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。     

Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome

The effect of infection of pigs with Ascaris suum on the microbial composition in the proximal colon and fecal matter was investigated using 16S rRNA gene sequencing. The infection significantly decreased various microbial diversity indices including Chao1 richness, but the effect on Chao1 in the colon luminal contents was worm burden-independent. The abundance of 49 genera present in colon contents, such as Prevotella and Faecalibacterium, and 179 operational taxonomic units was significantly changed as a result of infection. Notably, infection was also associated with a significant shift in the metabolic potential of the proximal colon microbiome, where the relative abundance of at least 30 metabolic pathways including carbohydrate metabolism and amino acid metabolism was reduced, while the abundance of 28 pathways was increased by infection. Furthermore, the microbial co-occurrence network in infected pigs was highly modular. Two of 52 modules or subnetworks were negatively correlated with fecal butyrate concentrations (r?<??0.7; P?<?0.05) while one module with 18 members was negatively correlated with fecal acetate, propionate and total short-chain fatty acids. A partial Mantel test identified a strong positive correlation between node connectivity of the operational taxonomic units assigned to β-Proteobacteria (especially the family Alcaligenaceae) and fecal acetate and propionate levels (r?=?0.82 and 0.74, respectively), while that of the family Porphyromonadaceae was positively correlated with fecal egg counts. Overall, Ascaris infection was associated with a profound change in the gut microbiome, especially in the proximity of the initial site of larval infection, and should facilitate our understanding of the pathophysiological consequence of gastrointestinal nematode infections.     

Gut microbiome composition is linked to whole grain-induced immunological improvements

The involvement of the gut microbiota in metabolic disorders, and the ability of whole grains to affect both host metabolism and gut microbial ecology, suggest that some benefits of whole grains are mediated through their effects on the gut microbiome. Nutritional studies that assess the effect of whole grains on both the gut microbiome and human physiology are needed. We conducted a randomized cross-over trial with four-week treatments in which 28 healthy humans consumed a daily dose of 60 g of whole-grain barley (WGB), brown rice (BR), or an equal mixture of the two (BR+WGB), and characterized their impact on fecal microbial ecology and blood markers of inflammation, glucose and lipid metabolism. All treatments increased microbial diversity, the Firmicutes/Bacteroidetes ratio, and the abundance of the genus Blautia in fecal samples. The inclusion of WGB enriched the genera Roseburia, Bifidobacterium and Dialister, and the species Eubacterium rectale, Roseburia faecis and Roseburia intestinalis. Whole grains, and especially the BR+WGB treatment, reduced plasma interleukin-6 (IL-6) and peak postprandial glucose. Shifts in the abundance of Eubacterium rectale were associated with changes in the glucose and insulin postprandial response. Interestingly, subjects with greater improvements in IL-6 levels harbored significantly higher proportions of Dialister and lower abundance of Coriobacteriaceae. In conclusion, this study revealed that a short-term intake of whole grains induced compositional alterations of the gut microbiota that coincided with improvements in host physiological measures related to metabolic dysfunctions in humans.     

Maize rhizosphere modulates the microbiome diversity and community structure to enhance plant health

Metagenomic has been explored in investigating microbiome diversity. However, there is limited available information on its application towards securing plant health. Hence, this study adopts the metagenomic approach to unravel the microbiome diversity associated with healthy (LI and MA) and Northern corn leaf blight (NCLB) infected (LID and MAD) maize rhizosphere in the maize growing field at Lichtenburg and Mafikeng, North-West province of South Africa. The extraction of whole DNA from the respective healthy and diseased rhizosphere soils was conducted and sequenced using shotgun metagenomics. A total of 12 bacteria, 4 archaea and 2 fungal phyla were found as predominant across the fields with the use of the SEED subsystem database. The most predominant bacteria phyla included Proteobacteria, Dienococcus-Thermus, Gemmatimonadetes, Chlorobi, Cyanobacteria, Planctomycetes, Verrucomicrobia, Acidobacteria, Firmicutes, Chloroflexi and Bacteroidetes. Archaea consisted of Euryarchaeota, Thaumarchaeota, Crenarchaeota and Korachaeota, while Ascomycota and Basidiomycota were the dominant fungal phyla. Microbial abundance and diversity were higher in the rhizosphere of healthy maize (LI and MA) rhizosphere as compared to the NCLB diseased (LID and MAD), in the order LI > MA > LID > MAD. At phylum and genus level, alpha diversity index showed no significant (p > 0.05) difference in the abundance of the microbial community of healthy and NCLB infected maize rhizosphere, while beta analysis produced a significant (p = 0.01) difference in the microbial diversity in the soil. Taken together, the study revealed that the abundance of microbial diversity in the maize rhizosphere influences the efficacy of the rhizosphere microbiome to modulate microbial functions towards managing and sustaining plant health.     

Comparative and functional analyses of fecal microbiome in Asian elephants

Asian elephant is large herbivorous animal with elongated hindgut. To explore fecal microbial community composition with various ages, sex and diets, and their role in plant biomass degrading and nutrition conversation. We generated 119 Gb by metagenome sequencing from 10 different individual feces and identified 5.3 million non-redundant genes. The comprehensive analysis established that the Bacteroidetes, Firmicutes and Proteobacteria constituted the most dominant phyla in overall fecal samples. In different individuals, the alpha diversity of the fecal microbiota in female was lower than male, and the alpha diversity of the fecal microbiota in older was higher than younger, and the fecal microbial diversity was the most complex in wild elephant. But the predominant population compositions were similar to each other. Moreover, the newborn infant elephant feces assembled and maintained a diverse but host-specific fecal microbial population. The discovery speculated that Asian elephant maybe have start to building microbial populations before birth. Meanwhile, these results illustrated that host phylogeny, diets, ages and sex are significant factors for fecal microbial community composition. Therefore, we put forward the process of Asian elephant fecal microbial community composition that the dominant populations were built first under the guidance of phylogeny, and then shaped gradually a unique and flexible gut microbial community structure under the influences of diet, age and sex. This study found also that the Bacteroidetes were presumably the main drivers of plant fiber-degradation. A large of secondary metabolite biosynthetic gene clusters, and genes related to enediyne biosynthesis were found and showed that the Asian elephant fecal microbiome harbored a diverse and abundant genetic resource. A picture of antibiotic resistance genes (ARGs) reservoirs of fecal microbiota in Asian elephants was provided. Surprisingly, there was such wide range of ARGs in newborn infant elephant. Further strengthening our speculation that the fetus of Asian elephant has colonized prototypical fecal microbiota before birth. However, it is necessary to point out that the data give a first inside into the gut microbiota of Asian elephants but too few individuals were studied to draw general conclusions for differences among wild and captured elephants, female and male or different ages. Further studies are required. Additionally, the cultured actinomycetes from Asian elephant feces also were investigated, which the feces of Asian elephants could be an important source of actinomycetes.

     

Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene

The intestinal tract houses one of the richest and most complex microbial populations on the planet, and plays a critical role in health and a wide range of diseases. Limited studies using new sequencing technologies in horses are available. The objective of this study was to characterize the fecal microbiome of healthy horses and to compare the fecal microbiome of healthy horses to that of horses with undifferentiated colitis. A total of 195,748 sequences obtained from 6 healthy horses and 10 horses affected by undifferentiated colitis were analyzed. Firmicutes predominated (68%) among healthy horses followed by Bacteroidetes (14%) and Proteobacteria (10%). In contrast, Bacteroidetes (40%) was the most abundant phylum among horses with colitis, followed by Firmicutes (30%) and Proteobacteria (18%). Healthy horses had a significantly higher relative abundance of Actinobacteria and Spirochaetes while horses with colitis had significantly more Fusobacteria. Members of the Clostridia class were more abundant in healthy horses. Members of the Lachnospiraceae family were the most frequently shared among healthy individuals. The species richness reported here indicates the complexity of the equine intestinal microbiome. The predominance of Clostridia demonstrates the importance of this group of bacteria in healthy horses. The marked differences in the microbiome between healthy horses and horses with colitis indicate that colitis may be a disease of gut dysbiosis, rather than one that occurs simply through overgrowth of an individual pathogen.     

A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development

Companion animals provide an excellent model for studies of the gut microbiome because potential confounders such as diet and environment can be more readily controlled for than in humans. Additionally, domestic cats and dogs are typically neutered early in life, enabling an investigation into the potential effect of sex hormones on the microbiome. In a longitudinal study to investigate the potential effects of neutering, neutering age and gender on the gut microbiome during growth, the faeces of kittens (16 male, 14 female) were sampled at 18, 30 and 42 weeks of age. DNA was shotgun sequenced on the Illumina platform and sequence reads were annotated for taxonomy and function by comparison to a database of protein coding genes. In a statistical analysis of diversity, taxonomy and functional potential of the microbiomes, age was identified as the only factor with significant associations. No significant effects were detected for gender, neutering, or age when neutered (19 or 31 weeks). At 18 weeks of age the microbiome was dominated by the genera Lactobacillus and Bifidobacterium (35% and 20% average abundance). Structural and functional diversity was significantly increased by week 30 but there was no further significant increase. At 42 weeks of age the most abundant genera were Bacteroides (16%), Prevotella (14%) and Megasphaera (8%). Significant differences in functional potential included an enrichment for genes in energy metabolism (carbon metabolism and oxidative phosphorylation) and depletion in cell motility (flagella and chemotaxis). We conclude that the feline faecal microbiome is predominantly determined by age when diet and environment are controlled for. We suggest this finding may also be informative for studies of the human microbiome, where control over such factors is usually limited.     

Phylogenetic distribution of genes encoding β-glucuronidase activity in human colonic bacteria and the impact of diet on faecal glycosidase activities

Bacterial β-glucuronidase in the human colon plays an important role in cleaving liver conjugates of dietary compounds and xenobiotics, while other glycosidase activities are involved in the conversion of dietary plant glycosides. Here we detected an increase in β-glucuronidase activity in faecal samples from obese volunteers following a high-protein moderate carbohydrate weight-loss diet, compared with a weight maintenance diet, but little or no changes were observed when the type of fermentable carbohydrate was varied. Other faecal glycosidase activities showed little or no change over a fivefold range of dietary NSP intake, although α-glucosidase increased on a resistant starch-enriched diet. Two distinct groups of gene, gus and BG, have been reported to encode β-glucuronidase activity among human colonic bacteria. Degenerate primers were designed against these genes. Overall, Firmicutes were found to account for 96% of amplified gus sequences, with three operational taxonomic units particularly abundant, whereas 59% of amplified BG sequences belonged to Bacteroidetes and 41% to Firmicutes. A similar distribution of operational taxonomic units was found in a published metagenome dataset involving a larger number of volunteers. Seven cultured isolates of human colonic bacteria that carried only the BG gene gave relatively low β-glucuronidase activity that was not induced by 4-nitrophenyl-β-D-glucuronide. By comparison, in three of five isolates that possessed only the gus gene, β-glucuronidase activity was induced.     

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.     

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。     

Abundant and diverse fungal microbiota in the murine intestine

Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4',6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.     

Deep Illumina-Based Shotgun Sequencing Reveals Dietary Effects on the Structure and Function of the Fecal Microbiome of Growing Kittens

Background

Previously, we demonstrated that dietary protein:carbohydrate ratio dramatically affects the fecal microbial taxonomic structure of kittens using targeted 16S gene sequencing. The present study, using the same fecal samples, applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome.

Methodology & Principal Findings

Fecal samples from kittens fed one of two diets differing in protein and carbohydrate content (high–protein, low–carbohydrate, HPLC; and moderate-protein, moderate-carbohydrate, MPMC) were collected at 8, 12 and 16 weeks of age (n = 6 per group). A total of 345.3 gigabases of sequence were generated from 36 samples, with 99.75% of annotated sequences identified as bacterial. At the genus level, 26% and 39% of reads were annotated for HPLC- and MPMC-fed kittens, with HPLC-fed cats showing greater species richness and microbial diversity. Two phyla, ten families and fifteen genera were responsible for more than 80% of the sequences at each taxonomic level for both diet groups, consistent with the previous taxonomic study. Significantly different abundances between diet groups were observed for 324 genera (56% of all genera identified) demonstrating widespread diet-induced changes in microbial taxonomic structure. Diversity was not affected over time. Functional analysis identified 2,013 putative enzyme function groups were different (p<0.000007) between the two dietary groups and were associated to 194 pathways, which formed five discrete clusters based on average relative abundance. Of those, ten contained more (p<0.022) enzyme functions with significant diet effects than expected by chance. Six pathways were related to amino acid biosynthesis and metabolism linking changes in dietary protein with functional differences of the gut microbiome.

Conclusions

These data indicate that feline feces-derived microbiomes have large structural and functional differences relating to the dietary protein:carbohydrate ratio and highlight the impact of diet early in life.     

Supragingival Microbial Profiles of Permanent and Deciduous Teeth in Children with Mixed Dentition

Objectives

The present study was designed to investigate the microbial profiles of teeth in different locations in mixed-dentition-stage children, and to compare the microbiomes of permanent and deciduous teeth in the same healthy oral cavity.

Methods

Supragingival plaque samples of teeth in various locations—the first permanent molars, deciduous molars, deciduous canines and incisors and permanent incisors—were collected from 20 healthy mixed-dentition-stage children with 10–12 permanent teeth erupted. Plaque DNA was extracted, and the V3–V4 hypervariable region of the bacterial 16S rRNA gene was amplified and subjected to sequencing.

Results

On average, 18,051 high-quality sequences per sample were generated. Permanent tooth sites tended to host more diverse bacterial communities than those of deciduous tooth sites. A total of 12 phyla, 21 classes, 38 orders, 66 families, 74 genera were detected ultimately. Five predominant phyla (Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria and Actinobacteria) were highly variable among sites. Of 26 genera with a mean relative abundance of >0.1%, 16 showed significant differences in relative abundance among the groups. More than 20% of the total operational taxonomical units were detected only in permanent or deciduous teeth. The variation in the microbial community composition was due mainly to permanent teeth being enriched in Actinomyces and deciduous teeth in Treponema. The core microbiome of supragingival plaque in mixed dentition comprised 19 genera with complex correlationships.

Conclusion

Our results suggest differences in microbial diversity and composition between permanent and deciduous teeth sites in mixed dentition. Moreover, the core microbiome of these sites was determined. These findings enhance our understanding of the development of the native oral microbiota with age.     

Rumen Microbiome from Steers Differing in Feed Efficiency

The cattle rumen has a diverse microbial ecosystem that is essential for the host to digest plant material. Extremes in body weight (BW) gain in mice and humans have been associated with different intestinal microbial populations. The objective of this study was to characterize the microbiome of the cattle rumen among steers differing in feed efficiency. Two contemporary groups of steers (n=148 and n=197) were fed a ration (dry matter basis) of 57.35% dry-rolled corn, 30% wet distillers grain with solubles, 8% alfalfa hay, 4.25% supplement, and 0.4% urea for 63 days. Individual feed intake (FI) and BW gain were determined. Within contemporary group, the four steers within each Cartesian quadrant were sampled (n=16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the harvested bovine rumen fluid samples using next-generation sequencing technology. No significant changes in diversity or richness were indicated, and UniFrac principal coordinate analysis did not show any separation of microbial communities within the rumen. However, the abundances of relative microbial populations and operational taxonomic units did reveal significant differences with reference to feed efficiency groups. Bacteroidetes and Firmicutes were the dominant phyla in all ruminal groups, with significant population shifts in relevant ruminal taxa, including phyla Firmicutes and Lentisphaerae, as well as genera Succiniclasticum, Lactobacillus, Ruminococcus, and Prevotella. This study suggests the involvement of the rumen microbiome as a component influencing the efficiency of weight gain at the 16S level, which can be utilized to better understand variations in microbial ecology as well as host factors that will improve feed efficiency.     

Changes in microbial diversity in fed-batch reactor operation with wastewater containing nitroaromatic residues

This study targeted the diversity of bacteria isolated from activated biomass of an ETP that treated wastewater from the dye industry. Phylogenetic analysis of 5'-partial 16S rDNA sequences revealed that the Proteobacteria (alpha, beta, and gamma) and Firmicutes were the major phyla in microbial community. Five unidentified culturable bacteria were also isolated. The activated biomass changed when acclimatized to wastewater with nitroaromatic residues. It was observed that the diversity of genera was reduced, but the degradative capacity of sludge was enhanced.     

Age‐related changes in the marmoset gut microbiome

The gut microbiome is known to play a significant role in human health but its role in aging remains unclear. The objective of this study was to compare the gut microbiome composition between young adult and geriatric non‐human primates (marmosets) as a model of human health and disease. Stool samples were collected from geriatric (8+ years) and young adult males (2–5 years). Stool 16S ribosomal RNA V4 sequences were amplified and sequenced on the Illumina MiSeq platform. Sequences were clustered into operational taxonomic units and classified via Mothur's Bayesian classifier referenced against the Greengenes database. A total of 10 young adult and 10 geriatric marmosets were included. Geriatric marmosets had a lower mean Shannon diversity compared with young marmosets (3.15 vs. 3.46; p = 0.0191). Geriatric marmosets had a significantly higher mean abundance of Proteobacteria (0.22 vs. 0.09; p = 0.0233) and lower abundance of Firmicutes (0.15 vs. 0.19; p = 0.0032) compared with young marmosets. Geriatric marmosets had a significantly higher abundance of Succinivibrionaceae (0.16 vs. 0.01; p = 0.0191) and lower abundance of Porphyromonadaceae (0.07 vs. 0.11; p = 0.0494). In summary, geriatric marmosets had significantly altered microbiome diversity and composition compared with young adult marmosets. Further studies are needed to test microbiome‐targeted therapies to improve healthspan and lifespan.     

基于16S rDNA高通量测序的短尾猴口腔微生物多样性

口腔微生物群落结构是维持机体健康的重要因素,了解动物口腔微生物多样性有助于认识和理解动物的生态学适应。本研究以栖息于安徽黄山的短尾猴为研究对象,采用非损伤性取样法收集了鱼鳞坑YA1群体中19个短尾猴口腔样本,采用改进高盐提取法提取微生物DNA,利用Illumina Miseq测序平台对微生物16S rDNA V3-V4区扩增产物进行双端测序,分析微生物群落结构多样性。研究共获得206 533条优质序列,发现4 685个OTU,归属20个门、310个属。结果表明：短尾猴口腔微生物物种丰富,以变形菌门(Proteobacteria,占总条带44.58%)、厚壁菌门(Firmicutes, 30.28%)、拟杆菌门(Bacteroidetes, 12.27%)、梭杆菌门(Fusobacteria, 7.72%) 和放线菌门(Actinobacteria,3.70%)为主;24个微生物属在所有样本中均有分布,为其核心微生物属;短尾猴口腔中存在大量与口腔疾病相关的微生物和多种低丰富度的潜在病原菌。本研究为进一步研究短尾猴口腔微生物群落结构形成与适应性提供了基础资料,也提示在保护和管理野生猴群中需要应对人畜共患病传播的潜在风险。     

High through put 16S rRNA gene-based pyrosequencing analysis of the fecal microbiota of high FCR and low FCR broiler growers

The performance of birds appears to vary among the flock of growing broilers which may in part be due to variation in their gut microbiota. In the view of poultry industry, it is desirable to minimise such variation. We investigated metagenomic profile of fecal bacteria in birds with high and low feed conversion ratio (FCR) to identify microbial community linked to low and high FCR by employing high throughput pyrosequencing of 16S rRNA genomic targets. Therefore feeding trial was investigated in order to identify fecal bacteria consistently linked with better feed conversion ratio in bird performance as measured by body weight gain. High-throughput 16S rRNA gene based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. The fecal microbial community of birds was predominated by Proteobacteria (48.04?% in high FCR and 49.98?% in low FCR), Firmicutes (26.17?% in high FCR and 36.23?% in low FCR), Bacteroidetes (18.62?% in high FCR and 11.66?% in low FCR), as well as unclassified bacteria (15.77?% in high FCR and 14.29?% in low FCR), suggesting that a large portion of fecal microbiota is novel and could be involved in currently unknown functions. The most prevalent bacterial classes in high FCR and low FCR were Gammaproteobacteria, Clostridia and Bacteroidia. However in low FCR birds Phascolarctobacterium, Faecalibacterium and Clostridium predominated among the Clostridia. In FCR comparison of fecal bacteria, about 36 genera were differentially abundant between high and low FCR birds. This information could be used to formulate effective strategies to improve feed efficiency and feed formulation for optimal gut health.