A Comparative Metagenome Survey of the Fecal Microbiota of a Breast- and a Plant-Fed Asian Elephant Reveals an Unexpectedly High Diversity of Glycoside Hydrolase Family Enzymes

A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal. The microbial diversity was examined via 16S rRNA gene analysis. We generated more than 44,000 GS-FLX+454 reads for each animal. For the baby elephant, 380 operational taxonomic units (OTUs) were identified at 97% sequence identity level; in the six-years-old animal, close to 3,000 OTUs were identified, suggesting high microbial diversity in the older animal. In both animals most OTUs belonged to Bacteroidetes and Firmicutes. Additionally, for the baby elephant a high number of Proteobacteria was detected. A metagenomic sequencing approach using Illumina technology resulted in the generation of 1.1 Gbp assembled DNA in contigs with a maximum size of 0.6 Mbp. A KEGG pathway analysis suggested high metabolic diversity regarding the use of polymers and aromatic and non-aromatic compounds. In line with the high phylogenetic diversity, a surprising and not previously described biodiversity of glycoside hydrolase (GH) genes was found. Enzymes of 84 GH families were detected. Polysaccharide utilization loci (PULs), which are found in Bacteroidetes, were highly abundant in the dataset; some of these comprised cellulase genes. Furthermore the highest coverage for GH5 and GH9 family enzymes was detected for Bacteroidetes, suggesting that bacteria of this phylum are mainly responsible for the degradation of cellulose in the Asian elephant. Altogether, this study delivers insight into the biomass conversion by one of the largest plant-fed and land-living animals.     

早期灌喂母源粪菌对新生仔猪肠道菌群发育的影响

【目的】粪菌移植(fecal microbiota transplantation,FMT)作为一种治疗手段,已在人类肠道疾病治疗中有较多应用,但在干预新生仔猪肠道菌群上的研究未见报道。本文旨在研究早期母源粪菌移植对新生仔猪肠道菌群发育的影响。【方法】选取一窝12头杜长大新生仔猪,随机分为粪菌处理组(feces treatment,FT)和对照组(control,CO)。FT组仔猪出生后1–5 d每日灌注母源粪菌接种液,CO组灌注等量生理盐水。于1、3、5、7、10、14、18和22日龄采集仔猪粪样,Miseq高通量测序分析仔猪粪便菌群。【结果】灌喂母源粪菌有增加仔猪肠道菌群丰富度的趋势;主坐标分析显示,两组仔猪粪样菌群结构簇并未分开,并在18和22日龄时靠近母猪粪样菌群结构簇;随日龄增加,两组仔猪肠道中的变形菌门丰度均显著降低,而厚壁菌门的丰度显著增加,且从10日龄起拟杆菌门和厚壁菌门之和约为90%;与对照组相比,灌喂母源粪菌增加了10日龄时Escherichia-Shigella的丰度,而降低了18日龄时该菌属的丰富度,18日龄时肠球菌属和普氏菌属的丰度则显著增加。【结论】1–3日龄口服灌喂母源粪菌液并不能影响仔猪肠道菌群的定殖,这一阶段主要受母体微生物结构的影响;灌喂粪菌液对仔猪肠道菌群定殖的影响最多持续10–14 d;而且仔猪在22 d左右,肠道菌群结构逐渐趋同于母猪肠道菌群。     

Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses

Disease susceptibility and resistance are important factors for the conservation of endangered species, including elephants. We analyzed pathology data from 26 zoos and report that Asian elephants have increased neoplasia and malignancy prevalence compared with African bush elephants. This is consistent with observed higher susceptibility to tuberculosis and elephant endotheliotropic herpesvirus (EEHV) in Asian elephants. To investigate genetic mechanisms underlying disease resistance, including differential responses between species, among other elephant traits, we sequenced multiple elephant genomes. We report a draft assembly for an Asian elephant, and defined 862 and 1,017 conserved potential regulatory elements in Asian and African bush elephants, respectively. In the genomes of both elephant species, conserved elements were significantly enriched with genes differentially expressed between the species. In Asian elephants, these putative regulatory regions were involved in immunity pathways including tumor-necrosis factor, which plays an important role in EEHV response. Genomic sequences of African bush, forest, and Asian elephant genomes revealed extensive sequence conservation at TP53 retrogene loci across three species, which may be related to TP53 functionality in elephant cancer resistance. Positive selection scans revealed outlier genes related to additional elephant traits. Our study suggests that gene regulation plays an important role in the differential inflammatory response of Asian and African elephants, leading to increased infectious disease and cancer susceptibility in Asian elephants. These genomic discoveries can inform future functional and translational studies aimed at identifying effective treatment approaches for ill elephants, which may improve conservation.     

Bacterial diversity and the antimicrobial resistome in the southwestern highlands of Saudi Arabia

Soil is a reservoir of microbial diversity and the most supportive habitat for acquiring and transmitting antimicrobial resistance. Resistance transfer usually occurs from animal to soil and vice versa, and it may ultimately appear in clinical pathogens. In this study, the southwestern highlands of Saudi Arabia were studied to assess the bacterial diversity and antimicrobial resistance that could be affected by the continuous development of tourism in the region. Such effects could have a long-lasting impact on the local environment and community. Culture-dependent, quantitative polymerase chain reaction (qPCR), and shotgun sequencing-based metagenomic approaches were used to evaluate the diversity, functional capabilities, and antimicrobial resistance of bacteria isolated from collected soil samples. Bacterial communities in the southwestern highlands were mainly composed of Proteobacteria, Bacteroidetes, and Actinobacteria. A total of 102 antimicrobial resistance genes (ARGs) and variants were identified in the soil microbiota and were mainly associated with multidrug resistance, followed by macrolide, tetracycline, glycopeptide, bacitracin, and beta-lactam antibiotic resistance. The mechanisms of resistance included efflux, antibiotic target alteration, and antibiotic inactivation. qPCR confirmed the detection of 18 clinically important ARGs. In addition, half of the 49 identified isolates were phenotypically resistant to at least one of the 15 antibiotics tested. Overall, ARGs and indicator genes of anthropogenic activities (human-mitochondrial [hmt] gene and integron-integrase [int1]) were found in relatively lower abundance. Along with a high diversity of bacterial communities, variation was observed in the relative abundance of bacterial taxa among sampling sites in the southwestern highlands of Saudi Arabia.     

腹泻柴达木马亚成体粪便微生物多样性分析及其生物标记物的筛选

为比较青藏高原柴达木马亚成体腹泻与健康个体粪便微生物群落多样性和结构组成的差异, 我们利用16S rRNA测序技术对采集的腹泻 (n = 3) 和健康 (n = 13) 个体粪便样本细菌的组成与分布进行分析比较,并利用实时荧光定量PCR测定相关菌属的含量。结果显示,无论健康还是腹泻,厚壁菌门、拟杆菌门、疣微菌门、变形杆菌门和螺旋体门是柴达木马亚成体粪便中的优势菌门。相比健康组,腹泻组粪便微生物的Alpha多样性显著下降 (P < 0.05),厚壁菌门相对丰度下降而变形杆菌门的相对丰度显著增加 (P < 0.05),推断这两个门中的梭菌属、普雷沃菌属、纤杆菌属等丰度的失衡可能是导致柴达木马腹泻的原因之一。此外,通过机器学习的随机森林算法筛选出12个对健康和腹泻柴达木马亚成体粪便微生物差异具有较大影响的特征菌属,包括甲烷短杆菌属、纤杆菌属、Paludibacter、肉食杆菌属和迷踪菌属等。研究揭示了健康和腹泻柴达木马亚成体粪便微生物组的变化,为进一步研究青藏高原地区家畜腹泻提供一定的数据支持。     

Dysbiosis of gut microbiota was closely associated with psoriasis

Psoriasis is an autoimmune disease and gut microbiota participate in the establishment of intestinal immunity. This study was performed to identify the fecal microbial composition of psoriasis patients, and investigated the influence of subgroup(type and severity) on the fecal microbial composition, and to define the key microbiota in the pathogenesis of psoriasis. Fecal samples from 35 psoriasis patients and 27 healthy controls were sequenced by 16 S rRNA and then analyzed by informatics methods. We found that the microbiota of the psoriasis group differed from that of the heathy group. The relative abundances of Firmicutes and Bacteroidetes were inverted at the phylum level, and 16 kinds of phylotype at the genus level were found with significant difference. No microbial diversity and composition alteration were observed among the four types of psoriasis. The microbiota of psoriasis patients in the severe state differs from those of psoriasis patients with more mild conditions and also the healthy controls. The veillonella in fecal microbiota showed a positive relationship with h-CRP in blood. This research proved that psoriasis patients have a significant disturbed microbiota profiles. Further study of psoriasis based on microbiota may provide novel insights into the pathogenesis of psoriasis and more evidence for the prevention and treatment of psoriasis.     

Molecular Fingerprinting of the Fecal Microbiota of Children Raised According to Different Lifestyles

In this population-based study, 90 children from three European countries were examined to determine the impact of lifestyle on the fecal microbiota. The study was designed to assess the impact of two extreme lifestyles that we hypothesized could impact the microbial composition in the gut: i.e., an anthroposophic lifestyle (restricted use of antibiotics, greater consumption of fermented vegetables, etc.) versus living on a farm (greater consumption of farm milk, contact with animals, etc.). In previous studies, these lifestyles correlated with lower prevalence of allergies. Terminal restriction fragment length polymorphism (T-RFLP) was used to assess the bacterial composition in fecal samples since recent studies have shown that the majority of this community cannot be cultivated. The T-RFLP data were used to calculate richness and evenness of the fecal microbiota. Children that were attending Steiner schools (anthroposophic children) had a significantly higher diversity of microbes in their feces than farm children, who in turn also had lower diversity than the control groups. Specific primers were also used to focus on the Lactobacillus-like community (lactic acid bacteria [LAB]). Large differences were found in the LAB subpopulations in the sampled groups. In some children, the LAB subpopulation was dominated by a species that has not yet been cultivated.     

Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach

The bovine fecal microbiota impacts human food safety as well as animal health. Although the bacteria of cattle feces have been well characterized using culture-based and culture-independent methods, techniques have been lacking to correlate total community composition with community function. We used high throughput sequencing of total DNA extracted from fecal material to characterize general community composition and examine the repertoire of microbial genes present in beef cattle feces, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that traditional 16S sequencing using “universal” primers to generate full-length sequence may under represent Acitinobacteria and Proteobacteria. Over eight percent (8.4%) of the sequences from our beef cattle fecal pool sample could be categorized as virulence genes, including a suite of genes associated with resistance to antibiotic and toxic compounds (RATC). This is a higher proportion of virulence genes found in Sargasso sea, chicken cecum, and cow rumen samples, but comparable to the proportion found in Antarctic marine derived lake, human fecal, and farm soil samples. The quantitative nature of metagenomic data, combined with the large number of RATC classes represented in samples from widely different habitats indicates that metagenomic data can be used to track relative amounts of antibiotic resistance genes in individual animals over time. Consequently, these data can be used to generate sample-specific and temporal antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats.     

土壤动物肠道微生物多样性研究进展

随着分子生物学技术方法的快速发展,动物肠道微生物已成为医学、动物生理学与微生物生态学等研究领域热点。土壤动物种类繁多,分布广泛,其作为陆地生态系统重要组分,是驱动生态系统功能的关键因子。土壤动物体内的微生物由于与宿主长期共存,在与宿主协同进化中形成了丰富多样的群落结构,能够影响土壤动物本身的健康,进而介导土壤动物生态功能的实现。近些年,土壤动物肠道微生物工作方兴未艾,日渐得到重视。总结了四个部分内容：1)首先总结了土壤动物肠道微生物多样性领域的研究现状,该领域年发文量逐年增长,且近十年增长快速。土壤模式生物肠道微生物多样性研究较多且更为深入。土壤动物肠道微生物多样性组成与驱动机制、共存机制及群落构建的理论研究是该领域前沿;2)进而展示了土壤动物肠道微生物多样性组成和研究方法,土壤动物肠道菌群组成以变形菌门、厚壁菌门、放线菌门和拟杆菌门为主。早期工作基于传统分离培养,近年来新一代测序技术推动了该领域发展;3)接着关注了土壤动物肠道微生物的生态学功能,总体上体现在肠道微生物能帮助宿主分解食物基质、参与营养利用、影响寿命和繁殖及提高宿主免疫能力,且其能够影响土壤动物的气体排放及介导其对生态系...     

Short-Term Effect of Antibiotics on Human Gut Microbiota

From birth onwards, the human gut microbiota rapidly increases in diversity and reaches an adult-like stage at three years of age. After this age, the composition may fluctuate in response to external factors such as antibiotics. Previous studies have shown that resilience is not complete months after cessation of the antibiotic intake. However, little is known about the short-term effects of antibiotic intake on the gut microbial community. Here we examined the load and composition of the fecal microbiota immediately after treatment in 21 patients, who received broad-spectrum antibiotics such as fluoroquinolones and β-lactams. A fecal sample was collected from all participants before treatment and one week after for microbial load and community composition analyses by quantitative PCR and pyrosequencing of the 16S rRNA gene, respectively. Fluoroquinolones and β-lactams significantly decreased microbial diversity by 25% and reduced the core phylogenetic microbiota from 29 to 12 taxa. However, at the phylum level, these antibiotics increased the Bacteroidetes/Firmicutes ratio (p = 0.0007, FDR = 0.002). At the species level, our findings unexpectedly revealed that both antibiotic types increased the proportion of several unknown taxa belonging to the Bacteroides genus, a Gram-negative group of bacteria (p = 0.0003, FDR<0.016). Furthermore, the average microbial load was affected by the treatment. Indeed, the β-lactams increased it significantly by two-fold (p = 0.04). The maintenance of or possible increase detected in microbial load and the selection of Gram-negative over Gram-positive bacteria breaks the idea generally held about the effect of broad-spectrum antibiotics on gut microbiota.     

The Microbial Community in the Feces of the White Rhinoceros (Ceratotherium simum) as Determined by Barcoded Pyrosequencing Analysis

As a non-ruminant herbivore, the white rhinoceros has the ability to utilize fibrous plant matter through microbial fermentation in the hindgut. So far, there has been no report using molecular techniques to study the gut microbiota of the white rhinoceros. We used barcoded pyrosequencing to characterize 105,651 sequences of 16S rRNA genes obtained from fecal samples from five white rhinoceroses. Results showed that Firmicutes and Bacteroidetes were the predominant phyla in the samples, which were comprised largely of unclassified bacteria. The microbiota of one animal treated with drug therapy differed from those in other healthy animals, and was dominated by Aerococcus -related bacteria. The core microbiota in the healthy rhinoceros were dominated by phyla Firmicutes and Bacteroidetes, represented by the Ruminococcaceae, Lachnospiraceae, Rikenellaceae and Prevotellaceae families. The present work provides a phylogenetic framework for understanding the complex microbial community of the rhinoceros; however, further studies are required to link the distinctive microbiota with their digestive role in the hindgut of the white rhinoceros.     

成年与未成年圈养林麝粪便菌群多样性的比较

本研究旨在解析林麝未成年组(n=10)和成年组(n=10)之间的菌群差异。收集林麝新鲜粪便,提取总DNA,利用带标签的通用引物扩增16S rRNA V3-V4区,使用Illumina Miseq 300PE测序平台对扩增产物进行Miseq双端测序,通过计算ACE和Shannon等多样性指数,以及微生物组成成分和距离聚类分析,揭示组成结构与差异。α多样性分析表明成年组微生物的多样性丰富度略高于未成年组,但不存在显著差异性(P>0.05)。未成年组和成年组均是厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)和变形菌门(Proteobacteria)所占的比例较高。成年组Proteobacteria比例明显高,而Firmicutes比例较低。LEfSe分析表明有12个显著差异的细菌分类。两组在Firmicutes门存在显著差异的细菌较少,而在Proteobacteria上存在显著差异的细菌较多。本研究证明在不同年龄阶段,微生物的丰富度和多样性不存在显著差异,细菌的组成成分也相同。但是在组成比例上存在差异性,间接反映了不同年龄阶段营养吸收的不同需求。     

Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons

The diversity of the equine fecal bacterial community was evaluated using pyrosequencing of 16S rRNA gene amplicons. Fecal samples were obtained from horses fed cool-season grass hay. Fecal bacteria were characterized by amplifying the V4 region of bacterial 16S rRNA gene. Of 5898 mean unique sequences, a mean of 1510 operational taxonomic units were identified in the four fecal samples. Equine fecal bacterial richness was higher than that reported in humans, but lower than that reported in either cattle feces or soil. Bacterial classified sequences were assigned to 16 phyla, of which 10 were present in all samples. The largest number of reads belonged to Firmicutes (43.7% of total bacterial sequences), Verrucomicrobia (4.1%), Proteobacteria (3.8%), and Bacteroidetes (3.7%). The less abundant Actinobacteria, Cyanobacteria, and TM7 phyla presented here have not been previously described in the gut contents or feces of horses. Unclassified sequences represented 38.1% of total bacterial sequences; therefore, the equine fecal microbiome diversity is likely greater than that described. This is the first study to characterize the fecal bacterial community in horses by the use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the fecal microbiota of forage-fed horses.     

象科动物对当地森林生态系统的影响

现存的象科动物(Elephantidae)分为非洲草原象(Loxodonta africana)、非洲森林象(Loxodonta cyclotis)和亚洲象(Elephas maximus)3 种,作为森林生态系统的关键物种,它们对当地森林生态系统的影响非常复杂,在一定环境条件下,既可能是积极的作用,也可能是消极的作用。积极的作用包括:帮助植物传播种子;促进种子萌发;创造断层,维持群落多样性;为其他动物增加食物资源;为其他动物创造栖息地。消极的作用包括:使一些物种的种群数量减小;使森林变成灌木丛和草原等。而由于活动受限导致的种群密度过高是象科动物对森林生态系统产生消极作用的主要原因。当前象科动物的3 个物种均面临种群数量锐减和生存空间不断缩小的危机,为此迫切需要针对其对生物多样性和生态平衡的影响开展深入和全面的研究,并且应根据实际情况因地制宜地制定管理措施。     

Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers

Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to identify the microbial diversity and metabolic potential in low and high FCR birds. The domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %), archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria (78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 % in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR) predominated in the fecal microbial community. Poultry fecal metagenomes revealed the sequences related to 33 genera in both low and high FCR with significantly different proportion. Functional analysis revealed that genes for the metabolism of carbohydrates, amino acids and derivatives and protein metabolism were most abundant in SEED subsystem in both samples. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Indeed, genes associated with sulphur assimilation, flagellum and flagellar motility were over represented in low FCR birds. This information could help in developing strategies to improve feed efficiency and feed formulation for broiler chickens.     

Targeted (PCR-based) screening of antibiotic resistance genes’ prevalence in the gut microbiota of tribal people of Nabarangpur,Odisha, India

Antibiotic resistance is a major public health concern worldwide. The gut microbiota harbours multiple antibiotic resistant genes (ARGs) that contribute to the existing and future microbial population in a community or ecosystem. This study aimed to investigate the prevalence of 35 antibiotic resistance genes (ARGs) in the gut microbiota of the tribal people of Nabarangpur, Odisha, India. A total of 83 faecal samples were collected from three different tribes (Bhatra, Gond, and Paraja). Total faecal DNA was extracted, and the simplex polymerase chain reaction was performed to detect selected ARGs. Further analysis was done to estimate the incidence of these ARGs across these tribes based on alcohol consumption habits. We identified a higher prevalence of tetracycline resistance genes (tetW, tetQ and tetM) in the gut microbiota among three populations. Furthermore, a significant (P = 0·024) difference in ARG prevalence against vancomycin in individuals with and without alcohol consumption habits was noticed. The overall distribution of ARGs among the three major tribes of this location was found to be very similar. Together, irrespective of the tribes, the people of this location have gut microbiota harbouring different kinds of ARGs and tetracycline-resistant genes are the most commonly found ARGs.     

Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study, DNA was extracted either directly or following freeze storage of three homogenized human fecal samples using three different extraction methods. No consistent differences were observed in DNA yields between extractions on fresh and frozen samples; however, differences were observed between extraction methods. Quantitative PCR analysis was subsequently performed on all DNA samples using six different primer pairs targeting 16S rRNA genes of significant bacterial groups, and the community composition was evaluated by comparing specific ratios of the calculated abundances. In seven of nine cases, the Firmicutes to Bacteroidetes 16S rRNA gene ratio was significantly higher in fecal samples that had been frozen compared to identical samples that had not. This effect was further supported by qPCR analysis of bacterial groups within these two phyla. The results demonstrate that storage conditions of fecal samples may adversely affect the determined Firmicutes to Bacteroidetes ratio, which is a frequently used biomarker in gut microbiology.     

Effects of diet,habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis)

The gut microbiome, or the community of microorganisms inhabiting the digestive tract, is often unique to its symbiont and, in many animal taxa, is highly influenced by host phylogeny and diet. In this study, we characterized the gut microbiome of the African savanna elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), sister taxa separated by 2.6–5.6 million years of independent evolution. We examined the effect of host phylogeny on microbiome composition. Additionally, we examined the influence of habitat types (forest versus savanna) and diet types (crop‐raiding versus noncrop‐raiding) on the microbiome within L. africana. We found 58 bacterial orders, representing 16 phyla, across all African elephant samples. The most common phyla were Firmicutes, Proteobacteria, and Bacteroidetes. The microbiome of L. africana was dominated by Firmicutes, similar to other hindgut fermenters, while the microbiome of L. cyclotis was dominated by Proteobacteria, similar to more frugivorous species. Alpha diversity did not differ across species, habitat type, or diet, but beta diversity indicated that microbial communities differed significantly among species, diet types, and habitat types. Based on predicted KEGG metabolic pathways, we also found significant differences between species, but not habitat or diet, in amino acid metabolism, energy metabolism, and metabolism of terpenoids and polyketides. Understanding the digestive capabilities of these elephant species could aid in their captive management and ultimately their conservation.     

Novel Polyfermentor Intestinal Model (PolyFermS) for Controlled Ecological Studies: Validation and Effect of pH

In vitro gut fermentation modeling offers a useful platform for ecological studies of the intestinal microbiota. In this study we describe a novel Polyfermentor Intestinal Model (PolyFermS) designed to compare the effects of different treatments on the same complex gut microbiota. The model operated in conditions of the proximal colon is composed of a first reactor containing fecal microbiota immobilized in gel beads, and used to continuously inoculate a set of parallel second-stage reactors. The PolyFermS model was validated with three independent intestinal fermentations conducted for 38 days with immobilized human fecal microbiota obtained from three child donors. The microbial diversity of reactor effluents was compared to donor feces using the HITChip, a high-density phylogenetic microarray targeting small subunit rRNA sequences of over 1100 phylotypes of the human gastrointestinal tract. Furthermore, the metabolic response to a decrease of pH from 5.7 to 5.5, applied to balance the high fermentative activity in inoculum reactors, was studied. We observed a reproducible development of stable intestinal communities representing major taxonomic bacterial groups at ratios similar to these in feces of healthy donors, a high similarity of microbiota composition produced in second-stage reactors within a model, and a high time stability of microbiota composition and metabolic activity over 38 day culture. For all tested models, the pH-drop of 0.2 units in inoculum reactors enhanced butyrate production at the expense of acetate, but was accompanied by a donor-specific reorganization of the reactor community, suggesting a concerted metabolic adaptation and trigger of community-specific lactate or acetate cross-feeding pathways in response to varying pH. Our data showed that the PolyFermS model allows the stable cultivation of complex intestinal microbiota akin to the fecal donor and can be developed for the direct comparison of different experimental conditions in parallel reactors continuously inoculated with the exact same microbiota.     

Lentinula edodes-Derived Polysaccharide Alters the Spatial Structure of Gut Microbiota in Mice

Lentinula edodes-derived polysaccharides possess many therapeutic characteristics, including anti-tumor and immuno-modulation. The gut microbes play a critical role in modulation of immune function. However, the impact of Lentinula edodes-derived polysaccharides on the gut microbes have not yet been explored. In this study, high-throughput pyrosequencing technique was employed to investigate the effects of a new heteropolysaccharide L2 from Lentinula edodes on microbiota diversity and composition of small intestine, cecum, colon and distal end of colon (feces) in mice. The results demonstrated that along mouse intestine the microbiota exhibit distinctly different space distribution. L2 treatment reduced the diversity and evenness of gut microbiota along the intestine, especially in the cecum and colon. In the fecal microbial communities, the decrease of Bacteroidetes by significantly increasing Proteobacteria were observed, which were characterized by the increased Helicobacteraceae and reduced S24-7 at family level. Some OTUs, corresponding to Bacteroides acidifaciens, Alistipes and Helicobacter suncus, were found to be significantly increased in L2 treated-mice. In particular, 4 phyla Chloroflexi, Gemmatimonadetes, Nitrospirae and Planctomycetes are exclusively present in L2-treated mice. This is helpful for further demonstrating healthy action mechanism of Lentinula edodes-derived polysaccharide L2.