Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota

Age-dependent development trends (models) of intestinal significant microbiota species and Eimeria oocysts in coccidia-challenged broiler chickens as affected by dietary encapsulated organic acids and anticoccidial drugs

ABSTRACTThe study was conducted to investigate the effect of dietary encapsulated organic acids (EOAs) and anticoccidials on the age-dependent development trend of intestinal Lactobacillus, E. coli, coliforms, and Eimeria in Eimeria spp.-infected broiler chickens from reused litter. In total, 525 mixed-sex 1-day-old broiler chickens were used in an uninfected/un-supplemented control plus a 2 (no EOA or 0.1% EOA) × 3 (no anticoccidial, 0.05% maduramicin, and 0.02% diclazuril) factorial arrangement of treatments as a completely randomized design with five replicates of 15 chickens. Results indicated that the cubic model is the best model for explaining the development trends of the intestinal microbial population in uninfected and infected chickens (affected by the EOAs and anticoccidials). Based on the cubic models, the microbial populations had development trends with a decreasing slope from 1-day-old until the early or middle finisher period. EOAs and anticoccidials, especially their simultaneous usage, improved (P < 0.05) the linear and cubic models' slope (affected negatively by Eimeria infection). A polynomial model (order = 6) was determined as the best model for explaining the EOAs and anticoccidial effects on the trend of intestinal Eimeria oocysts in infected chickens. The infection peak (which happened at 25 days) was reduced by EOAs and anticoccidials, especially their simultaneous usage. In conclusion, cubic and polynomial (order = 6) regressions are the best models fitted for explaining the microbiota and Eimeria oocysts trends, respectively. EOAs and anticoccidials, especially their simultaneous usage, had beneficial effects on the microbiota and Eimeria development trends and gastrointestinal health in coccidia-infected broiler chickens.‏RESEARCH HIGHLIGHTSCubic regression is the best model for explaining intestinal microbiota development.Polynomial regression is the best model for intestinal Eimeria oocysts development.Age-development trends are affected by dietary encapsulated organic acids and anticoccidials.

The role of the fecal microbiota in inflammatory bowel disease

The understanding of the potential role of the microbiota in the pathogenesis of inflammatory bowel disease (IBD) is ever-evolving. Traditionally, the management of IBD has involved medical therapy and/or surgical intervention. IBD can be characterized by gut microbiome alterations through various pathological processes. Various studies delve into nontraditional methods such as probiotics and fecal microbiota transplant and their potential therapeutic effects. Fecal microbiota transplant involves the delivery of a balanced composition of gut microorganisms into an affected patient via multiple possible routes and methods, while probiotics consist of live microorganisms given via the oral route. At present, neither method is considered first-line treatment, however, fecal microbiota transplant has shown potential success in inducing and maintaining remission in ulcerative colitis. In a study by Kruis and colleagues, Escherichia coli Nissle 1917 was considered to be equivalent to mesalamine in mild ulcerative colitis. Alteration of the microbiome in the management of Crohn's disease is less well defined. Furthermore, variation in the clinical usefulness of 5-aminosalicylic acid medication has been attributed, in part, to its acetylation and inactivation by gut microbes. In summary, our understanding of the microbiome's role is continually advancing, with the possibility of paving the way for personalized medicine based on the microbiome.

The Association between Broiler Litter Microbiota and the Supplementation of Bacillus Probiotics in a Leaky Gut Model

Probiotics provided from hatch have a major influence on microbiota development, and together with environmental and bedding microbiota, shape the microbial community of the litter. We investigated the influence of probiotic supplementation and a leaky gut challenge induced using dexamethasone (DEX) on the litter microbial community and litter parameters. The probiotic product was a mix of three Bacillus amyloliquefaciens strains. The litter microbiota were compared to the microbial communities from other gut sections. The litter samples had higher microbial diversity compared to the caecum, gizzard, jejunum, and jejunal mucosa. The high similarity between the litter phylum-level microbiota and gizzard microbiota detected in our study could be a consequence of ingested feed and litter passing through the gizzard. Moreover, the litter microbial community is fundamentally distinct from the intestinal microbiota, as evidenced by the number of genera present in the litter but absent from all the intestinal sections and vice versa. Furthermore, LEfSe analysis identified distinct microbial taxa across different groups, with specific genera associated with different treatments. In terms of litter quality, the birds in the DEX groups had a significantly higher moisture content, indicating successful leaky gut challenge, while probiotic supplementation did not significantly affect the moisture levels. These findings provide comprehensive insights into the distinct microbiota characteristics of litter.

Validation of gavage sampling as tool for longitudinal sampling of microbiota of the mouse gastric lumen

BACKGROUND

Fecal samples are commonly used for longitudinal studies of the gut lumen microbiome to track the course of response to infection or drug treatment, but no comparable method has been evaluated for longitudinal analysis of the gastric lumen microbiome in mice. Herein, a buffer flush of the stomach with a flexible gavage needle was used to collect gastric contents at one or several time points without harming the mouse. These samples were compared to samples collected by sacrifice and dissection of the mouse stomach. Microbiota from these samples were sequenced and evaluated in two ways: the composition of samples as measured by beta diversity and the richness of samples as measured by alpha diversity. Additionally, the effect of multiple sampling every two days on these metrics were studied. DNA was extracted from each of these samples and Illumina 16S rRNA gene sequencing was performed.

RESULTS

First, taxonomic richness of gavage and dissection samples was compared. A greater number of taxa was detected in gavage samples than in dissection samples. Second, taxonomic richness was analyzed over time. No significant difference in taxonomic richness was observed with repeated gavage flushes. Third, a comparison was made of the taxonomic composition of samples collected by gavage versus dissection followed by a comparison of samples collected over multiple samplings. Nonmetric multidimensional scaling analysis revealed no clear differences between collection by gavage flushing or dissection. Using weighted Unifrac and Aitchison taxonomic distances between gavage and dissection samples were not significantly different from distances between gavage samples themselves, and no significant difference was found in the taxonomic composition of mice which were sampled repeatedly. Finally, relative abundances of specific identified taxa were compared, and eleven taxa were found to differ in frequency between collection methods. Using the more stringent Analysis of Composition of Microbiomes (ANCOM), seven was found to differ. Similarly, no significant differences were uncovered using these analyses over multiple samples by gastric flush.

CONCLUSION

In summary, the consistency of the microbiota collected by gastric flushing recommends its use for microbiome analysis of gastric fluid similar to the use of fecal sampling to study the gut lumen microbiome.

Investigating antibiotic free feed additives for growth promotion in poultry: effects on performance and microbiota

The poultry industry is evolving towards antibiotic-free production to meet market demands and decelerate the increasing spread of the antimicrobial resistance. The growing need for antibiotic free products has challenged producers to decrease or completely stop using antimicrobials as feed supplements in broiler diet to improve feed efficiency, growth rate, and intestinal health. Natural feed additives (e.g., probiotics and phytobiotics) are promising alternatives to substitute antimicrobial growth promoters. The goal of our study was to characterize the effects of a Probiotic and an Essential Oils blend on broilers' performance and perform a time-series analysis to describe their excreta microbiome. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 d in 32 randomly allocated cages. Treatments consisted of 4 experimental diets: a basal diet, and a basal diet mixed with an Antibiotic (bacitracin methylene disalicylate), an essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Body weight (on 1, 10, and 21d), and feed intake (10d and 21d) were recorded and feed conversion ratio was calculated. Droppings were collected daily (1-21d) to characterize broilers' excreta microbiota by targeted sequencing of the bacterial 16S rRNA gene. The Probiotic significantly improved feed conversion ratio for starter phase 1 to 10d (P = 0.03), grower phase 10 to 21d (P = 0.05), and total period 1 to 21d (P = 0.01) compared to the Antibiotic. Feed supplements did not affect alpha diversity but did impact microbial beta diversity (P < 0.01). Age also impacted microbiome turnover as differences in alpha and beta diversity were detected. Furthermore, when compared to the basal diet, the probiotic and antibiotic significantly impacted relative abundance of Bifidobacterium (log2 fold change -1.44, P = 0.03), Intestinimonas (log2 fold change 0.560, P < 0.01) and Ligilactobacillus (log2 fold change -1.600, P < 0.01). Overall, Probiotic supplementation but not essential oils supplementation positively impacted broilers' growth performance by directly causing directional shifts in broilers' excreta microbiota structure.

Winged resistance: Storks and gulls increase carriage of antibiotic resistance by shifting from paddy fields to landfills

Waterbirds are vectors for the dissemination of antimicrobial resistance across environments, with some species increasingly reliant on highly anthropized habitats for feeding. However, data on the impact of their feeding habits on the carriage of antibiotic resistance genes (ARGs) are still scarce. To fill this gap, we examined the microbiota (16S rRNA amplicon gene sequencing) and the prevalence of ARG (high-throughput qPCR of 47 genes) in faeces from white storks (Ciconia ciconia) and lesser black-backed gulls (Larus fuscus) feeding in highly (landfill) and less (paddy fields) polluted habitats. Faecal bacterial richness and diversity were higher in gulls feeding upon landfills and showed a greater abundance of potential pathogens, such as Staphylococcus. In contrast, faecal bacterial communities from storks were similar regardless of habitat preferences, maybe due to a less intense habitat use compared to gulls. In addition, birds feeding in the landfill carried a higher burden of ARGs compared to the surrounding soil and surface waters. Network analysis revealed strong correlations between ARGs and potential pathogens, particularly between tetM (resistance to tetracyclines), blaCMY (beta-lactam resistance), sul1 (sulfonamide resistance) and members of the genera Streptococcus, Peptostreptococcus, and Peptoclostridium. Our work demonstrates how transitioning from paddy fields to landfills fosters the carriage of ARGs and potential pathogens in the bird gut, shedding light on the ecological role of these avian vectors in antimicrobial resistance dissemination.

Exposure to a fungicide for a field-realistic duration does not alter bumble bee fecal microbiota structure

Social bees are frequently exposed to pesticides when foraging on nectar and pollen. Recent research has shown that pesticide exposure not only impacts social bee host health but can also alter the community structure of social bee gut microbiotas. However, most research on pesticide-bee gut microbiota interactions has been conducted in honey bees; bumble bees, native North American pollinators, have received less attention and, due to differences in their ecology, may be exposed to certain pesticides for shorter durations than honey bees. Here, we examine how exposure to the fungicide chlorothalonil for a short, field-realistic duration alters bumble bee fecal microbiotas (used as a proxy for gut microbiotas) and host performance. We expose small groups of Bombus impatiens workers (microcolonies) to field-realistic chlorothalonil concentrations for 5 days, track changes in fecal microbiotas during the exposure period and a recovery period, and compare microcolony offspring production between treatments at the end of the experiment. We also assess the use of fecal microbiotas as a gut microbiota proxy by comparing community structures of fecal and gut microbiotas. We find that chlorothalonil exposure for a short duration does not alter bumble bee fecal microbiota structure or affect microcolony production at any concentration but that fecal and gut microbiotas differ significantly in community structure. Our results show that, at least when exposure durations are brief and unaccompanied by other stressors, bumble bee microbiotas are resilient to fungicide exposure. Additionally, our work highlights the importance of sampling gut microbiotas directly, when possible.IMPORTANCEWith global pesticide use expected to increase in the coming decades, studies on how pesticides affect the health and performance of animals, including and perhaps especially pollinators, will be crucial to minimize negative environmental impacts of pesticides in agriculture. Here, we find no effect of exposure to chlorothalonil for a short, field-realistic period on bumble bee fecal microbiota community structure or microcolony production regardless of pesticide concentration. Our results can help inform pesticide use practices to minimize negative environmental impacts on the health and fitness of bumble bees, which are key native, commercial pollinators in North America. We also find that concurrently sampled bumble bee fecal and gut microbiotas contain similar microbes but differ from one another in community structure and consequently suggest that using fecal microbiotas as a proxy for gut microbiotas be done cautiously; this result contributes to our understanding of proxy use in gut microbiota research.

Are fecal samples an appropriate proxy for amphibian intestinal microbiota?

The intestinal microbiota, an invisible organ supporting a host's survival, has essential roles in metabolism, immunity, growth, and development. Since intestinal microbiota influences a host's biology, application of such data to wildlife conservation has gained interest. There are standard protocols for studying the human intestinal microbiota, but no equivalent for wildlife. A major challenge is sampling the intestinal microbiota in an effective, unbiased way. Fecal samples are a popular proxy for intestinal microbiota because collection is non-invasive and allows for longitudinal sampling. Yet it is unclear whether the fecal microbiota is representative of the intestinal microbiota. In wildlife studies, research on the sampling methodology is limited. In this study focusing on amphibians, we characterize and compare the microbiota (small intestine, large intestine, and feces) of two Hong Kong stream-dwelling frog species: Lesser Spiny Frog (Quasipaa exilispinosa) and Hong Kong Cascade Frog (Amolops hongkongensis). We found that the microbiota of both species are similar at the level of phylum and family, but diverge at the level of genus. When we assessed the performance of fecal microbiota in representing the intestinal microbiota in these two species, we found that (1) the microbiota of the small and large intestine differs significantly, (2) feces are not an appropriate proxy of either intestinal sections, and (3) a set of microbial taxa significantly differs between sample types. Our findings raise caution equating fecal and intestinal microbiota in stream-dwelling frogs. Sampling feces can avoid sacrifice of an animal, but researchers should avoid over-extrapolation and interpret results carefully.

Mechanisms of hepatic steatosis in chickens: integrated analysis of the host genome, molecular phenomics and gut microbiome

Hepatic steatosis is the initial manifestation of abnormal liver functions and often leads to liver diseases such as nonalcoholic fatty liver disease in humans and fatty liver syndrome in animals. In this study, we conducted a comprehensive analysis of a large chicken population consisting of 705 adult hens by combining host genome resequencing; liver transcriptome, proteome, and metabolome analysis; and microbial 16S ribosomal RNA gene sequencing of each gut segment. The results showed the heritability (h2 = 0.25) and duodenal microbiability (m2 = 0.26) of hepatic steatosis were relatively high, indicating a large effect of host genetics and duodenal microbiota on chicken hepatic steatosis. Individuals with hepatic steatosis had low microbiota diversity and a decreased genetic potential to process triglyceride output from hepatocytes, fatty acid β-oxidation activity, and resistance to fatty acid peroxidation. Furthermore, we revealed a molecular network linking host genomic variants (GGA6: 5.59-5.69 Mb), hepatic gene/protein expression (PEMT, phosphatidyl-ethanolamine N-methyltransferase), metabolite abundances (folate, S-adenosylmethionine, homocysteine, phosphatidyl-ethanolamine, and phosphatidylcholine), and duodenal microbes (genus Lactobacillus) to hepatic steatosis, which could provide new insights into the regulatory mechanism of fatty liver development.

Smart capsules for sensing and sampling the gut: status, challenges and prospects

Smart capsules are developing at a tremendous pace with a promise to become effective clinical tools for the diagnosis and monitoring of gut health. This field emerged in the early 2000s with a successful translation of an endoscopic capsule from laboratory prototype to a commercially viable clinical device. Recently, this field has accelerated and expanded into various domains beyond imaging, including the measurement of gut physiological parameters such as temperature, pH, pressure and gas sensing, and the development of sampling devices for better insight into gut health. In this review, the status of smart capsules for sensing gut parameters is presented to provide a broad picture of these state-of-the-art devices while focusing on the technical and clinical challenges the devices need to overcome to realise their value in clinical settings. Smart capsules are developed to perform sensing operations throughout the length of the gut to better understand the body's response under various conditions. Furthermore, the prospects of such sensing devices are discussed that might help readers, especially health practitioners, to adapt to this inevitable transformation in healthcare. As a compliment to gut sensing smart capsules, significant amount of effort has been put into the development of robotic capsules to collect tissue biopsy and gut microbiota samples to perform in-depth analysis after capsule retrieval which will be a game changer for gut health diagnosis, and this advancement is also covered in this review. The expansion of smart capsules to robotic capsules for gut microbiota collection has opened new avenues for research with a great promise to revolutionise human health diagnosis, monitoring and intervention.

Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle

The biological mechanisms underlying meat quality remain unclear. Currently, many studies report that the gastrointestinal microbiota is essential for animal growth and performance. However, it is uncertain which bacterial species are specifically associated with the meat quality traits. In this study, 16S rDNA and metagenomic sequencing were performed to explore the composition and function of microbes in various gastrointestinal segments of Tan sheep and Dorper sheep, as well as the relationship between microbiota and meat quality (specifically, the fatty acid content of the muscle). In the ruminal, duodenal, and colonic microbiome, several bacteria were uniquely identified in respective breeds, including Agrobacterium tumefaciens, Bacteroidales bacterium CF, and several members of the family Oscillospiraceae. The annotation of GO, KEGG, and CAZYme revealed that these different bacterial species were linked to the metabolism of glucose, lipids, and amino acids. Additionally, our findings suggested that 16 microbial species may be essential to the content of fatty acids in the muscle, especially C12:0 (lauric acid). 4 bacterial species, including Achromobacter xylosoxidans, Mageeibacillus indolicus, and Mycobacterium dioxanotrophicus, were positively correlated with C12:0, while 13 bacteria, including Methanobrevibacter millerae, Bacteroidales bacterium CF, and Bacteroides coprosuis were negatively correlated with C12:0. In a word, this study provides a basic data for better understanding the interaction between ruminant gastrointestinal microorganisms and the meat quality traits of hosts.

Convergent remodelling of the gut microbiome is associated with host energetic condition over long-distance migration

The gut microbiome can be thought of as a virtual organ given its immense metabolic capacity and profound effects on host physiology. Migratory birds are capable of adaptively modulating many aspects of their physiology to facilitate long-distance movements, raising the hypothesis that their microbiome may undergo a parallel remodeling process that helps to meet the energetic demands of migration.To test this hypothesis, we investigated changes in gut microbiome composition and function over the fall migration of the Blackpoll Warbler (Setophaga striata), which exhibits one of the longest known autumnal migratory routes of any songbird and rapidly undergoes extensive physiological remodeling during migration.Overall, our results showed that the Blackpoll Warbler microbiome differed significantly across phases of fall migration. This pattern was driven by a dramatic increase in the relative abundance of Proteobacteria, and more specifically a single 16S rRNA gene amplicon sequence variant belonging to the family Enterobacteriaceae. Further, Blackpoll Warblers exhibited a progressive reduction in microbiome diversity and within-group variance over migration, indicating convergence of microbiome composition among individuals during long-distance migration. Metagenomic analysis revealed that the gut microbiome of staging individuals was enriched in bacterial pathways involved in vitamin, amino acid, and fatty acid biosynthesis, as well as carbohydrate metabolism, and that these pathways were in turn positively associated with host body mass and subcutaneous fat deposits.Together, these results provide evidence that the gut microbiome of migratory birds may undergo adaptive remodeling to meet the physiological and energetic demands of long-distance migration.

Assessment of the inclusion of a feed additive of sodium humate derived from freshwater sapropel in diets for broiler chickens

Background and Aim

Poultry production is the fastest growing livestock industry in the world, as the rapid growth of and efficient absorption of feed by poultry ensure the production of poultry meat with a relatively low carbon footprint. Seeking new ways to increase livestock productivity as well as poultry product quality, the number of research studies on the use of humic substances of various origins in livestock farming has increased significantly, emphasizing the role of feed additives derived from local resources. The unique capability of humic substances to improve metabolic processes allows the immune protection of the bird body to be strengthened and production efficiency to be increased. This study aimed to identify the effects of sodium humate (NaHum) on the growth performance of broiler chickens and selected blood and ileum microbiota parameters.

Materials and Methods

Dietary research was conducted 2 times under production conditions in a poultry facility of a commercial company, with 210 1-day-old, unsorted broiler chickens of both sexes (Ross 308). The broiler chickens were fed with standard commercial feed, the rearing period of 35 days, and slaughtered on day 36. Sodium humate additive was added to drinking water for the research groups of broilers in period from 8th to 35th day of life, 25 mL (Group 1, n = 2 × 35) and 50 mL (Group 2, n = 2 × 35) per liter of drinking water. Sodium humate contained an average of 4.48% dry matter, a kilogram of dry matter containing 104.3 g of crude protein, 3.6 g of crude fiber and 0.9 g of crude fat, 14.3 MJ of metabolic energy, and 5.8 MJ of energy for live weight gain, as well as a very high content of crude ash -759.8 g, including 4.2 g Ca, 4.2 g Na, and 4.81 g Fe, the dry matter digestibility of NaHum was 87.0%, and the absorption capacity of dry matter was 113.2%., the pH level was 13.0, i.e., alkaline. At the end of the dietary research, the productivity and economic efficiency of the research groups of broilers were calculated by live weight gain, carcass weight, feed conversation ratio, and blood and intestinal samples of broilers were analyzed to identify the effects of NaHum on the growth performance and health status of broilers.

Results

Dietary research found that adding 25 mL/L and 50 mL/L of NaHum to drinking water for the broiler chickens increased their live weights at the selling age, average live weight gains by 3.06-3.93%, and carcass weights by 5.07-6.06%, while feed conversion increased in terms of both live weight (1.5 and 1.51) and carcass weight (1.84 and 1.86) compared with the control group. The best economic performance in terms of the economic efficiency index and the cost index (CI) was found in Group 1, which was fed with the NaHum additive at an intake rate of 25 mL/L. The NaHum additive modulated the ileal microbiota and metabolic processes in the broiler body. At the same time, a significant decrease in the levels of total protein, alkaline phosphatase and phosphorus (P) in blood was found in the research groups.

Conclusion

Considering the positive effects of NaHum derived from freshwater sapropel on the productivity and economic efficiency of broiler chickens, the NaHum feed additive should be further investigated on a larger scale to obtain results that could reasonably be used in practice. This study concluded that a decrease in P levels in the blood was observed when NaHum was added to the drinking water; therefore, it is important to continue the research to draw reasonable conclusions on the effects of NaHum in liquid form on the health performance of farm animals.

Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data

Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.

Comparison of the Gut Microbial Communities of Domestic and Wild Mallards (Anas platyrhynchos) Based on High-Throughput Sequencing Technology

Mallards (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there have been no studies comparing the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis showed significant differences in gut microbial communities between the two groups of mallards, and the diversity and richness of gut microbial communities were significantly higher in wild mallards than in domestic mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCoA) plot. In domestic mallards, Firmicutes (68.0% ± 26.5%) was the most abundant bacterial phylum, followed by Proteobacteria (24.5% ± 22.9%), Bacteroidetes (3.1% ± 3.2%), Fusobacteria (2.2% ± 5.9%), and Actinobacteria (1.1% ± 1.8%). The dominant bacterial phyla in wild mallards were Firmicutes (79.0% ± 10.2%), Proteobacteria (12.9% ± 9.5%), Fusobacteria (3.4% ± 2.5%), and Bacteroidetes (2.8% ± 2.4%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogenic genera (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.

Comparative Analysis of Structural Composition and Function of Intestinal Microbiota between Chinese Indigenous Laiwu Pigs and Commercial DLY Pigs

Intestinal microbiota has an important impact on pig phenotypes. Previous studies mainly focused on the microbiota of feces and worldwide farmed commercial pigs, while research on the microbiota of various intestinal sections and indigenous pig breeds is very limited. This study aimed to characterize and compare the biogeography of intestinal microbiota in pigs of one Chinese indigenous breed and one commercial crossbred. In this study, we sequenced the microbiota of six intestinal segments in the grown-up pigs of a Chinese indigenous breed, Laiwu pigs, and the worldwide farmed crossbred Duroc × Landrace × Yorkshire (DLY) pigs by 16S rRNA sequencing, characterized the biogeography of intestinal microbiota, and compared the compositional and functional differences between the two breeds. The results showed that there were obvious differences in microbial structure and abundance between the small and large intestines. Laiwu pigs had higher large intestinal diversity than DLY pigs, while DLY pigs had higher small intestinal diversity than Laiwu pigs. Moreover, some specific bacterial taxa and Kyoto Encyclopedia of Genes and Genomes pathways were found to be related to the high fat deposition and good meat quality of Laiwu pigs and the high growth speed and lean meat rate of DLY pigs. This study provides an insight into the shifts in taxonomic composition, microbial diversity, and functional profile of intestinal microbiota in six intestinal segments of Laiwu and DLY pigs, which would be essential for exploring the potential influence of the host's genetic background on variation in microbiota composition and diversity.

Investigating the modulatory effects of Moringa oleifera on the gut microbiota of chicken model through metagenomic approach

Introduction

This study aimed to assess the effects of supplementing chicken feed with Moringa oleifera leaf powder, a phytobiotic, on the gastrointestinal microbiota. The objective was to examine the microbial changes induced by the supplementation.

Methods

A total of 40, one-day-old chickens were fed their basal diet for 42 days and then divided into two groups: SG1 (basal diet) and SG2 (basal diet + 10 g/kg Moringa oleifera leaf powder). Metagenomics analysis was conducted to analyze operational taxonomic units (OTUs), species annotation, and biodiversity. Additionally, 16S rRNA sequencing was performed for molecular characterization of isolated gut bacteria, identified as Enterococcus faecium. The isolated bacteria were tested for essential metabolites, demonstrating antibacterial, antioxidant, and anticancer activities.

Results and discussion

The analysis revealed variations in the microbial composition between the control group (SG1) and the M. oleifera-treated group (SG2). SG2 showed a 47% increase in Bacteroides and a 30% decrease in Firmicutes, Proteobacteria, Actinobacteria, and Tenericutes compared to SG1. TM7 bacteria were observed exclusively in the M. oleifera-treated group. These findings suggest that Moringa oleifera leaf powder acts as a modulator that enhances chicken gut microbiota, promoting the colonization of beneficial bacteria. PICRUSt analysis supported these findings, showing increased carbohydrate and lipid metabolism in the M.oleifera-treated gut microbiota.

Conclusion

This study indicates that supplementing chicken feed with Moringa oleifera leaf powder as a phytobiotic enhances the gut microbiota in chicken models, potentially improving overall health. The observed changes in bacterial composition, increased presence of Bacteroides, and exclusive presence of TM7 bacteria suggest a positive modulation of microbial balance. The essential metabolites from isolated Enterococcus faecium bacteria further support the potential benefits of Moringa oleifera supplementation.

Strategies to Assess the Impact of Sustainable Functional Food Ingredients on Gut Microbiota

Nowadays, it is evident that food ingredients have different roles and distinct health benefits to the consumer. Over the past years, the interest in functional foods, especially those targeting gut health, has grown significantly. The use of industrial byproducts as a source of new functional and sustainable ingredients as a response to such demands has raised interest. However, the properties of these ingredients can be affected once incorporated into different food matrices. Therefore, when searching for the least costly and most suitable, beneficial, and sustainable formulations, it is necessary to understand how such ingredients perform when supplemented in different food matrices and how they impact the host's health. As proposed in this manuscript, the ingredients' properties can be first evaluated using in vitro gastrointestinal tract (GIT) simulation models prior to validation through human clinical trials. In vitro models are powerful tools that mimic the physicochemical and physiological conditions of the GIT, enabling prediction of the potentials of functional ingredients per se and when incorporated into a food matrix. Understanding how newly developed ingredients from undervalued agro-industrial sources behave as supplements supports the development of new and more sustainable functional foods while scientifically backing up health-benefits claims.

Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study

BACKGROUND

Oxidative stress (OS) is a key pathophysiological mechanism in Crohn's disease (CD). OS-related genes can be affected by environmental factors, intestinal inflammation, gut microbiota, and epigenetic changes. However, the role of OS as a potential CD etiological factor or triggering factor is unknown, as differentially expressed OS genes in CD can be either a cause or a subsequent change of intestinal inflammation. Herein, we used a multi-omics summary data-based Mendelian randomization (SMR) approach to identify putative causal effects and underlying mechanisms of OS genes in CD.

METHODS

OS-related genes were extracted from the GeneCards database. Intestinal transcriptome datasets were collected from the Gene Expression Omnibus (GEO) database and meta-analyzed to identify differentially expressed genes (DEGs) related to OS in CD. Integration analyses of the largest CD genome-wide association study (GWAS) summaries with expression quantitative trait loci (eQTLs) and DNA methylation QTLs (mQTLs) from the blood were performed using SMR methods to prioritize putative blood OS genes and their regulatory elements associated with CD risk. Up-to-date intestinal eQTLs and fecal microbial QTLs (mbQTLs) were integrated to uncover potential interactions between host OS gene expression and gut microbiota through SMR and colocalization analysis. Two additional Mendelian randomization (MR) methods were used as sensitivity analyses. Putative results were validated in an independent multi-omics cohort from the First Affiliated Hospital of Sun Yat-sen University (FAH-SYS).

RESULTS

A meta-analysis from six datasets identified 438 OS-related DEGs enriched in intestinal enterocytes in CD from 817 OS-related genes. Five genes from blood tissue were prioritized as candidate CD-causal genes using three-step SMR methods: BAD, SHC1, STAT3, MUC1, and GPX3. Furthermore, SMR analysis also identified five putative intestinal genes, three of which were involved in gene-microbiota interactions through colocalization analysis: MUC1, CD40, and PRKAB1. Validation results showed that 88.79% of DEGs were replicated in the FAH-SYS cohort. Associations between pairs of MUC1-Bacillus aciditolerans and PRKAB1-Escherichia coli in the FAH-SYS cohort were consistent with eQTL-mbQTL colocalization.

CONCLUSIONS

This multi-omics integration study highlighted that OS genes causal to CD are regulated by DNA methylation and host-microbiota interactions. This provides evidence for future targeted functional research aimed at developing suitable therapeutic interventions and disease prevention.

Dietary Impacts on Changes in Diversity and Abundance of the Murine Microbiome during Progression and Treatment of Cancer

The intestinal microbial population is recognized for its impact on cancer treatment outcomes. Little research has reported microbiome changes during cancer progression or the interplay of disease progression, dietary sugar/fat intake, and the microbiome through surgery and chemotherapy. In this study, the murine gut microbiome was used as a model system, and changes in microbiome diversity, richness, and evenness over the progression of the cancer and treatment were analyzed. Mice were categorized into four diet cohorts, combinations of either high or low sucrose and high or low omega-3 fatty acids, and two treatment cohorts, saline vehicle or chemotherapy, for a total of eight groups. Fecal samples were collected at specific timepoints to assess changes due to diet implementation, onset of cancer, lumpectomy, and chemotherapy. Akkermansia muciniphila abundance was very high in some samples and negatively correlated with overall Amplicon Sequence Variant (ASV) richness (r(64) = -0.55, p = 3 × 10-8). Throughout the disease progression, ASV richness significantly decreased and was impacted by diet and treatment. Alpha-diversity and differential microbial abundance were significantly affected by disease progression, diet, treatment, and their interactions. These findings help establish a baseline for understanding how cancer progression, dietary macronutrients, and specific treatments impact the murine microbiome, which may influence outcomes.

A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies

As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.

Genetic and microbiome analysis of feed efficiency in laying hens

Improving feed efficiency is an important target for poultry breeding. Feed efficiency is affected by host genetics and the gut microbiota, but many of the mechanisms remain elusive in laying hens, especially in the late laying period. In this study, we measured feed intake, body weight, and egg mass of 714 hens from a pedigreed line from 69 to 72 wk of age and calculated the residual feed intake (RFI) and feed conversion ratio (FCR). In addition, fecal samples were also collected for 16S ribosomal RNA gene sequencing (V4 region). Genetic analysis was then conducted in DMU packages by using AI-REML with animal model. Moderate heritability estimates for FCR (h² = 0.31) and RFI (h² = 0.52) were observed, suggesting that proper selection programs can directly improve feed efficiency. Genetically, RFI was less correlated with body weight and egg mass than that of FCR. The phenotypic variance explained by gut microbial variance is defined as the microbiability (m²). The microbiability estimates for FCR (m² = 0.03) and RFI (m² = 0.16) suggested the gut microbiota was also involved in the regulation of feed efficiency. In addition, our results showed that the effect of host genetics on fecal microbiota was minor in three aspects: 1) microbial diversity indexes had low heritability estimates, and genera with heritability estimates more than 0.1 accounted for only 1.07% of the tested fecal microbiota; 2) the genetic relationship correlations between host genetics and different microbial distance were very weak, ranging from -0.0057 to -0.0003; 3) the microbial distance between different kinships showed no significant difference. Since the RFI has the highest microbiability, we further screened out three genera, including Anaerosporobacter, Candidatus Stoquefichus, and Fournierella, which were negatively correlated with RFI and played positive roles in improving the feed efficiency. These findings contribute to a great understanding of the genetic background and microbial influences on feed efficiency.

Gut microbiota and transcriptome analysis reveals a genetic component to dropping moisture in chickens

High dropping moisture (DM) in poultry production has deleterious effects on the environment, feeding cost, and public health of people and animals. To explore the contributing genetic components, we classified DM of 67-wk-old Rhode Island Red (RIR) hens at 4 different levels and evaluated the underlying genetic heritability. We found the heritability of DM to be 0.219, indicating a moderately heritable trait. We then selected chickens with the highest and lowest DM levels. Using transcriptome, we only detected 12 differentially expressed genes (DEGs) between these 2 groups from the spleen, and 1,507 DEGs from intestinal tissues (jejunum and cecum). The low number of DEGs observed in the spleen suggests that differing moisture levels are not attributed to pathogenic infection. Fourteen of the intestinal high expressed genes are associated with water-salt metabolism (WSM). We also investigated the gut microbial composition by 16S rRNA gene amplicon sequencing. Six different microbial operational taxonomic units (OTUs) (Cetobacterium, Sterolibacterium, Elusimicrobium, Roseburia, Faecalicoccus, and Megamonas) between the 2 groups from jejunum and cecum are potentially biomarkers related to DM levels. Our results identify a genetic component to chicken DM, and can guide breeding strategies.

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

BACKGROUND

The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries.

RESULTS

Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes.

CONCLUSIONS

Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task. Video Abstract.

Correlation between postmortem microbial signatures and substance abuse disorders

The microbiota gut-brain-axis is a bidirectional circuit that links the neural, endocrine, and immunological systems with gut microbial communities. The gut microbiome plays significant roles in human mind and behavior, specifically pain perception, learning capacity, memory, and temperament. Studies have shown that disruptions in the gut microbiota have been associated with substance use disorders. The interplay of gut microbiota in substance abuse disorders has not been elucidated; however, postmortem microbiome profiles may produce promising avenues for future forensic investigations. The goal of the current study was to determine gut microbiome composition in substance abuse disorder cases using transverse colon tissues of 21 drug overdose versus 19 non-overdose-related cases. We hypothesized that postmortem samples of the same cause of death will reveal similar microbial taxonomic relationships. We compared microbial diversity profiles using amplicon-based sequencing of the 16S rRNA gene V4 hypervariable region. The results demonstrated that the microbial abundance in younger-aged cases were found to have significantly more operational taxonomic units than older cases. Using weighted UniFrac analysis, the influence of substances in overdose cases was found to be a significant factor in determining microbiome similarity. The results also revealed that samples of the same cause of death cluster together, showing a high degree of similarity between samples and a low degree of similarity among samples of different causes of death. In conclusion, our examination of human transverse colon microflora in decomposing remains extends emerging literature on postmortem microbial communities, which will ultimately contribute to advanced knowledge of human putrefaction.

Gastrointestinal Biogeography of Luminal Microbiota and Short-Chain Fatty Acids in Sika Deer (Cervus nippon)

The gut microbiota of sika deer has been widely investigated, but the spatial distribution of symbiotic microbes among physical niches in the gastrointestinal tract remains to be established. While feces are the most commonly used biological samples in these studies, the accuracy of fecal matter as a proxy of the microbiome at other gastrointestinal sites is as yet unknown. In the present study, luminal contents obtained along the longitudinal axis of deer gastrointestinal tract (rumen, reticulum, omasum, abomasum, small intestine, cecum, colon, and rectum) were subjected to 16S rRNA gene sequencing for profiling of the microbial composition, and samples from the rumen, small intestine, and cecum were subjected to metabolomic analysis to evaluate short-chain fatty acid (SCFA) profiles. Prevotella bacteria were the dominant gastric core microbes, while Christensenellaceae_R-7_group was predominantly observed in the intestine. While the eight gastrointestinal sites displayed variations in microbial diversity, abundance, and function, they could be clustered into stomach, small intestine, and large intestine segments, and the results further highlighted a specific microbial niche of the small intestine. SCFA levels in the rumen, small intestine, and cecum were significantly different, with Bacteroidetes and Spirochaetes were shown to play a critical role in SCFA production. Finally, the rectal microbial composition was significantly correlated with colonic and cecum communities but not those of the small intestine and four gastric sites. Quantification of the compositions and biogeographic relationships between gut microbes and SCFAs in sika deer should provide valuable insights into the interactions contributing to microbial functions and metabolites. IMPORTANCE Feces or specific segments of the gastrointestinal tract (in particular, the rumen) were sampled to explore the gut microbiome. The gastrointestinal biogeography of the luminal microbiota in ruminants, which is critical to guide accurate sampling for different purposes, is poorly understood at present. The microbial community of the rectal sample (as a proxy of fecal sample) showed higher correlation with those of other large intestinal sites relative to the small intestine or stomach, suggesting that the microbial composition is specifically shaped by the unique physiological characteristics of different gastrointestinal niches. In addition, significant differences in microbiomes and SCFAs were observed among the different gastrointestinal sites.

Early life environment affects behavior, welfare, gut microbiome composition, and diversity in broiler chickens

This study aimed to identify whether early-life conditions in broiler chickens could affect their behavior and welfare, and whether or not this was associated with an altered gut microbiome composition or diversity. Broilers were tested in a 2 x 2 factorial design with hatching conditions [home pen (OH) or at the hatchery (HH)] and enrichment (dark brooder (EE) or no brooder (NE) until 14 days of age) as factors (N = 6 per treatment combination). Microbiota composition was measured in the jejunum on days (d) 7, 14, and 35 and in pooled fecal samples on day 14. A novel environment test (NET) was performed on days 1 and 11, and the behavior was observed on days 6, 13, and 33. On day 35, composite asymmetry was determined and footpad dermatitis and hock burn were scored. In their home pen, HH showed more locomotion than OH (P = 0.05), and NE were sitting more and showed more comfort behavior than EE at all ages (P <0.001 and P = 0.001, respectively). On days 6 and 13 NE showed more eating and litter pecking while sitting, but on day 33 the opposite was found (age^*enrichment: P = 0.05 and P <0.01, respectively). On days 1 and 11, HH showed more social reinstatement in the NET than OH, and EE showed more social reinstatement than NE (P <0.05). Composite asymmetry scores were lower for EE than NE (P <0.05). EE also had less footpad dermatitis and hock burn than NE (P <0.001). Within OH, NE had a more diverse fecal and jejunal microbiome compared to EE on day 14 (feces: observed richness: P = 0.052; jejunum: observed richness and Shannon: P <0.05); the principal component analysis (PCA) showed differences between NE and EE within both HH and OH in fecal samples on day 14, as well as significant differences in bacterial genera such as Lactobacillus and Lachnospiraceae (P <0.05). On day 35, PCA in jejunal samples only showed a trend (P = 0.068) for differences between NE vs. EE within the OH. In conclusion, these results suggest that especially the dark brooder affected the behavior and had a positive effect on welfare as well as affected the composition and diversity of the microbiome. Whether or not the behavior was modulated by the microbiome or vice versa remains to be investigated.

Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure

BACKGROUND

The emergence of antimicrobial resistance is a major threat to global health and has placed pressure on the livestock industry to eliminate the use of antibiotic growth promotants (AGPs) as feed additives. To mitigate their removal, efficacious alternatives are required. AGPs are thought to operate through modulating the gut microbiome to limit opportunities for colonization by pathogens, increase nutrient utilization, and reduce inflammation. However, little is known concerning the underlying mechanisms. Previous studies investigating the effects of AGPs on the poultry gut microbiome have largely focused on 16S rDNA surveys based on a single gastrointestinal (GI) site, diet, and/or timepoint, resulting in an inconsistent view of their impact on community composition.

METHODS

In this study, we perform a systematic investigation of both the composition and function of the chicken gut microbiome, in response to AGPs. Birds were raised under two different diets and AGP treatments, and 16S rDNA surveys applied to six GI sites sampled at three key timepoints of the poultry life cycle. Functional investigations were performed through metatranscriptomics analyses and metabolomics.

RESULTS

Our study reveals a more nuanced view of the impact of AGPs, dependent on age of bird, diet, and intestinal site sampled. Although AGPs have a limited impact on taxonomic abundances, they do appear to redefine influential taxa that may promote the exclusion of other taxa. Microbiome expression profiles further reveal a complex landscape in both the expression and taxonomic representation of multiple pathways including cell wall biogenesis, antimicrobial resistance, and several involved in energy, amino acid, and nucleotide metabolism. Many AGP-induced changes in metabolic enzyme expression likely serve to redirect metabolic flux with the potential to regulate bacterial growth or produce metabolites that impact the host.

CONCLUSIONS

As alternative feed additives are developed to mimic the action of AGPs, our study highlights the need to ensure such alternatives result in functional changes that are consistent with site-, age-, and diet-associated taxa. The genes and pathways identified in this study are therefore expected to drive future studies, applying tools such as community-based metabolic modeling, focusing on the mechanistic impact of different dietary regimes on the microbiome. Consequently, the data generated in this study will be crucial for the development of next-generation feed additives targeting gut health and poultry production. Video Abstract.

The avian gut microbiota: Diversity, influencing factors, and future directions

The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.

Effects of compound probiotics on intestinal barrier function and caecum microbiota composition of broilers

Probiotics are beneficial microorganisms existing in nature and animals and can be used in livestock and poultry breeding. Here, 240 1-day-old Arbor Acre (AA) broilers were used to study the effects of compound probiotics (CP) on antioxidant capacity, intestinal barrier function and cecum microorganisms. 2‰, 3‰ and 4‰ CP were added to the basal diet and fed to broilers for 60d. Blood, jejunum, cecum and cecum contents of broilers on day 60 were collected for jejunum histopathological observation, assessment of oxidative stress status and caecum microbiota composition. Additionally, the mRNA levels of intestinal barrier function were also analyzed. The results showed that CP significantly improved the growth performance of broilers in 1-30 days (P < 0.05 or P < 0.01). 3‰ CP could prominently enhance the ratio of villus height to crypt depth (P < 0.01). Moreover, CP supplementation resulted in a significant elevation in superoxide dismutase (SOD) activity (P < 0.01), accompanied by a significant reduction in malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) contents (P < 0.01) in serum. Additionally, Dietary CP supplementation increased the mRNA levels of zona occludens 1 (ZO-1), Claudin -1 and Occlodin in the jejunum of broilers (P < 0.01). 3‰ CP observably increased the abundance of the genus Rikenellaceae_RC9_gut_group and Phascolarctobacterium (P < 0.01), and significantly decreased the abundance of the genus Ruminococcaceae_UCG-014 (P < 0.05), together with regulations on several genes that are responsible for signaling pathways involved in carbohydrate metabolism, amino acid metabolism and endocrine and metabolic diseases. Taken together, the supplementation of CP could reduce oxidative stress level, increase the mRNA expression levels of tight junction (TJ) related genes, and the colonization of beneficial bacteria in the cecum, as well as improve intestinal health, which has a promoting effect on the growth performance in broilers.

Innovative Use of Olive, Winery and Cheese Waste By-Products as Functional Ingredients in Broiler Nutrition

The purpose of this study was to evaluate the dietary use of novel silage that was created by combining three agro-industrial wastes produced in bulk, i.e., olive mill wastewater, grape pomace, and deproteinized feta cheese whey, in the diets of broiler chickens. A total of 216 one-day-old male Ross-308 chicks were randomly allocated to three treatment groups with six replications (12 chicks per pen). Three isocaloric and isonitrogenous diets were formulated to include the examined silage at 0%, 5%, or 10%. Commercial breeding and management procedures were employed throughout the trial. At the end of the trial (day 35), tissue samples were collected for analysis. Feeding 10% silage resulted in increased (p ≤ 0.001) final body weight (p ≤ 0.001) and feed intake. Jejunum and cecum microflora, as well as breast and thigh meat microflora, were modified (p ≤ 0.05) by the dietary inclusion. Thigh meat oxidative stability was improved (p < 0.01) by the silage supplementation. In addition, breast and thigh meat fatty acid profiles were different, respectively, (p < 0.05) in the supplemented treatments compared to the control. The examined silage was successfully tested in broiler diets with potential benefits for their performance and meat quality.

Regulatory Effects of Combined Dietary Supplementation With Essential Oils and Organic Acids on Microbial Communities of Cobb Broilers

The emergence and spread of antibiotic resistance genes in pathogenic microorganisms have resulted in many countries restricting the use of antibiotics as growth promoters in animal feed. The combined use of essential oils and organic acids can help maintain intestinal health, improve animal growth performance, and alleviate the negative effects of banned antibiotics for certain economically important animals. Although the modes of action for the combined dietary supplementation of essential oils and organic acids such as thymol-citric acid (EOA1) and thymol-butyric acid (EOA2) remain unclear, it is speculated that their activities are achieved through beneficial modulation of gastrointestinal microbial communities and inhibition of pathogen growth. In this study, 16S rDNA amplicon sequencing was used to analyze the effects of treatment with EOA1 and EOA2 on the jejunal, cecal, and fecal microbial communities of Cobb broilers while also evaluating effects over different broiler ages. The intestinal microbial communities of broilers developed with increasing age, and Lactobacillus gradually came to dominate the intestinal communities of treated broilers. Further, the microbial communities of feces were more complex than those of the jejuna and ceca. We systematically elucidate that the longitudinal changes in the intestinal microbial communities of Cobb broiler chickens at different ages. Meanwhile, we found that the addition of EOA1 or EOA2 to the diet: (1) inhibited the proliferation of Ralstonia pickettii and Alcaligenaceae in the jejuna on day 28, (2) promoted the colonization and growth of beneficial bacteria such as Lactobacillus, Clostridia, and Bacteroidia at various growth stages, and (3) enriched the abundance of certain microbiota functions, including biological pathways related to metabolism (e.g., enzyme families). Taken together, the results of this study demonstrate that EOA1 and EOA2 dietary supplementation can affect various microbial metabolic pathways related to the metabolism and absorption of nutrients via regulation of the intestinal microbial community structures of Cobb broilers.

Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems

The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (¹³C) and nitrogen (¹⁵N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.

Potential improvements of the cognition of piglets through a synbiotic supplementation from 1 to 28 days via the gut microbiota

The influence of feed supplements on behavior and memory has been recently studied in livestock. The objectives of the study were to evaluate the effects of a synbiotic on: an episodic-like (SOR: Spontaneous Object Recognition), a working (BARR: Fence barrier task), a long-term (TMAZE: Spatial T-maze task) memory test and on gut microbiota composition. Eighteen female piglets were supplemented from 1 to 28 days of age with a synbiotic (SYN), while 17 served as control (CTL). Feces were collected on days 16, 33 and 41 for 16S rRNA gene composition analyses. In the SOR, SYN piglets interacted more quickly with the novel object than CTL piglets. In the BARR, SYN piglets had shorter distances to finish the test in trial 3. In the TMAZE, SYN piglets were quicker to succeed on specific days and tended to try the new rewarded arm earlier during the reversal stage. Difference of microbiota composition between treatments was nonexistent on D16, a tendency on D33 and significant on D41. The synbiotic supplement may confer memory advantages in different cognitive tasks, regardless of the nature of the reward and the memory request. Difference in memory abilities can potentially be explained by differences in microbiota composition.

The Role of Segmented Filamentous Bacteria in Immune Barrier Maturation of the Small Intestine at Weaning

The microbiological, physical, chemical, and immunological barriers of the gastrointestinal tract (GIT) begin developing in utero and finish maturing postnatally. Maturation of these barriers is essential for the proper functioning of the GIT. Maturation, particularly of the immunological barrier, involves stimulation by bacteria. Segmented filamentous bacteria (SFB) which are anaerobic, spore-forming commensals have been linked to immune activation. The presence and changes in SFB abundance have been positively correlated to immune markers (cytokines and immunoglobulins) in the rat ileum and stool samples, pre- and post-weaning. The abundance of SFB in infant stool increases from 6 months, peaks around 12 months and plateaus 25 months post-weaning. Changes in SFB abundance at these times correlate positively and negatively with the production of interleukin 17 (IL 17) and immunoglobulin A (IgA), respectively, indicating involvement in immune function and maturation. Additionally, the peak in SFB abundance when a human milk diet was complemented by solid foods hints at a diet effect. SFB genome analysis revealed enzymes involved in metabolic pathways for survival, growth and development, host mucosal attachment and substrate acquisition. This narrative review discusses the current knowledge of SFB and their suggested effects on the small intestine immune system. Referencing the published genomes of rat and mouse SFB, the use of food substrates to modulate SFB abundance is proposed while considering their effects on other microbes. Changes in the immune response caused by the interaction of food substrate with SFB may provide insight into their role in infant immunological barrier maturation.

Poultry gut health - microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies

The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.

Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents

Host-microbe interactions within the gastrointestinal tract (GIT) play a pivotal role in shaping host physiology, ecology, and life history. However, these interactions vary across gut regions due to changes in the physical environment or host immune system activity, thereby altering the microbial community. Each animal species may harbor their own unique microbial community due to host species-specific ecological traits such as dietary habits, micro-habitat preferences, and mating behavior as well as physiological traits. While the gut microbiota in wild animals has received much attention over the last decade, most studies comparing closely related species only utilized fecal or colon samples. In this study, we first compared the gut microbial community from the small intestine, cecum, colon, and rectum within three sympatric species of wild rodents (i.e. Apodemus speciosus, A. argenteus, and Myodes rufocanus). We then compared each gut region among host species to determine the effect of both gut region and host species on the gut microbiota. We found that the small intestine harbored a unique microbiome as compared to the lower GIT in all three host species, with the genus Lactobacillus in particular having higher abundance in the small intestine of all three host species. There were clear interspecific differences in the microbiome within all gut regions, although some similarity in alpha diversity and community structure within the small intestine was found. Finally, fecal samples may be appropriate for studying the lower GIT in these species, but not the small intestine.

Comparative analysis of chicken cecal microbial diversity and taxonomic composition in response to dietary variation using 16S rRNA amplicon sequencing

BACKGROUND

Antibiotic resistance poses a grave threat to One-Health. By replacing antibiotics with non-antibiotic additives (are alternatives to antibiotics, ATAs) like phytogenic feed additives and organic acids in poultry feed. ATAs are a potential alternative as these decline the proliferation of pathogenic bacteria and strengthen gut function in broiler chickens. In this study, we use 16S rRNA amplicon sequencing of the V3-V4 region to evaluate phytogenic feed additives and organic acids on the cecal microbial diversity of broiler chickens.

METHODS AND RESULTS

Two hundred & forty broiler chicks were divided into five treatments comprising: a controlled basal diet (CON), antibiotic group (AB), phytogenic feed additives (PHY), organic acids (ORG), and a combination of PHY + ORG (COM). A distinctive microbial community structure was observed amongst different treatments with increased microbial diversity in AB, ORG, and COM (p < 0.05). The synergistic effects of PHY and ORG increased bacterial population of phyla: Firmicutes, Bacteroides, and Proteobacteria in the cecum. The presence of species, Akkermansia muciniphila (involved in mucin degradation) and Bacillus safensis (a probiotic bacterium) were noticed in COM and PHY, respectively. Clustering analysis revealed a higher relative abundance of similar microbial community composition between AB and ORG groups.

CONCLUSIONS

Treatments with PHY and ORG modified the relative abundance and presence/absence of specific microbiota in the chicken cecum. Hence, cecal microbiota modulation through diet is a promising strategy to reduce cross-contamination of zoonotic poultry pathogens, led to healthy and economical broiler meat.

Analysis of the Microbial Intestinal Tract in Broiler Chickens during the Rearing Period

Gut microbiota contributes to animal health. However, identifying which microorganisms or associated functions are involved remains, still, difficult to assess. In the present study, the microbiota of healthy broiler chickens, under controlled diet and farm conditions, was investigated by 16S rRNA gene sequencing in four intestine segments and at four ages. In detail, 210 Ross-308 male chickens were raised according to the EU guidelines and fed on a commercial diet. The duodenum, jejunum, ileum, and caecum microbiota were analyzed at 11, 24, 35, and 46 days of life. Although the microbial composition was revealed as homogeneous 11 days after chicks hatched, it was found to be similar in the proximal intestine segments and different in ileum and caecum, where almost the same genera and species were detected with different relative abundances. Although changes during the later growth stage were revealed, each genus remained relatively unchanged. Lactobacillus mostly colonized the upper tract of the intestine, whereas the Escherichia/Shigella genus the ileum. Clostridium and Bacteroides genera were predominant in the caecum, where the highest richness of bacterial taxa was observed. We also analyze and discuss the predicted role of the microbiota for each intestine segment and its potential involvement in nutrient digestion and absorption.

The Spatial and Temporal Characterization of Gut Microbiota in Broilers

The gut microbiota of chickens plays an important role in host physiology. However, the colonization and prevalence of gut microbiota have not been well-characterized. Here, we performed 16S rRNA gene sequencing on the duodenal, cecal and fecal microbiota of broilers at 1, 7, 21, and 35 days of age and characterized the dynamic succession of microbiota across the intestinal tract. Our results showed that Firmicutes was the most abundant phylum detected in each gut site at various ages, while the microbial diversity and composition varied among the duodenum, cecum, and feces at different ages. The microbial diversity and complexity of the cecal microbiota increased with age, gradually achieving stability at 21 days of age. As a specific genus in the cecum, Clostridium_sensu_stricto_1 accounted for 83.50% of the total abundance at 1 day of age, but its relative abundance diminished with age. Regarding the feces, the highest alpha diversity was observed at 1 day of age, significantly separated from the alpha diversity of other ages. In addition, no significant differences were observed in the alpha diversity of duodenal samples among 7, 21, and 35 days of age. The predominant bacterium, Lactobacillus, was relatively low (0.68–6.04%) in the intestinal tract of 1-day-old chicks, whereas its abundance increased substantially at 7 days of age and was higher in the duodenum and feces. Escherichia-Shigella, another predominant bacterium in the chicken intestinal tract, was also found to be highly abundant in fecal samples, and the age-associated dynamic trend coincided with that of Lactobacillus. In addition, several genera, including Blautia, Ruminiclostridium_5, Ruminococcaceae_UCG-014, and [Ruminococcus]_torques_group, which are related to the production of short-chain fatty acids, were identified as biomarker bacteria of the cecum after 21 days of age. These findings shed direct light on the temporal and spatial dynamics of intestinal microbiota and provide new opportunities for the improvement of poultry health and production.

The Impact of Host Genotype, Intestinal Sites and Probiotics Supplementation on the Gut Microbiota Composition and Diversity in Sheep

Three sampling strategies with a 16s rRNA high-throughput sequencing and gene expression assay (by RT-PCR) were designed, to better understand the host and probiotics effect on gut microbiota in sheep. Sampling: (1) colon contents and back-fat tissues from small-tailed Han sheep (SHS), big-tailed Hulun Buir sheep (BHBS), and short-tailed Steppe sheep (SHBS) (n = 12, 14, 12); (2) jejunum, cecum and colon contents, and feces from Tan sheep (TS, n = 6); (3) feces from TS at 4 time points (nonfeeding, 30 and 60 feeding days, and stop feeding 30 days) with probiotics supplementation (n = 7). The results indicated SHS had the highest Firmicutes abundance, the thinnest back-fat, and the lowest expression of C/EBPβ, C/EBPδ, ATGL, CFD, and SREBP1. Some bacteria orders and families could be potential biomarkers for sheep breeds with a distinct distribution of bacterial abundance, implying the host genotype is predominant in shaping unique microbiota under a shared environment. The microbiota diversity and Bifidobacterial populations significantly changed after 60 days of feeding but restored to its initial state, with mostly colonies, after 30 days ceased. The microbiota composition was greatly different between the small and large intestines, but somewhat different between the large intestine and feces; feces may be reliable for studying large intestinal microbiota in ruminants.

Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum

Traditional sampling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative sampling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive samples (excreta, litter and poultry dust) are representative of invasive samples (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene amplicon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive samples were detected in non-invasive samples, the relative abundance of members of the microbial communities of these groups were different, as shown by beta diversity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes, and excreta as a proxy of caecal contents for the detection of Tenericutes. Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes. However, none of the non-invasive samples could be used to infer the overall abundance of OTUs observed in invasive samples. In conclusion, non-invasive samples could be used to detect the presence and absence of the majority of the OTUs found in invasive samples, but could not accurately reflect the microbial community structure of invasive samples.

Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death

Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.

Major histocompatibility complex class II genetic diversity and the genetic influence on gut microbiota in Guizhou minipigs

Major histocompatibility complex (MHC) is an important complex that presents antigen to T cells. The second exon of swine MHC (SLA) class II genes has antigen binding sites that bind with extracellular antigen. Populations with high MHC gene diversity result in low gut microbiota, and individuals with MHC gene heterozygote have lower gut microbiota diversity than that of homozygote. The pig is an animal with organs physiologically and anatomically similar to humans than any other mammal, and the pig is also suitably developed as a laboratory animal to establish the animal models of human disease. However, the relationship between SLA genetic diversity and the gut microbes of the pig is ambiguous. We studied the characterization of SLA class II genes and calculated the genetic diversity, and then we selected experimental animal groups divided by different SLA genotypes to investigate the gut microbiota composition by sequencing V3 to V4 hypervariable regions of bacterial 16 s rRNA from fecal samples. Our results showed that Guizhou minipigs had a low SLA genetic diversity, which may be due to the small founder population. The Guizhou minipig population deviated from neutral selection and balancing selection, which shows that Guizhou minipigs experience a strong artificial selection in recent years. We observed that the sex differences influenced gut microbiota much more deeply than that of genetics. Our results also showed that the individual with heterozygote of genes at the SLA class II region had much higher abundant gut microbiota than that of the homozygote.

Comparative Metagenomic Analysis of Chicken Gut Microbial Community, Function, and Resistome to Evaluate Noninvasive and Cecal Sampling Resources

When conducting metagenomic analysis on gut microbiomes, there is no general consensus concerning the mode of sampling: non-contact (feces), noninvasive (rectal swabs), or cecal. This study aimed to determine the feasibility and comparative merits and disadvantages of using fecal samples or rectal swabs as a proxy for the cecal microbiome. Using broiler as a model, gut microbiomes were obtained from cecal, cloacal, and fecal samples and were characterized according to an analysis of the microbial community, function, and resistome. Cecal samples had higher microbial diversity than feces, while the cecum and cloaca exhibited higher levels of microbial community structure similarity compared with fecal samples. Cecal microbiota possessed higher levels of DNA replicative viability than feces, while fecal microbiota were correlated with increased metabolic activity. When feces were excreted, the abundance of antibiotic resistance genes like tet and ErmG decreased, but some antibiotic genes became more prevalent, such as fexA, tetL, and vatE. Interestingly, Lactobacillus was a dominant bacterial genus in feces that led to differences in microbial community structure, metabolism, and resistome. In conclusion, fecal microbiota have limited potential as a proxy in chicken gut microbial community studies. Thus, feces should be used with caution for characterizing gut microbiomes by metagenomic analysis.

Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies

Understanding the roles of microorganisms in the animal gastrointestinal microenvironment is highly important for the development of effective strategies to manage and manipulate these microbial communities. In order to guide future animal gut microbiota research projects and standardization efforts, we have conducted a systematic comparison of 10 currently used sample preservation and DNA extraction approaches for pig and chicken microbiota samples and quantified their effects on bacterial DNA yield, quality, integrity, and on the resulting sequence-based bacterial composition estimates. The results showed how key stages of conducting a microbiota study, including the sample storage and DNA extraction, can substantially affect DNA recovery from the microbial community, and therefore, biological interpretation in a matrix-dependent manner. Our results highlight the fact that the influence of storage and extraction methods on the resulting microbial community structure differed by sample type, even within the same species. As the effects of these technical steps are potentially large compared with the real biological variability to be explained, standardization is crucial for accelerating progress in the area of livestock microbiota research. This study provided a framework to assist future animal gut microbiota research projects and standardization efforts.

Serotoninergic system targeting in multiple sclerosis: the prospective for pathogenetic therapy

Serotonin (5-hydroxytryptamine) (5-HT) is a neurotransmitter, which mediates neuropsychological functions of the central nervous system (CNS). Recent studies have shown the modulatory effect of 5-HT on gut microbiota functions, which play an essential role in developing CNS inflammatory diseases. Finally, 5-HT is a direct mediator of neuroimmune interaction. The article reviews the literature data on the role of 5-HT in the regulation of neuroinflammation in multiple sclerosis (MS). The influence of 5-HT and selective serotonin reuptake inhibitors (SSRIs) on experimental autoimmune encephalomyelitis (EAE) and MS pathogenesis, as well as the therapeutic potential of serotoninergic drugs as a pathogenetic therapy of MS, are discussed.

Species Differences in in vitro and Estimated in vivo Kinetics for Intestinal Microbiota Mediated Metabolism of Acetyl-deoxynivalenols

SCOPE

Deoxynivalenol (DON) and its acetylated derivatives 3-acetyl-DON (3-Ac-DON) and 15-acetyl-DON (15-Ac-DON) are important mycotoxins of concern in the modern food chain.

METHODS AND RESULTS

The present study reveals that the rate of de-acetylation in in vitro anaerobic fecal incubations decreased in the order rat > mouse > human > pig for 3-Ac-DON, and mouse > human > rat > pig for 15-Ac-DON. The ratio between the de-acetylation rate of 3-Ac-DON and 15-Ac-DON varies with the species. Scaling of the kinetic parameters to the in vivo situation results in catalytic efficiencies decreasing in the order human > rat > pig > mouse for 3-Ac-DON and human > pig > rat > mouse for 15-Ac-DON. The results obtained indicate that in mice, 3-Ac-DON can be fully deconjugated while 15-Ac-DON cannot. In rats, pigs, and humans, both 3-Ac-DON and 15-Ac-DON can be totally transformed by gut fecal microbiota during the estimated intestinal residence time. A correlation analysis between the deacetylation rate and the relative abundance of the microbiome suggests Lachnospiraceae may be involved in the deacetylation process.

CONCLUSION

It is concluded that interspecies differences in deacetylation of acetylated DONs exist but that in risk assessment assumption of complete intestinal deconjugation provides an adequate approach.

The pelvic flexure separates distinct microbial communities in the equine hindgut

As hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota from each sample was characterized by profiling the V4 region of the 16S rRNA. Principal coordinate analysis of the beta diversity results revealed significant (p = 0.0001; F = 5.2393) similarities between the microbial populations from cecal and ventral colon and the dorsal colon and fecal samples, however, there was little overlap between the proximal and distal ends of the hindgut. These distinct population structures observed in our results coincide with the pelvic flexure, which itself separates intestinal compartments with distinct roles in digestive physiology. An indicator species analysis confirmed the population differences, supported by the identification of several microbial families characteristic of the compartments upstream of the pelvic flexure that were not represented following it. Our data suggest that the fecal microbiota is not informative of the proximal hindgut but can provide insight into communities of the distal compartments. Further, our results suggest that the pelvic flexure might be an important anatomical landmark relative to the microbial communities in the equine large intestine.