Comparative Metagenomic Analysis of Chicken Gut Microbial Community, Function, and Resistome to Evaluate Noninvasive and Cecal Sampling Resources.
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ABSTRACT:
SUBMITTER: Kang K
PROVIDER: S-EPMC8228302 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs), the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas.
| S-EPMC3962364 | biostudies-literature
Project description:The chicken gut microbiota, as a reservoir of antibiotic resistance genes (ARGs), poses a high risk to humans and animals worldwide. Yet a comprehensive exploration of the chicken gut antibiotic resistomes remains incomplete. In this study, we established the largest chicken gut resistance gene catalogue to date through metagenomic analysis of 629 chicken gut samples. We found significantly higher abundance of ARGs in the Chinese chicken gut than that in the Europe. tetX, mcr, and blaNDM, the genes resistant to antibiotics of last resort for human and animal health, were detected in the Chinese chicken gut. The abundance of ARGs was linearly correlated with that of mobile genetic elements (MGEs). The host-tracking analysis identified Escherichia, Enterococcus, Staphylococcus, Klebsiella, and Lactobacillus as the major ARG hosts. Especially, Lactobacillus, an intestinal probiotic, carried multiple drug resistance genes, and was proportional to ISLhe63, highlighting its potential risk in agricultural production processes. We first established a reference gene catalogue of chicken gut antibiotic resistomes. Our study helps to improve the knowledge and understanding of chicken antibiotic resistomes for knowledge-based sustainable chicken meat production. IMPORTANCE The prevalence of antibiotic resistance genes in the chicken gut environment poses a serious threat to human health; however, we lack a comprehensive exploration of antibiotic resistomes and microbiomes in the chicken gut environment. The results of this study demonstrate the diversity and abundance of antibiotic resistance genes and flora in the chicken gut environment and identify a variety of potential hosts carrying antibiotic resistance genes. Further analysis showed that mobile genetic elements were linearly correlated with antibiotic resistance genes abundance, implying that we should pay attention to the role played by mobile genetic elements in antibiotic resistance genes transmission. We established a reference genome of gut antibiotic resistance genes in chickens, which will help to rationalize the use of drugs in poultry farming.
| S-EPMC9045286 | biostudies-literature
Project description:A gnotobiotic Gallus gallus (chicken) model was developed to study the dynamics of intestinal microflora from hatching to 18 days of age employing metagenomics. Intestinal samples were collected from a local population of feral chickens and administered orally to germfree 3-day-old chicks. Animals were euthanized on days 9 and 18 postinoculation, and intestinal samples were collected and subjected to metagenomic analysis. On day 18, the five most prevalent phyla were Bacteroidetes (43.03 ± 3.19%), Firmicutes (38.51 ± 2.67%), Actinobacteria (6.77 ± 0.7%), Proteobacteria (6.38 ± 0.7%), and Spirochaetes (2.71 ± 0.55%). Principal-coordinate analysis showed that the day 18 variables clustered more closely than the day 9 variables, suggesting that the microbial communities had changed temporally. The Morista-Horn index values ranged from 0.7 to 1, indicating that the communities in the inoculum and in the day 9 and day 18 samples were more similar than dissimilar. The predicted functional profiles of the microbiomes of the inoculum and the day 9 and day 18 samples were also similar (values of 0.98 to 1). These results indicate that the gnotobiotic chicks stably maintained the phylogenetic diversity and predicted metabolic functionality of the inoculum community.IMPORTANCE The domestic chicken is the cornerstone of animal agriculture worldwide, with a flock population exceeding 40 billion birds/year. It serves as an economically valuable source of protein globally. The microbiome of poultry has important effects on chicken growth, feed conversion, immune status, and pathogen resistance. The aim of our research was to develop a gnotobiotic chicken model appropriate for the study chicken gut microbiota function. Our experimental model shows that young germfree chicks are able to colonize diverse sets of gut bacteria. Therefore, besides the use of this model to study mechanisms of gut microbiota interactions in the chicken gut, it could be also used for applied aspects such as determining the safety and efficacy of new probiotic strains derived from chicken gut microbiota.
| S-EPMC6437271 | biostudies-literature
Project description:Background: Japanese quail (Coturnix japonica) are important and widely distributed poultry in China. Researchers continue to pursue genetic selection for heavier quail. The intestinal microbiota plays a substantial role in growth promotion; however, the mechanisms involved in growth promotion remain unclear. Results: We generated 107.3 Gb of cecal microbiome data from ten Japanese quail, providing a series of quail gut microbial gene catalogs (1.25 million genes). We identified a total of 606 main microbial species from 1,033,311 annotated genes distributed among the ten quail. Seventeen microbial species from the genera Anaerobiospirillum, Alistipes, Barnesiella, and Butyricimonas differed significantly in their abundances between the female and male gut microbiotas. Most of the functional gut microbial genes were involved in metabolism, primarily in carbohydrate transport and metabolism, as well as some active carbohydrate-degrading enzymes. We also identified 308 antibiotic-resistance genes (ARGs) from the phyla Bacteroidetes, Firmicutes and Euryarchaeota. Studies of the differential gene functions between sexes indicated that abundances of the gut microbes that produce carbohydrate-active enzymes varied between female and male quail. Bacteroidetes was the predominant ARG-containing phylum in female quail; Euryarchaeota was the predominant ARG-containing phylum in male quail. Conclusion: This article provides the first description of the gene catalog of the cecal bacteria in Japanese quail as well as insights into the bacterial taxa and predictive metagenomic functions between male and female quail to provide a better understanding of the microbial genes in the quail ceca.
| S-EPMC8517240 | biostudies-literature
Project description:Spatial structuring is important for the maintenance of natural ecological systems1,2. Many microbial communities, including the gut microbiome, display intricate spatial organization3-9. Mapping the biogeography of bacteria can shed light on interactions that underlie community functions10-12, but existing methods cannot accommodate the hundreds of species that are found in natural microbiomes13-17. Here we describe metagenomic plot sampling by sequencing (MaPS-seq), a culture-independent method to characterize the spatial organization of a microbiome at micrometer-scale resolution. Intact microbiome samples are immobilized in a gel matrix and cryofractured into particles. Neighboring microbial taxa in the particles are then identified by droplet-based encapsulation, barcoded 16S rRNA amplification and deep sequencing. Analysis of three regions of the mouse intestine revealed heterogeneous microbial distributions with positive and negative co-associations between specific taxa. We identified robust associations between Bacteroidales taxa in all gut compartments and showed that phylogenetically clustered local regions of bacteria were associated with a dietary perturbation. Spatial metagenomics could be used to study microbial biogeography in complex habitats.
| S-EPMC6679743 | biostudies-literature
Project description:BACKGROUND:The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability to harvest energy from dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics (n = 72). RESULTS:Time and wheat content in feed explained most of the variation of the microbiota as assessed by 16S rRNA gene sequencing in weanling pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic and 1 archaeal phylum. Analysis of carbohydrate metabolism in these genomes revealed that starch fermentation is carried out by a consortium of Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) and Bacteroidetes expressing periplasmic neopullulanase (GH13) and α-glucosidase (GH97). Fructans were degraded by extracellular GH32 enzymes from Bacteriodetes and Lactobacillus. Lactose fermentation by β-galactosidases (GH2 and GH42) was identified in Firmicutes. In conclusion, the assembly of 360 high-quality genomes as the first metagenomic reference for swine intestinal microbiota allowed identification of key microbial contributors to degradation of starch, fructans, and lactose. CONCLUSIONS:Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. Our study thus enables improvement of feeding models with higher feed efficiency and better pathogen control for weanling pigs.
| S-EPMC6436221 | biostudies-literature
Project description:Background:Metagenomic analysis of the gut microbiome and resistome is instrumental for understanding the dynamics of diarrheal pathogenesis and antimicrobial resistance transmission (AMR). Metagenomic sequencing of 20 diarrheal fecal samples from Kolkata was conducted to understand the core and variable gut microbiota. Five of these samples were used for resistome analysis. The pilot study was conducted to determine a microbiota signature and the source of antimicrobial resistance genes (ARGs) in the diarrheal gut. Results:16S rRNA amplicon sequencing was performed using Illumina MiSeq platform and analysed using the MGnify pipeline. The Genome Taxonomy Database (GTDB-Tk) was used for bacterial taxonomic identification. Diarrheal etiology was determined by culture method. Phylum Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were consistently present in 20 samples. Firmicutes was the most abundant phylum in 11 samples. The Bacteroidetes/Firmicutes ratio was less than 1 in 18 samples. 584 genera were observed. 18 of these were present in all the 20 samples. Proteobacteria was the dominant phylum in 6 samples associated with Vibrio cholerae infection. Conservation of operational taxonomic units (OTUs) among all the samples indicated the existence of a core microbiome. Asymptomatic carriage of pathogens like Vibrio cholerae and Helicobacter pylori was found. Signature of Candidate phyla or "microbial dark matter" occurred. Significant correlation of relative abundance of bacterial families of commensals and pathogens were found. Whole-genome sequencing (WGS) on Illumina MiSeq system and assembly of raw reads using metaSPAdes v3.9.1 was performed to study the resistome of 5 samples. ABRicate was used to assign ARG function. 491 resistance determinants were identified. In 80% of the samples tetracycline resistance was the most abundant resistance determinant. High abundance of ARGs against ?-lactams, aminoglycosides, quinolones and macrolides was found. Eschericia sp. was the major contributor of ARGs. Conclusions:This is the first comparative study of the gut microbiome associated with different diarrheal pathogens. It presents the first catalogue of different bacterial taxa representing the core and variable microbiome in acute diarrheal patients. The study helped to define a trend in the gut microbiota signature associated with diarrhea and revealed which ARGs are abundantly present and the metagenome-assembled genomes (MAGs) contributing to AMR.
| S-EPMC7339541 | biostudies-literature
Project description:Despite the convenience and non-invasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum, and feces samples, for 16S rRNA amplicon sequencing analyses. In this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11-87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54-0.71 and 0.71-0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the four gut segments, and these correlations were not high (ρ = -0.2-0.4, P < 0.05) for most genera. Our results suggest that fecal microbial community has a good potential to identify most taxa in the chicken gut and could moderately mirror the microbial structure in the intestine at the microbial population level with phylum specificity. However, it should be interpreted with caution by using feces as a proxy to study associations for microbial structure at individual microorganism level.
| S-EPMC6753641 | biostudies-literature
Project description:To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
| S-EPMC3779803 | biostudies-literature
Project description:Hospitalized preterm infants receive frequent and often prolonged exposures to antibiotics because they are vulnerable to infection. It is not known whether the short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic, culture-based and machine learning techniques to study the gut microbiota and resistome of antibiotic-exposed preterm infants during and after hospitalization, and we compare these readouts to antibiotic-naive healthy infants sampled synchronously. We find a persistently enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug-resistant Enterobacteriaceae and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants that received early-life antibiotics. The collateral damage of early-life antibiotic treatment and hospitalization in preterm infants is long lasting. We urge the development of strategies to reduce these consequences in highly vulnerable neonatal populations.
| S-EPMC6879825 | biostudies-literature