatial pattern, there is a significant spatial gradient in the east, central and western regions, with the overall PLE scores of the four major regions in descending order: eastern region > central region > western region > northeastern region. The regions with high scores in the “production, living and ecological” environmental quality of cities can be divided into three types: multi-core, dual-core and single-core. (5) In terms of influencing factors, there is a logarithmic curve relationship between the combined production, living and ecological environmental quality (PLE) score and the built-up area (BUA) of cities. The study proposes to optimize the layout of urban production, strengthen the industrial links of urban clusters, improve the level of public services, ensure the equalization of urban public services, strengthen the management of ecological environment and improve the quality of ecological environment in order to optimize the quality of urban “production, living and ecological” environment. With rapid industrialization and urbanization, China’s economy and society have grown at a rapid pace, with the gross regional product rising from US $149.5 billion in 1978 to US $17.73 trillion in 2021, and the urbanization rate rising from 17.90% in 1978 to 64.72% in 2021. However, the rapid urbanization development has brought about increasingly serious problems. China’s development is facing the crisis and challenge of approaching resource and environmental constraints, increasing environmental pollution and degradation of ecosystems [In order to change the mode of economic growth, we must follow the path of sustainable development, respect the laws of urban development, implement the new development concept of innovation, coordination, green, openness and sharing, meet the growing needs of the people for a better life, and support the role of the United Nations development system in implementing sustainable development goals. Western developed countries have all faced the same dilemma in the process of industrialization, and they have all adopted development strategies that optimize territorial space and attach importance to environmental protection ,7,8,9,10Firstly, researchers have analyzed different perspectives on the integrated assessment of the “production, living and ecological” environmental quality of cities. ① Research on indicators for the spatial allocation of “production, living and ecology” resources. The scientific issues of the quantity ratio and spatial allocation of “production, living and ecological” space was elaborated , and it Secondly, the evaluation of the quality of the urban “production, living and ecology” environment was performed. ① The spatial perspective of “production, life and ecology”. Based on the perspective of “production, living and ecological space”, a spatial evaluation system of production, living and ecological functions was constructed . ② The pThirdly, the analysis of the factors influencing the quality of the urban “production, living and ecological” environment was conducted. ① The study of the factors influencing production space. To measure the spatial and temporal efficiency of industrial production space, the spatial and temporal evolution characteristics and driving mechanisms of the industrial production space in the Pearl River Delta city cluster were revealed , the spaIn summary, the above-mentioned studies provide a solid analytical basis for this paper, as scholars have discussed the issue of urban “production, living and ecological” environmental quality, but have focused more on the spatial land use aspect of “production, living and ecological”, lacking a comprehensive measurement of urban “production, living and ecological” environmental quality, and lacking spatial and temporal analysis of continuous data. This paper is based on the data matrix of the “production, living and ecological” environmental quality of 285 cities in China from 2010 to 2020, and reveals the spatial and temporal characteristics of the “production, living and ecological” environmental quality of cities. This paper will be divided into four parts. The first part is the introduction, which introduces the progress of research on urban “production, living and ecological” environmental quality; the second part is the methods and data, which introduces the research methods, indicator system and data sources; the third part is the results and analysis, which is the main focus of the paper, and the research will develop the empirical analysis of the overall differences, time-series differences, comprehensive rankings, spatial and temporal patterns of the “production, living and ecological” environmental quality of cities and their influencing factors; the fourth part is the main conclusion of the paper, and proposes targeted countermeasures.Our study covers 285 cities at prefecture level and above in China, which are located in the eastern, central, western and northeastern regions of China, with 86, 80, 85 and 34 cities involved in the four major regions, respectively. The study includes all important cities in China, comprising municipalities directly under the central government, provincial capitals and large cities, and the samples are representative and significant. Our study will measure the “production, living and ecological” environmental quality of 285 cities and analyze their subsystems to reveal the overall differences, time-series differences, overall rankings and spatial and temporal patterns in the development of the “production, living and ecological” environmental quality of cities. This study uses the entropy method to comprehensively evaluate the level of PLE of 285 prefecture-level and above cities in China. The entropy method can profoundly reflect the utility value of the entropy value of indicator information, and the indicator weight value given has higher credibility than the hierarchical analysis method and the expert experience assessment method, which is suitable for the comprehensive evaluation of multiple indicators, and its main steps are  describem programs to be evaluated and n evaluation indicators, forming the original indicator data matrix:ijx is the indicator value of the jth indicator of the ith program to be evaluated.Step one: construct the original indicator data matrix. Assume there are Step two: data standardization. As the scale, order of magnitude and positive and negative orientation of the indicators are different, the initial data should be standardized.Define the normalization matrix:k = 1/lnm, and calculate the entropy value of the evaluation indicator:Step three: let Step four: calculate the coefficient of variability of the evaluation indicators and define the weights of the evaluation indicators.jw of the jth indicator and the proximity ijx′ of the jth evaluation indicator of the ith sample in the standardized matrix is used as the evaluation value ijf of ijx, and the evaluation value if of the ith sample.Step five: calculate the evaluation value of the sample. The product of the weight Theil index examines inequality and disparity from the concepts of information quantity and entropy, and it decomposes overall disparity into disparity between parts and disparity within parts, which has wide applications for analyzing and decomposing disparity ,62,63. TIn Equation (9), the parameter c is used to determine the sensitivity of the exponential change. In general, when c < 2, the exponential change it determines is sensitive. When c = 0.1, it is the well-known Theil index.Due to its property of dividing overall differences into within-group differences and between-group differences, the Theil index is widely used in empirical studies of overall spatial heterogeneity, as well as inter-spatial heterogeneity. The calculation formula isIf the area under study is divided into groups according to certain methods, the Theil index can be further decomposed into intra-group differences and inter-group differences.WR is the differences within the four regional groups of northeast, east, central, and west regions; TBR is the differences between the four regional groups; ndb, nd, nz, and nx are the number of cities within the northeast, eastern, central, and western regions, respectively; Ti is the carbon emission index of region in and the national average ratio; Tdb, Td, Tz, and Tx are the ratios of carbon emission indexes of the northeast, east, central, and west regions to the national average, respectively. A total of 285 cities at the prefecture level and above are included in our study. The northeast region includes 34 cities in Liaoning, Jilin, and Heilongjiang; the east region includes 86 cities in Beijing, Tianjin, Hebei, Shanghai, Jiangsu, Zhejiang, Shandong, Fujian, Guangdong, and Hainan; the central region includes 80 cities in Shanxi, Henan, Anhui, Hubei, Hunan, and Jiangxi, and the west region includes 85 cities in Inner Mongolia, Chongqing, Sichuan, Guangxi, Guizhou, Yunnan, Shaanxi, Gansu, Ningxia, Tibet, Qinghai, and Xinjiang.In Equations (10)–(12), Theil is Theil index; n is the number of cities in the sample region; TThe scatter plot is the most visual method used to express correlation analysis. The correlation coefficient is a collective term for a class of indicators that measure the correlation between variables ,67,68.The common correlations are linear correlation, curvilinear correlation, positive correlation, and negative correlation. The Pearson correlation coefficient, also known as the product–difference correlation coefficient, is a common metric for quantitatively describing the degree of linear correlation ,70,71,72i and yi are the variables, i and yi, and r is the correlation coefficient. The maximum correlation coefficient is 1. The closer the absolute value of the correlation coefficient is to 1, the stronger the correlation between the variables. Our study will measure the correlation coefficient between PLE and BUA using correlation coefficients, and visually express the relationship between them by means of scatter plots.In Equation (13), xThe index system for the evaluation of the “production, living and ecological” environmental quality of the city consists of a target level, secondary indicators and tertiary indicators. The target level includes three aspects: production environment quality, living environment quality and ecological environment quality. The secondary indicators of production environment quality cover four aspects: industry, wholesale and retail, postal and telecommunications, and energy use. The secondary indicators for the quality of the living environment cover four aspects: employment, education, healthcare and social security. The secondary indicators for the quality of the ecological environment cover three aspects: greening, industrial waste discharge and environmental management. There are a total of 24 specific evaluation indicators for the three levels of indicators, of which 21 have positive attributes and 3 have negative attributes .The indicator data involved in our study were collected from secondary data publicly available to the government and processed appropriately. Data on the quality of the urban “production, living and ecological” environment are mainly obtained from the 2011–2021 China Urban Statistical Yearbook compiled by the National Bureau of Statistics of China and the China Urban Construction Statistical Yearbook for the past years. Data on the population size of urban areas were obtained from the “2020 China Population Census Sub-County Information” published in October 2022 and compiled by the State Council’s Seventh National Census Leading Group Office.The overall difference in the “production, living and ecological” environmental quality scores of 285 cities in China between 2010 and 2020 underwent a process of “narrowing–widening–narrowing”. The Theil Index narrowed from 0.490 in 2010 to 0.466 in 2012, then widened to 0.543 in 2016, and then narrowed to 0.488 in 2020 . AlthougIn terms of trends, the differences between the northeast, east, central and west zones show a general trend of “narrowing–expanding–narrowing”, and the differences in the environmental quality indices of “production, living and ecology” between the four zones also show a trend of “narrowing–expanding–narrowing” . The difIn terms of contribution rate, the differences within the four major zones of the country are much higher than the differences between the four major zones, and the differences within the zones show an increasing trend year by year . The conIn summary, internal differences in the four major zones were the main drivers of variation in the quality of the urban “production, living and ecological” environment, with internal differences in the eastern region being the main driver, while internal differences in the north-eastern region contributed the least, and internal differences in the central and western regions were second only to those in the eastern region.The PLE scores of the 285 cities were summed to obtain the changes in the PLE scores from 2010 to 2020 . The oveIn terms of the score contribution of production environment, living environment and ecological environment , the scoAnalysis of factors influencing changes in production environment, living environment, and ecological scores was performed. Firstly, data structural factors were considered. As the differences of some indicators are relatively small, the entropy method of processing brought about changes in weights, resulting in a low score for this part of the indicators, while the differences of some indicators are large and the weights given are high, resulting in a relatively high score for this part of the indicators. Secondly, the deep transformation of China’s economic structure was considered. The study uses the number of large-scale industrial enterprises and the number of foreign-invested enterprises as positive indicators in consideration of its importance to the national economy and social development. Currently, one of China’s greatest strengths is its manufacturing sector, and to hold on to it and to deal with issues such as supply-side shocks in the face of exposure to the risks of counter-globalization, there is an urgent need to open up all aspects of production, distribution, circulation and consumption, and to promote a freer flow of production factors. Relatively speaking, the significant reduction in emissions of the “three wastes” by Chinese enterprises indicates that the government and enterprises have been effective in managing the ecological environment; industrial wastewater, industrial Sulphur dioxide and industrial smoke (dust) emissions in 285 cities were reduced from 225,493,900 tonnes, 16,978,337 tonnes and 54,165,563 tonnes in 2010 to 12,671,570 tonnes, 229,770 tonnes and 4,221,750 tonnes in 2020, a reduction of 43.81%, 86.47% and 22.06%, respectively. At the same time, China’s economic structure is undergoing a deep transformation, the energy structure, economic structure and industrial structure are being adjusted at an accelerated pace, and the manufacturing industry has started to move from the middle and low end to the middle and high end. The number of industrial enterprises above the national scale decreased from 452,872 in 2010 to 399,375 in 2020, a decrease of 11.81%, while the total profit of industrial enterprises above the national scale rose from 530.5 billion yuan in 2010 to 68.465 billion yuan in 2020, a rise of 29.06%, and the number of industrial enterprises above the scale indicator of the “one down, one up” indicates that its intrinsic structure is undergoing deep adjustments and the trend of industrial scale and concentration is strengthening. Thirdly, the impact of major public health events was considered. In response to COVID-19, China has adopted a strict epidemic prevention policy, adopting a general policy of “dynamic zero” means to eliminate an outbreak if one is detected so that there is no continuous community transmission or large-scale rebound. When a city is sealed, the primary impact is on the industry. The data is visualized in the fact that the scores for both Quality of Production Environment (QoP) and Quality of Living Environment (QoL) drop from 7.308 and 6.552 in 2019 to 6.676 and 6.084 in 2020, a drop of 8.65% and 7.14%, respectively. For example, Shanghai was sealed in March–June 2022. As a result, people found that Shanghai has a very important position in China, and the sealing of Shanghai directly impacted China’s secondary industry. Shanghai is not only an international shipping center and financial center, but also the economic center of China. The world’s top industries are in Shanghai, and the Yangtze River Delta city cluster, the engine of China’s economic growth, was directly affected after Shanghai was sealed, and after the lifting of the sealing China’s economy has only gradually recovered.The production, living and ecological environmental quality (PLE) of cities shows a horse-trading effect, with the top scores being those of mega-cities or large cities, and the bottom scores being those of small and medium-sized cities .The top 10 cities in terms of PLE score are all mega-cities or large cities in Chin. From 2010 to 2020, Shanghai, Beijing, Guangzhou and Shenzhen, the most economically developed mega-cities in China, have maintained their PLE scores in the top four, with Shanghai consistently ranking first. Cities such as Shanghai, Beijing, Guangzhou, Shenzhen, Suzhou, Chongqing, Chengdu, Hangzhou, Dongguan and Tianjin are pivotal and important in China’s economic growth. These cities have large populations, concentrated production, and maintain full national rankings in terms of ecological and environmental quality and public service levels. Due to the concentration of production, job opportunities, development opportunities and ecological livability, the head cities pose a strong attraction to migrant populations and produce a strong siphoning effect on factors of production such as human, capital and technological resources, and are the growth poles of regional economic development. With the exception of Chengdu and Chongqing in the western region, the top cities with the highest PLE scores are mainly located in the eastern coastal region, because the eastern coastal region has excellent location conditions and is actively participating in the global division of labor, playing a leading role in linking Chinese industries to the world industrial system.The bottom 10 cities in terms of PLE score are all small and medium-sized cities with significant regional characteristics. In 2010, the bottom 10 cities in terms of PLE are mainly located in the western region, namely Fangchenggang, Longnan, Zhangye, Chongzuo, Qitaihe, Pingliang, Lincang, Zhongwei, Zhangjiajie and Baoshan. The bottom 10 cities in terms of “production, living and ecological” environmental quality (PLE) in 2020 are mainly located in the western region and the northeastern region: Hegang, Heihe, Shuangyashan, Liaoyuan, Pu’er, Tongchuan, Jinchang, Zhongwei, Fangchenggang and Wuzhong. In terms of spatial and temporal characteristics, the bottom 10 cities in the PLE composite score from 2010 to 2020 gradually change from a westernized character to a westernized and northeasterlies character. We performed an analysis of the reasons for the bottom 10 cities in the composite score. Firstly, some cities in the western region have a thin industrial base and public service level bottom, and the ecological and environmental quality in the process of rough economic growth is not good, which together lead to some cities’ low composite PLE score. Secondly, as the state attaches importance to ecological and environmental management, the degree of investment has deepened, prompting the overall ecological and environmental quality in the western region to rise, causing some cities in the western region to gradually move out of the bottom 10. Thirdly, in recent years, the hollowing out of industries, the loss of population and the decline in the level of public services in some cities in the Northeast have led to a significant reduction in the quality of the production, living and ecological environment (PLE) in the region. For example, in Hegang, one of the most popular cities on the internet, individual houses are sold for only RMB 15,000, which is equivalent to a month’s salary in Shanghai. In an era of high property prices, Hegang has become a place for young people to escape the fierce competitive large cities. However, the issue of strengthening the resilience of industrial and supply chains, revitalizing existing resources, building a modern economic system and improving the quality of the “production, living and ecological” environment (PLE) in some northeastern cities with “hollowed out” industries and high population outflows remains a huge challenge for local governments.The spatial gradient between the eastern, central and western regions is significant in terms of the overall scores of the four regions . The oveThe spatial and temporal distribution of the 285 cities in terms of their overall scores shows “cluster” distribution of cities with high environmental quality in terms of “production, living and ecology” from 2010 to 2020 . The fouAnalysis of the spatial distribution characteristics of cities with high production, living and ecological environmental quality. Firstly, the spatial pattern shows a significant spatial gradient of PLE scores from east to central to west, with the PLE scores decreasing as we move towards the western regions. Secondly, although the PLE composite score of the eastern coastal region is much higher than that of the central and western regions, the spatial differences are significant. It can be divided into two types: multinuclear and binuclear. The former is typified by the Yangtze River Delta city cluster and the Pearl River Delta city cluster, both of which have spatially contiguous cities with high PLE scores, while the latter is typified by the Shandong Peninsula city cluster, who’s high PLE scores are characterized by the “Jinan-Qingdao” twin core. Thirdly, most of the cities in the western region are spatially distributed in a double-core or single-core pattern. The Chengdu-Chongqing urban agglomeration is typical, while the Guanzhong urban agglomeration and the Beibu Gulf urban agglomeration are typical of the single-core spatial distribution. The spatial distribution of the above cities is basically consistent with the strategic spatial layout of the large urban agglomerations approved by the state, indicating that there is a great consistency between the level of urbanization and the quality of the urban “production, living and ecological” environment. The higher the level of urbanization, the higher the overall score of “production, living and ecological” environmental quality of the city.2 of 0.761 , 14 very large cities , 14 Type I large cities , 70 Type II large cities and over 500 small and medium-sized cities. Since four of the 105 large cities are county-level cities, including Kunshan , Yiwu , Cixi  and Jinjiang , the environmental quality of urban “production, living and ecology” is only counted at the prefecture-level city level, so excluding these four cities, there are 101 large cities left.2 value increasing from 0.761 to 0.779. Most of the 101 cities are in the top 25% in terms of their combined PLE scores, a result that is highly consistent with the “clustered” spatial distribution of cities with the highest PLE scores. This result is highly consistent with the “cluster-like” spatial distribution of the cities with the highest PLE scores. The coefficient before the ln(x) function in the model decreases, from 0.9625 to 0.823, indicating that as the PLE score increases, the built-up area does not increase indefinitely, but has certain limits, as exemplified by the mega-cities of Beijing and Shanghai. For Bottom184 cities, the logarithmic relationship between the combined PLE score and built-up area for small and medium-sized cities has weakened  and other aspects . These gSince the founding of New China, China has made certain achievements in transforming old cities and building new towns. However, for a long time, “focusing on production and neglecting life”, focusing only on industrial output value and ignoring urban construction, coupled with the tight and uncertain policies on population control and residential migration, led to different degrees of housing difficulties, tight traffic, environmental degradation, increased unemployment and other problems in various cities . In 2011The deep reason for the change of urban “production, living and ecological” environmental quality is the interweaving and promotion of industrialization and urbanization. Industrialization is also linked with globalization, which together cause profound changes in the “production, living and ecological” environmental quality of Asian cities. Due to multiple reasons such as economic transformation and development, political system reform, opening to the outside world, and world industrial specialization, the environmental quality of “production, life, and ecology” in Chinese cities has been accelerated. At the technical level, due to different starting points, there are also large differences in the urban “production, living, ecological” environmental evaluation index system. The high value areas of the ecological space quality index are mainly concentrated in the northeast and southeast coastal areas. Our research also shows that the characteristics of spatial gradient in the eastern, central and western regions are significant. The environmental quality of “production, life and ecology” in the eastern region is the highest, followed by the central region, and again in the western region. However, we take cities as the research object, which is more detailed in spatial scale compared with Li’s research .From the theoretical perspective of “elements structure function”, Liu (2017) used the national land use data to evaluate the utilization of “production, living and ecology” space in 1990 and 2010, and concluded that the production space is mainly distributed in the main urban agglomerations in the southeast of the Hu Huanyong Line, the living space is mainly concentrated in the major cities and urban agglomerations in China, and the ecological environment is mainly distributed in the northwest of the Hu Huanyong Line . Our resOf course, our research is also insufficient. Although the research reveals the temporal and spatial pattern of urban “production, life and ecology” environmental quality from the urban level, there is still a lack of dynamic mechanism analysis of urban “production, life and ecology” environmental quality change. In the discussion part, it is mentioned that industrialization and globalization have the power of changing each other and have an impact on the urban “production, life and ecological” environmental quality. However, this impact should be analyzed in combination with the national conditions and the background of the times. Through field research, micro data can be obtained to reveal the micro mechanism of urban “production, life and ecological” environmental quality changes.In this paper, we use the entropy method, the Theil index and correlation analysis, the study analyzed the spatial and temporal differences in “production, living and ecological” environmental quality of 285 cities in China from 2010 to 2020, and reached the following main conclusions.(1) In terms of overall differences, the overall differences in the “production, living and ecological” environmental quality indices of the 285 cities in the study period underwent a process of “narrowing–widening–narrowing”. The differences within the four major zones of the country are much higher than those between the four major zones, and the differences within the zones show an increasing trend year by year. The intra-belt contribution rate is, in descending order, Eastern Region > Western Region > Central Region > Northeast Region. Intra-provincial variation in the eastern region is the main driver, while the contribution of intra-difference in the northeastern region is the smallest, and the contribution of intra-difference in the central and western regions is second only to that of the eastern region.(2) In terms of time series differences, the overall scores of “production, living and ecological” environmental quality in the 285 cities in the study period show a decreasing trend, and the contribution of the PLE subsystem scores are, in descending order, production environmental quality > living environmental quality > ecological environmental quality, reflecting that the overall level of “production, living and ecological” environmental quality in the country is not satisfactory. “The unbalanced development between the production environment, living environment and ecological environment is still a prominent problem. Although the government is determined to continue to tackle the problem of ecological pollution during the study period and has achieved certain results, the current economic structure of China is undergoing a deep transformation and the industrial structure has not yet been renewed, and the transformation and upgrading pains of the energy and industrial structures are the underlying causes of the imbalance in the quality of the urban “production, living and ecological” environment.(3) In terms of overall ranking, the headline effect of the PLE score is significant during the study period, with the top 10 cities being all mega-cities and megacities in China, with Shanghai, Beijing, Guangzhou and Shenzhen remaining in the top 4. The bottom 10 cities in the composite score are all small and medium-sized cities with significant regionalization characteristics, and from 2010 to 2020 the bottom 10 cities in the PLE composite score gradually change from a westernized character to a westernized and northeasterlies character.(4) In terms of spatial pattern, there is a significant spatial gradient in the east, central and western regions, with the four major regions having the highest to lowest overall scores in terms of “production, living and ecological” environmental quality: eastern region > central region > western region > northeastern region. Regions with high scores in the “production, living and ecological” environment can be classified into three types: multinuclear, binuclear and mononuclear. The cities with high environmental quality in terms of production, living and ecology are mainly concentrated in China’s coastal areas, the Pearl River Delta, inland provincial capitals and other urban agglomerations. Some cities in the western part of the country have seen their scores rise faster, while some cities in the northeast have seen their scores fall significantly.(5) In terms of influencing factors, there is a logarithmic relationship between the combined PLE score and the area of the built-up area, while the area of the built-up area and the combined PLE score show an exponential curve. The logarithmic relationship between PLE and BUA is significantly influenced by the urban population control variable. The logarithmic relationship between PLE and BUA is weakened for small and medium-sized cities with an urban population of less than 1 million.


Fermented foods have been a part of human diet for almost 10,000 years, and their level of diversity in the 21st century is substantial. The health benefits of fermented foods have been intensively investigated; identification of bioactive peptides and microbial metabolites in fermented foods that can positively affect human health has consolidated this interest. Each fermented food typically hosts a distinct population of microorganisms. Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, which can now be resolved at the species and strain level by metagenomics. Transient or long-term colonization of the gut by fermented food strains or impacts of fermented foods on indigenous gut microbes can therefore be determined. This review considers the primary food fermentation pathways and microorganisms involved, the potential health benefits, and the ability of these foodstuffs to impact the gut microbiome once ingested either through compounds produced during the fermentation process or through interactions with microorganisms from the fermented food that are capable of surviving in the gastro-intestinal transit. This review clearly shows that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet. Fermented foods have been a component of the human diet from ancient times. Among the earliest evidence for the deliberate application of fermentation has been found in pottery vessels discovered in China dating from 7000 BC that were used to ferment rice, honey, and fruit . HoweverHowever, while the primary function of food fermentation revolves around enhanced food safety and extended shelf-life, fermented foods have become associated with health benefits as well. One of the earliest proponents of this hypothesis was Élie Metchnikoff, who was interested in the potential of food in promoting the elongation of life. In Metchnikoff’s essay entitled ‘Lactic Acid and Putrefaction’, he attributes the long lives of Bulgarian peasants to the staple foods of the country at the time, in particular soured milk. In his experiments, he found that lactic acid bacteria (LAB) cultures in the fermented food produced ‘disinfecting bodies’ beneficial to their human host . Thus, fConsequently, researchers have proposed that fermented foods be included as part of dietary guidelines. Chilton and colleagues argue that due to their long role as part of the human diet and their established and emerging nutritional and therapeutic benefits (which will be discussed in detail below), brought about in part by their own microbiome, they deserve to be considered for regular consumption and to be included in food consumption guidelines . In addiIn this review, a brief introduction to fermented foods and their potential health benefits is followed by a discussion of the ability of fermented foods to impact the gut microbiome, either through fermented food communities surviving gastric transit and becoming established transiently or permanently as part of the gut microbiome, or through provision of nutrients that support the growth of indigenous gut microbiota; in addition, we explore the potential nutritional and health benefits associated with such interactions.The earliest evidence of food fermentation dates from the Neolithic period, ~7000 BC, in China , a perioThe process of fermentation has been exploited by almost all peoples and has been applied to plant materials  and animal materials , reflecting the base foods available in different regions ,13.It is difficult to definitively establish the number of fermented foods produced globally; most estimates suggest that there are in excess of 5000 different kinds . HoweverAs a consequence of their ancient origins, there is a strong regional bias in the distribution and popularity of different fermented foods. For example, throughout much of East and South Asia and the southern regions of India fermented legumes, in particular soyabeans, as well as vegetables, fish, and meat are common components of the diet. In West Asia, Northern India, Europe, and North America, fermented cereals, including wheat, barley, and oats, are used to make bread, and fermented dairy and meat products are more common. In Africa and South America fermented seeds, including sorghum, maize, millet, cassava, and legumes, are an important component of the diet, as are fermented milk and meat products . A recenFermentation is a process whereby substrates are converted to alcohols, carbon dioxide, and/or organic acids, predominantly anaerobically . From thThe substrate for both lactic acid and ethanol fermentation consists of the sugars available in the food material, for example (though not limited to) lactose in milk and glucose from the breakdown of starch in plant products; the products of both pathways, in addition to influencing the sensory characteristics of the fermented food, play a critical role in extending its shelf life, as the accumulated lactic acid or ethanol inhibits the growth of undesirable spoilage and/or pathogenic microorganisms. Propionic or acetic acid fermentation is effectively secondary fermentation, the substrate being the product of lactic or ethanol fermentation, respectively. This contributes to extended shelf life and is critically important in impacting the sensory characteristics of the final product. Citric and malolactic fermentations use substrates available in the raw food material, which are converted into products that impact the sensory characteristics of the fermented food. It is important to note that during the food fermentation process, the microorganisms present can release amino acids and encrypted bioactive peptides from proteins, convert fats to more healthy formats such as conjugated linoleic acid, and produce a wide diversity of metabolites, including short chain fatty acids (SCFA), vitamins, exopolysaccharides, and gamma-aminobutyric acid; these impact the sensory characteristics and health-promoting potential of the final fermented food product .Lactococcus lactis, Streptococcus thermophilus, homofermentative Lactobacillaceae including Lactobacillus delbrueckii subspecies bulgaricus, Lactobacillus acidophilus, and Lactobacillus helveticus, and members of the Pediococcus and Enterococcus genera [Leuconostoc spp. and several lactobacilli, including Fructilactobacillus sanfranciscensis, Levilactobacillus brevis, Limosilactobacillus fermentum, and Limosilactobacillus reuteri. The most commonly encountered facultative LAB include Lactiplantibacillus plantarum, Lacticaseibacillus casei, and Latilactobacillus curvatus [The lactic acid fermentation pathway is arguably the most important fermentation pathway in terms of fermented foods. It is the basis of all dairy fermentation as well as the majority of fermentation processes using plant or animal source materials. The bacteria responsible are LAB, which are grouped depending on whether they are homo-, hetero-, or facultative fermenters . While hs genera . Heterofcurvatus .Saccharomyces cerevisiae, although Zymomonas mobilis (a gram-negative bacterium) is used for, among other products, the production of the fermented Mexican beverage Pulque [Zymomonas mobilis is used, the pathways differ [Zymomonas generates only one mole of ATP [Zymomonas uses a variation of this, the Entner–Doudoroff pathway [Ethanol fermentation is responsible for the production of wines from fermented fruits, beers from cereals such as wheat, barley and rye, and other stronger liquors involving distillation following fermentation such as sake from rice, vodka from potatoes, and rum from sugar cane . The orge Pulque ,28. Whils differ . While be of ATP . This di pathway . It is w pathway . Kefir,  pathway .Acetobacter and Komagataeibacter are of particular interest due to their high tolerance of both the substrate (ethanol) and product (acetate) present in their growth media [Acetic acid is an important component in vinegar and is derived from fermenting alcoholic beverages such as wine, cider, and beer; the end product differs depending on the region in which it is produced and the alcoholic beverage used . As discth media .2 giving rise to the characteristic flavour and holes or “eyes” associated with these cheese types [2 for every three moles of lactate catabolized [Emmental and other Swiss-type cheeses rely on the ability of Propionic Acid Bacteria (PAB) to ferment lactate to propionic acid, with the coproduction of acetate and COse types . Propionabolized . PAB useabolized .L. lactis subsp. lactis biovar diacetylactis and certain Leuconostoc species, respectively. The fermentation pathway and the end products produced vary depending on the LAB involved as well as environmental factors, including the availability of fermentable carbohydrate and the pH. Potential end products include acetate, formate, ethanol, 2,3-butanediol, diacetyl, acetoin, carbon dioxide, and lactate [Citrate fermentation is an important metabolic pathway for certain fermented foods, in particular in the dairy sector . This fe lactate , of whic lactate .Oenococcus oeni, although other Lactobacillaceae and Pediococcus species can be used [Lactic acid bacteria are responsible for the malolactic fermentation process that is involved in the production of wine as well; this predominantly takes place after alcohol fermentation by yeast . This re be used .The primary microorganisms responsible for the main fermentation pathways that occur in food are discussed above and are listed in Arthrobacter, Bacillus, Bifidobacterium, Brachybacterium, Brevibacterium, Enterobacter, Hafnia, Haloanaerobium, Halobacterium, Halococcus, Klebsiella, Kocuria, Micrococcus, Pseudomonas, and Staphylococcus have been recorded in different fermented foods [Brettanomyces, Candida, Cryptococcus, Debaryomyces, Dekkera, Galactomyces, Geotrichum, Hansenula, Hanseniaspora, Hyphopichia, Issatchenkia, Kazachstania, Kluyveromyces, Metschnikowia, Pichia, Rhodotorula, Rhodosporidium, Saccharomyces, Saccharomycodes, Saccharomycopsis, Schizosaccharomyces, Sporobolomyces, Torulaspora, Torulopsis, Trichosporon, Yarrowia, and Zygosaccharomyces, while the filamentous moulds include Actinomucor, Amylomyces, Aspergillus, Monascus, Mucor, Neurospora, Parcilomyces, Penicillium, Rhizopus, and Ustilago [However, even under modern food processing systems most of the ingredients used in the preparation of fermented foods and the processing equipment used in their manufacture are not sterilized; thus, in addition to known starter microbiota most fermented foods and beverages contain an indigenous microbiome, potentially consisting of a wide variety of microorganisms. Traditional microbiological methods demonstrate the existence of these indigenous microorganisms, often referred to as Non-Starter organisms; however, with the development and widespread application of affordable and reliable high-throughput DNA sequencing technologies numerous fermented foods have undergone metagenomic screening, revealing highly diverse and previously unrecognized populations of adventitious Non-Starter microorganisms ,16,39,40ed foods . The genLactococcus, Lactobacillus, Leuconostoc, Streptococcus, and Enterococcus, although certain varieties are more strongly associated with one type or another, which impacts the microbiome of a final product [Pseudomonas, Bacillus, Lactococcus, and Acinetobacter, the genera most common to raw camel’s milk include Enterococcus, Lactococcus, and Pediococcus [2–103 colony-forming units (CFU)/g), they proliferate and outcompete the starter cultures to become the dominant microbial populations during cheese ripening and are often responsible for the development of characteristic organoleptic properties [Penicillium roqueforti culture that emanate from the core outwards, has a very diverse microbiome that includes an outer rind that develops from different molds [The diversity that exists among fermented food microbiomes is exemplified by cheese. The microbiome that develops in cheese during ripening arises from the milk and other ingredients used for cheese manufacture, the starter cultures added at the beginning of manufacture, and the cheesemaking and ripening room environments . While t product ,45,46. Fiococcus ,48. The iococcus . For comiococcus ,51. NSLAoperties . Certainoperties ,54. Stilnt molds ,56.8 CFU/g; these can potentially gain entry to the human gastrointestinal tract, where they may interact with or become established as part of the gut microbiome [In addition, many fermented foods are eaten without further processing or preparation, and thus contain microbial populations of up to 10crobiome ,58.As discussed above, while fermented foods have a long history of safe use, there is a growing popular consensus that consumption of fermented foods results in positive health effects. Much of this is driven by popular observations that fermented foods in general use unprocessed raw ingredients, contain little or no added preservatives, colours or flavourings, and are made using long-established, sustainable, and in many cases traditional technologies. Consumers may be attracted to the concept that these are “live foods” containing natural and diverse microbiota.It is incumbent upon the relevant research community to generate data to clarify and identify the benefits of such foods, if any exist. In support of this, a number of controlled human dietary studies have recently been undertaken which sustain these popular perceptions of health benefits . These sIt well established that fermentation can enhance the digestibility of complex carbohydrates and proteins through the breakdown of starch to oligosaccharides and polypeptides to amino acids ,73. FermAdditionally, fermentation can facilitate transformations in raw foods that allow these foods to be tolerated by consumers that are intolerant of the original raw product. A good example of this is the ability of lactose-intolerant individuals to consume fermented dairy products, in particular ripened cheeses such as Cheddar. The reason for this is that during fermentation and cheese ripening, the LAB metabolize the lactose, significantly reducing the level of lactose in the resulting fermented food product. In addition, the presence of the lactase enzyme produced by bacteria present in the fermented matrix can help to further remove any residual lactose during ingestion and digestion . A similLactiplantibacillus plantarum, Lactobacillus delbrueckii, Limosilactobacillus reuteri), Propionibacterium, Bifidobacterium, and several species of Streptococcus [Leuconostoc and Pediococcus [In addition, bioactive compounds can be produced through protein, lipid, and carbohydrate catabolism during the fermentation process, and can result from the range of microbial metabolites produced during the process . Indeed,tococcus . Folic Atococcus . Non-daitococcus . Shalgamiococcus . This beiococcus ,85. Antiiococcus . Kombuchiococcus . Many otiococcus .Lactobacillus helveticus strain, a species known for its ability to release ACE-inhibitory peptides from milk protein, which significantly lowered blood pressure when compared with controls [Latilactobacillus sakei and Latilactobacillus curvatus [The release of bioactive peptides as a result of protein hydrolysis during fermentation has been investigated by multiple groups. A well-studied example of bioactive peptide release as a consequence of catabolism of protein involves angiotensin-1-converting enzyme (ACE)-inhibitory peptides, a group of peptides with hypertension-lowering capabilities . LAB frocontrols . Human tcontrols . ACE-inhcurvatus .Zymomonas, Leuconostoc, Pediococcus and Streptococcus species, and members of the Lactobacillaceae family [Pediococcus-produced β-glycans to lower serum cholesterol levels [Lacticaseibacillus paracasei to lower serum cholesterol in mice found that a significant decrease was observed when compared to control mice that were not given the EPS-producing Lacticaseibacillus strain [Lacticaseibacillus paracasei [Pediococcus damnosus strain [Bifidobacterium species  and total faecal bacterial counts [Many food fermentation microbes are capable of producing high molecular weight exopolysaccharides (EPS) from simple sugars present in the raw food product. EPS can be produced by e family . Examplee family . In terme family . Dendrite family . EPS prol levels . While pl levels . A paperl levels ,95. An is strain . Additioaracasei . A simils strain . This stl counts . Thus, fBacteroides spp., Pseudomonas spp., Dorea spp., Lachnospiraceae, Prevotella spp., Alistipes putredinis, Oscillospira spp., Enterobacteriaceae, Fusobacterium spp., Actinomyces spp., Achromobacter spp., Clostridium clostridioforme, Faecalibacterium prausnitzii, Bacteroides uniformis, Clostridiales, and Delftia spp. [Lactobacillus acidophilus, Levilactobacillus brevis, Lactobacillus kefiranofaciens, Lentilactobacillus parabuchneri, Lactobacillus helveticus, and Latilactobacillus sakei) and microbes not associated with fermented foods  [The ability of fermented foods to modulate the gut microbiome has been documented by several groups with varying degrees of success. Changes are generally recorded as overall shifts in microbial populations, and do not necessarily reflect the microbial content of the fermented foods in question. A recent study evaluated the effect of general fermented plant intake on microbial and metabolomic differences in consumers versus non-consumers , and determined that beta diversity was significantly different between consumers versus non-consumers [lyticus) . The dielyticus) .Bilophila wadsworthia  and an increase in two Clostridiales isolates (uncharacterized genera MGS203 and MGS126) known for butyrate production [Firmicutes/Bacteroidetes rand Ascomycota/Basidiomycota ratios at the phylum level [Bacteroidetes  species and a decrease in Firmicutes abundance  that reversed when the product was no longer being ingested [Firmicutes and yet a decrease in this phylum was observed, highlighting the varying and complex relationship between fermented foods and the gut microbiome. In contrast, Tillisch and colleagues (2013) reported no significant changes to the microbial composition of stool samples following ingestion of a probiotic-containing fermented milk [Helicobacter pylori exhibited lower stool Bifidobacterium than their healthy counterparts, which could be restored partially through ingestion of a probiotic yogurt that led to a significant increase in their stool Bifidobacterium spp./Escherichia coli ratio [Enterococcus populations and the ability of the cheese microbiome to be detected in faecal samples [Enterococcus faecalis populations in stool samples were significantly increased post-Camembert ingestion, while cheese populations of L. lactis and Ln. mesenteroides were detected in faeces during the trial [n = 544) and 16S rRNA sequencing  [Ruminococcaceae family, one Streptococcus, one unidentified genus belonging to the Lachnospiraceae family, and one belonging to the Christensenellacaea family) had significantly increased relative abundance [S. thermophilus and B. animalis and yogurt consumption, whereby greater levels of both species were present in participants who consumed higher quantities of yogurt in a dose-dependent manner, although this increased colonisation appears to be transient [Different groups have reported changes in gut microbe populations following ingestion of fermented milk, although parameters vary between studies ,100,101.oduction . A separum level . Healthyted milk . Childreli ratio . The effli ratio . Firmess samples ,106. Enthe trial ,105. Le  cohort) . For thebundance . Shotgunransient . Both ofransient .Bacteroides and Prevotella and a relative decrease in Blautia [Clostridiales order), although the unpasteurized group showed significantly greater numbers of sauerkraut-associated LAB (Lactiplantibacillus plantarum and Levilactobacillus brevis) than their pasteurized counterparts [Aspergillus luchuensis, and its effects on perturbations in the gut microbiota was investigated in mouse caecal and human faecal samples, showing significant increases in Clostridium clusters XI and XIVa (members of which are established butyrate producers), respectively [Bifidobacterium spp. were significantly increased following three weeks of coffee consumption by healthy adult volunteers, although inconsistencies between subjects were observed [E. coli and Clostridium perfringens [Lacticaseibacillus casei on in vitro and in vivo microbiome populations were assessed by Wu and colleagues (2021), with differences being seen in both instances [Lactobacillus, Akkermansia, E. coli, and butyric acid-producing bacteria, while Bacteroides and Ruminococcus decreased significantly. For their in vivo murine trial, the fermented beverage was freeze dried and fed to male Kun Ming mice in several concentrations, and was found to alter beta diversity and various genera depending on the concentration [The ability of fermented foods to impact gut microbial populations is not limited to fermented dairy products. The effect of both fresh and fermented kimchi on the gut microbiome of obese patients was examined in . Althoug Blautia . A studyterparts . Two septerparts ,110. Ingectively . Faecal observed . Fermentfringens . The effnstances . When thntration .Thus, fermented foods have been shown to have the capacity to modify gut microbiome populations, although it can often be unclear as to how these changes are brought about. While this has been shown in the above examples for a myriad of different fermented food types, the results cannot be directly compared due to highly variable parameters, including the use of both healthy and disease models and the various methods by which microbes are quantified. Fermented foods may interfere with the gut microbiome through its own microbiome or through the nutrients present in its matrix. Therefore, in an effort to provide objective evidence that clearly demonstrates whether or not fermented foods can modulate the human gut microbiome, more in-depth and well-defined human feeding studies need to be undertaken. In these studies, the microbiomes of both the fermented food and the human gut need to be established using the most advanced and sensitive tools available in order to permit changes at both the genus and the species level to be determined.In addition to the benefits of fermented foods to the host, certain chemicals present in fermented foods can affect the host’s gut microbiome directly. The production of two types of chemicals in particular have come under scrutiny due to their documented effects on microbial populations, polyphenols and dietary fibre, the latter of which leads to the in vivo production of short-chain fatty acids .Agaricus sp.) was compared; both fermented corns showed an increase in FPP content compared to the unfermented control, with one of the strains having an FPP content 88 times greater than the control [Fermentation can lead to increases in polyphenol bioavailability in fermented foods ,117,118. control . Unsurpr control . Thus, eH. pylori urease enzyme required for its ability to neutralize gastric acid [Various studies have shown that polyphenols can impact bacteria found in the gut, although the majority of these studies focus on pathogen inhibition ,124,125.ric acid ,131.Enterococcus, Prevotella, Bacteroides, Bifidobacterium, Eggerthella lenta, and Blautia coccoides–Eubacterium rectale groups in similarly healthy individuals who consumed wine once a day, although the dominant groups shifted throughout the duration of the study [Bifidobacterium and Prevotella with beverage consumption that was negatively correlated with LPS [Bifidobacterium and Lactobacillaceae levels, increased the levels of butyrate-producing Faecalibacterium prausnitzii and Roseburia, and decreased LPS-producing E. coli and Enterobacter cloacae [Firmicutes/Bacteroidetes ratio linked with high-fat diets, although Etxeberria et al. found that only quercetin was able to decrease microbial groups previously associated with diet-induced obesity, while Zhao et al. concluded that a combination of quercetin and resveratrol was capable of the same effect [Wine is a rich source of polyphenols, and manipulation of various factors during grape growth and processing can increase total polyphenol content . Red winhe study ,136. A pwith LPS . Similar cloacae . Two sep cloacae ,138. Bote effect ,138. As Bifidobacterium are established producers of these valuable components in vitro [Short chain fatty acids (SCFA) arise through the catabolism of carbohydrate fibres by microbes. This is important in human nutrition, as microbes indigenous to the colon are capable of this fermentative process and the SCFA thus produced are used as an energy source by colon cells; their formation benefits the human host, as it enables energy to be extracted from an otherwise-indigestible complex carbohydrate ,139. Welin vitro ,139. Whiin vitro . As alrein vitro . Acetatein vitro . More imin vitro . Mucus cin vitro ,145. A sin vitro ,147. ThuPropionibacterium freudenreichii, a species commonly used in the production of Swiss-type cheeses, to produce SCFA in rats; one strain in particular was found to significantly enhance the presence of these compounds within the caecum [Certain fermented foods have been shown to contain high levels of readily accessible SCFA . As state caecum .Thus, fermented foods have the potential to impact gut microbiota by modifying levels of particular compounds within food. Polyphenols have been shown to directly impact the microbial composition of the gut, while SCFA can induce a more favourable environment for the growth of beneficial gut microbes or impact mucus concentration, which acts as both an energy source and binding site for gut microbes.As discussed above, fermented foods contain large and diverse microbiomes, many species of which are to be found within the gut microbiota as well; thus, it is reasonable to propose that fermented foods could be a source of these microorganisms. However, in order for this to occur the fermented food microbiota must have the capacity to survive the environmental stresses of the digestive tract. This requires tolerance to low pH and bile, traits used in the selection of probiotic bacteria. Many groups have investigated the microbiota of fermented foods as a source of new probiotic bacteria, and many have found bacteria that are capable of surviving gastric transit, implying that this property may be common among the microbiota found in fermented foods. Potential to survive gastric transit can be investigated using a range of in vitro models and using either purified bacterial cultures grown in laboratory media or by incorporating the test organism into the model food matrix.Lactiplantibacillus plantarum isolates from both Argentinean and Italian cheeses for potential probiotic characteristics [Lactiplantibacillus plantarum strains tested showed excellent resistance to digestive stresses and on average about 40% tolerance to bile; the data reported were the average of three different bile concentrations, including one more than three times higher than physiological conditions, in which case their survival level in vivo may be much higher [Lactiplantibacillus plantarum is present in a myriad of fermented foods made from vegetables, meats and dairy products, and is found in the human intestine as well [Lactiplantibacillus plantarum has been investigated by other authors and has been found to survive well under gastric conditions. Haller and colleagues investigated a number of strains both from fermented foods and of intestinal origin and determined that, while the strains from the intestines performed the best under digestive stresses, the Lactiplantibacillus plantarum strains survival rates that are used to ferment fruit were broadly similar [Lactiplantibacillus plantarum, one Ln. mesenteroides ssp. mesenteroides/dextranicum, and one Levilactobacillus brevis strain, all of which were capable of surviving simulated digestion, including low pH, bile salts and digestive enzymes, at rates of above 5 log CFU/mL, resulting in only approximately 1 log CFU/mL reduction following exposure to simulated GIT conditions [Lacticaseibacillus casei strains from fermented dairy products to low pH  and high bile (1%–2%), revealing three acid-tolerant strains  and strains with varying levels of bile tolerance [Lacticaseibacillus casei strains appear to be less tolerant of simulated digestion, it should be taken into account that they would normally be found in a fermented food matrix, and the bile concentrations used were very high in comparison to physiological conditions [7 CFU/g could survive simulated gastric transit, a sufficient number to potentially impact the gut microbiome. This research demonstrates the in vitro potential of Lactobacillaceae strains from fermented foods to survive gastric transit, potentially allowing them to influence the gut microbiota. However, the importance of the fermented food itself to protect the bacteria during digestion needs more consideration.A study in 2011 screened eristics . The moseristics . Survivaeristics . The Lach higher . These dh higher . In this as well . While s similar . A study similar . While inditions . Mishra olerance . While tnditions . While mnditions . The obsLacticaseibacillus paracasei IMPC2.1 into the intestines of five human subjects, who were given 10–15 olives coated with 109–1010 CFU of lactobacilli [Lacticaseibacillus strain was absent in the faecal samples prior to ingestion of the olives, it was detected in four of five of the subjects post-consumption using a combination of Vancomycin-containing agar plates and PCR-Amplified Ribosomal DNA Restriction Analysis (ARDRA) [Lacticaseibacillus rhamnosus GG and LC705, Propionibacterium freudenreichii subsp. shermanii JS, and Bifidobacterium animalis subsp. lactis Bb12 when administered as either capsules or interred in yogurt or cheese [Lacticaseibacillus rhamnosus strain based on counts in faeces, both the P. freudenreichii and B. animalis strains showed higher survival levels when administered in the yogurt matrix, although counts in the other matrices were still high (log10) [In other cases, fermented foods are used as a delivery vehicle for probiotic strains that may not be autochthonous for that environment. In 2005, a group investigated the effectiveness of fermented olive varieties  at carrying the established probiotic obacilli . Faecal obacilli . While t (ARDRA) . Therefo (ARDRA) . A studyr cheese . In this (log10) . This stLacticaseibacillus casei 334e, with the added stage of refrigerating both matrices for time periods reflecting their shelf-life  in order to test their ability to sustain probiotics during storage [Lacticaseibacillus strain was inoculated into both fermented foods during the manufacturing process at 107 CFU/g and remained at this viable count after storage in both cases [Lacticaseibacillus casei remained higher following exposure to pH 2.0, stabilizing at approximately 104 CFU/g after 120 min of exposure in cheese, as opposed to less than 101 CFU/g in yogurt after only 30 min [Lacticaseibacillus paracasei and Lacticaseibacillus rhamnosus strains embedded in two dairy matrices, Cheddar cheese and fermented milk [Limosilactobacillus reuteri LR92, a strain with known potential probiotic properties, was tested for its ability to survive gastric transit using a fermented vegetable/fruit blended beverage as a matrix [In 2008, yogurt and low-fat cheese matrices were compared as barriers against acid exposure for the probiotic  storage . The Lacth cases . This sty 30 min . A recented milk . The baca matrix . Unlike a matrix , storagea matrix . While ia matrix . Fermenta matrix . TherefoBacteroides and other groups with high bile tolerance being present in the intestines of the human host due to the greater concentration of bile excreted to deal with animal fat digestion, while a high-carbohydrate diet is associated with the Prevotella enterotype [Bifidobacterium longum on a cohort of volunteers who were put onto an animal-based diet for five days, followed by a ‘recovery’ balanced diet for fourteen days [Bilophila, Odoribacter, Dorea, and Ruminococcus, all of which are associated with either a metabolic disorder  or other illness, including colon cancer [Bifidobacterium decreased in these two groups [Dorea group), indicating that the probiotic yogurt may have had a stabilizing capacity on the gut microbiota, although the authors stated that this may be attributed to the higher carbohydrate levels ingested in the YAB group [Bifidobacteria used in this study was known to produce bile salt hydrolase enzymes, it was proposed that this might limit the growth of the bile-metabolizing groups Bilophila and Odoribacter [Few studies that examine the microbial consequences of ingesting fermented foods have been reported in the literature, and those that are available are usually grouped together with a diet (such as cheese) or with the focus on a probiotic of interest that is present already or more likely has been added in high cell numbers, with the fermented food acting as a vehicle for said strain. It has previously been established that diets dominated by specific macronutrients and deficient in others effect the composition of the gut microbiome, with enterotypes (defining microbiotas based on their dominating taxa) developing when these eating patterns are long-term ,168. In terotype ,169. Proeen days . Three deen days . Followin cancer ,173,174.o groups . HoweverAB group . As the ribacter ,175,176.Bifidobacteria, Lactococcus and Streptococcus on the microbiome of seven sets of female monozygotic human twins while, in a parallel study, gnotobiotic mice were seeded with a model human gut microbiome of known species the genomic sequences of which were available [Bifidobacterium strain was recovered in the highest amounts from the faecal samples in comparison to its companion starter strains [In 2011, McNulty and colleagues used controlled conditions to ascertain the effects of a specific set of five known bacteria belonging to the family Lactobacillaceae and the genera vailable . The purvailable . The fivvailable . The micvailable . In any  strains . The aut strains . However strains . This maLactiplantibacillus pentosus strain and a Pediococcus pentosaceus strain) were not tracked through the experiment, and it is unclear whether these specific strains comprised a proportion of the LAB counts or whether they were even able to survive the initial gastric transit [Another study reported the impact of yogurt containing deep sea water  on the gut microbiome of clinical subjects . This tr transit . AdditioAlthough the relative abundance of fermented food microbiota are not uniform, the gut microbiome is exposed to and interacts with these allochthonous bacteria following ingestion either transiently or on a more long-term basis ,181. TheFermented foods have an important place in human history, and while their primary function was originally shelf life extension of seasonal foods, health benefits associated with their consumption have long been recognized . Almost As originally documented by Metchnikoff, fermented foods are being investigated for their ability to exert health benefits. There is growing scientific evidence to support this contention, including data demonstrating that fermented foods can be more easily digested due to partial protein digestion during fermentation as well as indications that they can be enriched in certain vitamins and antioxidants. It has been demonstrated that fermentation can result in the release of bioactive peptides, for example the well documented ACE inhibitory peptides and the production of bacterial EPS, which can help to reduce cholesterol. Controlled human clinical trials are the gold standard used to confirm benefits associated with foods or pharmaceuticals; however, while a number of studies have demonstrated health benefits associated with fermented foods , more sThe human gut microbiome has received much attention in recent years, with increasing evidence that it impacts both physical and mental health ,185 and