Fecal Communities Research Articles

Impact of antibiotic perturbation on fecal viral communities in mice.

Viruses and bacteriophages have a strong impact on intestinal barrier function and the composition and functional properties of commensal bacterial communities. Shifts of the fecal virome might be involved in human diseases, including inflammatory bowel disease (IBD). Loss-of-function variants in the nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene are associated with an increased risk of developing Crohn's disease, a subtype of human chronic IBD, where specific changes in fecal viral communities have also been described. To improve our understanding of the dynamics of the enteric virome, we longitudinally characterized the virome in fecal samples from wild-type C57BL/6J and NOD2 knock-out mice in response to an antibiotic perturbation. Sequencing of virus-like particles demonstrated both a high diversity and high interindividual variation of the murine fecal virome composed of eukaryotic viruses and bacteriophages. Antibiotics had a significant impact on the fecal murine virome. Viral community composition only partially recovered in the observation period (10 weeks after cessation of antibiotics) irrespective of genotype. However, compositional shifts in the virome and bacteriome were highly correlated, suggesting that the loss of specific phages may contribute to prolonged dysregulation of the bacterial community composition. We suggest that therapeutic interference with the fecal virome may represent a novel approach in microbiota-targeted therapies.

Enteroendocrine peptides, growth, and the microbiome during the porcine weaning transition

BackgroundGrowth rate in pigs can be affected by numerous factors that also affect feeding behavior and the microbiome. Recent studies report some communication between the microbiome and the enteroendocrine system. The present study examined if changes in the piglet microbiome between birth and during the weaning transition can be correlated either positively or negatively with growth rate and plasma concentrations of enteroendocrine peptides.ResultsDuring the post-weaning transition, a 49% reduction in average daily gain was observed at day 24 (P < 0.05) relative to day 21. Pigs recovered by day 28 with body weight and average daily gain increases of 17% and 175%, respectively relative to day 24 and the highest rate of gain was measured at day 35 (462 g/day). The time interval between day 21–24 had the highest number of correlations (n = 25) between the relative abundance differences in taxa over time and corresponding percent weight gain. Amplicon sequence variants with the greatest correlation with percent weight gain between day 21–24 belonged to families Prevotellaceae NK3B31 (ρ = 0.65, P < 0.001), Veillonellaceae (ρ = 0.63, P < 0.001) and Rikenellaceae RC9 (ρ = 0.62, P < 0.001). Seven taxa were positively correlated with percent weight gain between day 24–28. Eight taxa were positively correlated with percent weight gain between day 28–35, of which four were Clostridia. Only Lactobacillus reuteri was positively correlated across both day 24–28 and day 28–35 analyses. Insulin-like growth factor 1 (IGF-1; R2 = 0.61, P < 0.001), glucose-dependent insulinotropic polypeptide (GIP; R2 = 0.20, P < 0.001), glucagon-like peptide 1 (GLP-1; R2 = 0.51, P < 0.001), and glucagon-like peptide 2 (GLP-2; R2 = 0.21, P < 0.001) were significantly associated with the piglet fecal community NMDS, while serotonin showed no significant association (R2 = 0.03, P = 0.15). Higher concentrations of GLP-1 and GLP-2 characterized day 1 fecal communities, while GIP levels had the strongest relationship primarily with samples ordinated with the day 21 cluster.ConclusionsDemonstration of an association of certain taxa with individual gut peptides at specific ages suggests the potential for the microbiome to elicit changes in the gut enteroendocrine system during early postnatal development in the pig.

Using illustrated system analysis for qualitative risk assessment of emptying of pit latrines

Pit latrines as the primary means of sanitation for billions of people. Fecal sludge must be removed regularly when pit latrines fill up, and the workers who empty these latrines are essential service providers. Pit latrine emptying services and approaches are highly variable, ranging from highly trained teams using vacuum trucks with a suite of personal protective equipment to individuals with no protection using simple manual tools like buckets and shovels. While national governments and nonprofits endeavor to make pit latrine emptying safer, the people making day-to-day decisions such as local pit emptying associations, sanitation businesses, utilities, and local governments have limited resources to evaluate how different emptying practices vary in terms of risk. In this paper we describe the development of an open-source Illustrated System Analysis tool for the fecal sludge management community. This tool can be used in conjunction with a simple risk assessment matrix to help decision makers describe, compare, and prioritize risks for mitigation. We demonstrate this process by outlining how a pit emptying team can compare mechanical and manual emptying with respect to ingestion of fecal material and inhalation of fecal bioaerosols. Illustrated System Analysis can be a tool to analyze fecal sludge management systems, and the associated challenges and opportunities so that they could be understood and referenced by the wider public and used to spark innovation. We provide a library of graphics freely under creative commons.

Contrasting Fecal Methanogenic and Bacterial Profiles of Organic Dairy Cows Located in Northwest Washington Receiving Either a Mixed Diet of Pasture and TMR or Solely TMR.

Simple SummaryMethane is a by-product of the microbial fermentation process from a group of archaea known as methanogens. Ruminants harbor methanogens as a component of their normal gastrointestinal microbiota. In this study, we assessed the fecal microbiome of organic dairy cows across different time points receiving a mixed diet of pasture and TMR or TMR only. Our aim was to compare the archaea and bacterial fecal microbial structure, diversity and their interactions across diets. Cluster analysis based on the cows’ fecal microbial community identified four clusters. We found little difference in the relative abundance of methanogens across clusters. However, there was evidence of differences in diversity between pasture associated communities and those associated with TMR only. The cluster associated with cows receiving high-quality pasture and TMR, had higher diversity and a less robust co-occurrence network than those in TMR only or lower-quality pasture communities. The overall good pasture and TMR quality, combined with the organic allowance for feeding high levels of TMR, might have contributed to the lack of differences in the fecal archaeal community. The development of novel strategies that are independent of pasture management could have a greater impact in helping to reduce enteric CH4 emissions on organic dairies.Currently, little is known regarding fecal microbial populations and their associations with methanogenic archaea in pasture-based dairy cattle. In this study, we assessed the fecal microbiome of organic dairy cows across different time points receiving a mixed diet of pasture and total mixed ration (TMR) or TMR only. We hypothesized that the fecal methanogenic community, as well as co-occurrence patterns with bacteria, change across diets. To test these hypotheses, we analyzed TMR and pasture samples, as well as the V3-V4 region of 16S rRNA of fecal samples collected over the course of a one-year study period from 209 cows located on an organic dairy in Northwest Washington. The inherent variability in pasture quality, quantity, availability, and animal preference can lead to diverse dietary intakes. Therefore, we conducted a k-means clustering analysis to identify samples from cows that were associated with either a pasture-based diet or a solely TMR diet. A total of 4 clusters were identified. Clusters 1 and 3 were mainly associated with samples primarily collected from cows with access to pasture of varying quality and TMR, cluster 2 was formed by samples from cows receiving only TMR, and cluster 4 was a mix of samples from cows receiving high-quality pasture and TMR or TMR only. Interestingly, we found little difference in the relative abundance of methanogens between the community clusters. There was evidence of differences in diversity between pasture associated bacterial communities and those associated with TMR. Cluster 4 had higher diversity and a less robust co-occurrence network based on Spearman correlations than communities representing TMR only or lower-quality pasture samples. These findings indicate that varied bacterial communities are correlated with the metabolic characteristics of different diets. The overall good pasture and TMR quality in this study, combined with the organic allowance for feeding high levels of TMR even during the grazing season, might have contributed to the lack of differences in the fecal archaeal community from samples associated with a mixed pasture and TMR diet, and a TMR only diet. Mitigation strategies to decrease methane emissions such as increasing concentrate to forage ratio, decreasing pasture maturity and adopting grazing systems targeting high quality pasture have been shown to be efficient for pasture-based systems. However, the allowance for organic dairy producers to provide up to an average of 70% of a ruminant’s dry matter demand from dry matter fed (e.g., TMR), suggests that reducing enteric methane emissions may require the development of novel dietary strategies independent of pasture management.

Prebiotics enhance persistence of fermented-food associated bacteria in in vitro cultivated fecal microbial communities

It is well established that the gastrointestinal (GI) microbiota plays a major role in human health. Dietary interventions, and consumption of fermented foods that contain live microbes, in particular, are among the approaches being investigated to modulate the GI microbiota and improve health. However, the persistence of fermented food-associated bacteria (FAB) within the GI tract is typically limited by host factors that limit colonization and competition with autochthonous microbes. In this research, we examined if the addition of prebiotics, dietary substrates that are selectively metabolized by microbes to improve health, would enhance the persistence of FAB. We evaluated the persistence of bacteria from three live microbe-containing fermented foods—kefir, sausage, and sauerkraut—in fecal microbial communities from four healthy adults. Fecal communities were propagated in vitro and were inoculated with fermented food-associated microbes from kefir, sausage, or sauerkraut at ~107 CFU/mL. Communities were diluted 1:100 every 24 h into fresh gut simulation medium to simulate microbial community turnover in the GI tract. We measured the persistence of Lactobacillaceae from fermented foods by quantitative PCR (qPCR) and the persistence of other FAB through 16S rRNA gene sequencing. FAB were unable to persist in vitro, reaching undetectable levels within 96 h. Addition of prebiotics, including xylooligosaccharides and a mixture of fructooligosaccharides and galactooligosaccharides enhanced the persistence of some species of FAB, but the level of persistence varied by fecal donor, fermented food, and prebiotic tested. Addition of prebiotics also increased the relative abundance of Bifidobacterium species, which most likely originated from the fecal microbiota. Collectively, our results support previous in vivo studies demonstrating the transient nature of FAB in the GI tract and indicate that consumption of prebiotics may enhance their persistence.

Design, construction, and in vivo augmentation of a complex gut microbiome

Efforts to model the human gut microbiome in mice have led to important insights into the mechanisms of host-microbe interactions. However, the model communities studied to date have been defined or complex, but not both, limiting their utility. Here, we construct and characterize invitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2. In gnotobiotic mice, hCom2 exhibited increased stability to fecal challenge and robust colonization resistance against pathogenic Escherichia coli. Mice colonized by either hCom2 or a human fecal community are phenotypically similar, suggesting that this consortium will enable a mechanistic interrogation of species and genes on microbiome-associated phenotypes.

Comparison of Bacterial and Fungal Community Structure and Potential Function Analysis of Yak Feces before and after Weaning.

Weaning is one of the most stressful periods in yak growth. However, the impact of weaning on microbial diversity, structure, and potential function of yak feces is not clear. In this study, 12 Xinjiang yaks aged 3, 4, 5, and 6 months old were selected to collect fresh feces before and after weaning. Through 16S rRNA and ITS high-throughput sequencing, the dynamic distribution and potential function of yak fecal, bacterial, and fungal communities in each month were revealed. The study found that the richness of fungi had a significant impact on weaning. At the phylum level, Firmicutes, Bacteroidetes, Ascomycota, and Basidiomycota, and at the genus level, 5-7N15, Oscillospira, Roseburia, Dorea, Preussia, Neoascochyta, Naganishia, and Sporormiella were enriched in yak feces of different months old. The abundance and proportion of bacteria Firmicutes, Bacteroidetes, 5-7N15, and fungi Mucoromyceta changed significantly before and after weaning. With the increase of months, Verrucomicrobia and Akkermansia have shown a downward trend. Through the prediction and analysis of fecal microbial function, it was found that at the level of primary pathways, weaning has a significant impact on cellular processes, environmental information processing, genetic information processing, metabolism, and organismal systems. At the level of secondary metabolic pathways, weaning has a significant impact on cell motility, signal transduction, folding, sorting and degradation, translation, amino acid metabolism, glycan biosynthesis and metabolism, metabolism of terpenoids and polyketides, and xenobiotics biodegradation and metabolism. In addition, by analyzing the differences in functional pathways and microbial composition between sample groups of different months, it was found that the differences in functional pathways were related to the abundance differences of some microorganisms. In general, the changes in the composition and structure of yak fecal microflora may reflect the adaptability of the intestinal microbiota.

Dynamic alterations in the donkey fecal bacteria community and metabolome characteristics during gestation.

In donkeys, the gestation period is a dynamic and precisely coordinated process involving systemic and local alterations. Both the gut microbiota and its link with blood metabolites are thought to play significant roles in maintaining maternal health and supporting fetal development during the gestation period. This study was conducted to evaluate gut microbiota changes and the correlation with plasma metabolites in Dezhou donkeys during the gestation period. The donkeys were divided into the four following groups according to their pregnancy stages: the non-pregnant (NP), early stage of pregnancy (P1), middle stage of pregnancy (P2), and late stage of pregnancy (P3) groups. A total of 24 (n = 6 per group) samples of donkey feces and plasma were collected. The results showed that the diversity (Shannon index) of fecal bacteria significantly increased throughout the gestation period. The phyla Spirochaetota and Fibrobacterota varied significantly according to the stages of pregnancy (p < 0.05). At the genus level, the abundance of Treponema in pregnant donkeys was greater than that in non-pregnant donkeys (p < 0.05), and the genus Streptococcus reached its maximum abundance in the P2 period (p < 0.05). The abundance of Ruminococcaceae_NK4A214_group and norank_f_norank_o_WCHB1-41 linearly increased with the progression of pregnancy (p < 0.05). In addition, the host plasma metabolome was altered significantly during the gestation period. Testolic acid, estradiol-17beta 3-sulfate, equol 7'-o-glucuronide, equol 4'-o-glucuronide, estrone, estrone 3-glucuronide, and estradiol were the most significant differential enriched metabolites, and they increased gradually as gestation progressed. The altered metabolites were mainly enriched in pathways matched to bile secretion, ABC transporters, amino acid metabolism, protein digestion and absorption, mineral absorption, fatty acid degradation, glycerophospholipid metabolism, and steroid hormone biosynthesis. We also found a significant correlation between the shifts in donkey fecal bacteria and changes in the host metabolism. In summary, this study provided systematic data on the fecal bacterial changes and host plasma metabolism of donkeys throughout pregnancy. The results indicated that host-bacteria interactions during the gestation period influence the host metabolism. These interactions benefit the pregnant donkeys by providing a sufficient supply of nutrients and energy for fetal growth and maternal health.

Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet.

Simple SummaryComparison of bacterial diversity and composition of feces from cows and goats offered the same pasture-based diet revealed that the animal species had no effect on bacterial species richness and diversity, but significantly affected species evenness. Both diet and host species influence the gut microbiome.The aim of this study was to compare the diversity and composition of fecal bacteria in goats and cows offered the same diet and to evaluate the influence of animal species on the gut microbiome. A total of 17 female goats (Blond Adamellan) and 16 female cows (Brown Swiss) kept on an organic farm were fed pasture and hay. Bacterial structure in feces was examined by high-throughput sequencing using the V4–V5 region of the 16S rRNA gene. The Alpha diversity measurements of the bacterial community showed no statistical differences in species richness and diversity between the two groups of ruminants. However, the Pielou evenness index revealed a significant difference and showed higher species evenness in cows compared to goats. Beta diversity measurements showed statistical dissimilarities and significant clustering of bacterial composition between goats and cows. Firmicutes were the dominant phylum in both goats and cows, followed by Bacteroidetes, Proteobacteria, and Spirochaetes. Linear discriminant analysis with effect size (LEfSe) showed a total of 36 significantly different taxa between goats and cows. Notably, the relative abundance of Ruminococcaceae UCG-005, Christensenellaceae R-7 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-009, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Ruminococcus 1, Ruminococcaceae UCG-002, Lachnospiraceae NK4A136 group, Treponema 2, Lachnospiraceae AC2044 group, and Bacillus was higher in goats compared to cows. In contrast, the relative abundance of Turicibacter, Solibacillus, Alloprevotella, Prevotellaceae UCG-001, Negativibacillus, Lachnospiraceae UCG-006, and Eubacterium hallii group was higher in cows compared with goats. Our results suggest that diet shapes the bacterial community in feces, but the host species has a significant impact on community structure, as reflected primarily in the relative abundance of certain taxa.

Microbial communities associated with mounds of the Orange-footed scrubfowl Megapodius reinwardt.

Megapodius reinwardt, the orange-footed scrubfowl, belongs to a small family of birds that inhabits the Indo-Australian region. Megapodes are unique in incubating their eggs in mounds using heat from microbial decomposition of organic materials and solar radiation. Little is known about the microorganisms involved in the decomposition of organic matter in mounds. To determine the source of microbes in the mounds, we used 16S and 18S rRNA gene sequencing to characterize the microbial communities of mound soil, adjacent soil and scrubfowl faeces. We found that the microbial communities of scrubfowl faeces were substantially different from those of the mounds and surrounding soils, suggesting that scrubfowls probably do not use their faeces to inoculate their mounds although a few microbial sequence variants were present in both faeces and mound samples. Further, the mound microbial community structure was significantly different to the adjacent soils. For example, mounds had a high relative abundance of sequence variants belonging to Thermomonosporaceae, a thermophilic soil bacteria family able to degrade cellulose from plant residues. It is not clear whether members of Thermomonosporaceae disproportionately contribute to the generation of heat in the mound, or whether they simply thrive in the warm mound environment created by the metabolic activity of the mound microbial community. The lack of clarity in the literature between designations of heat-producing (thermogenic) and heat-thriving (thermophilic) microbes poses a challenge to understanding the role of specific bacteria and fungi in incubation.

Depicting Fecal Microbiota Characteristic in Yak, Cattle, Yak-Cattle Hybrid and Tibetan Sheep in Different Eco-Regions of Qinghai-Tibetan Plateau.

ABSTRACTThe gut microbiota is closely associated with the health and production performance of livestock. Partial studies on ruminant microbiota are already in progress in the Qinghai-Tibetan Plateau Area (QTPA) in China, but large-scale and representative profiles for the QTPA are still lacking. Here, 16S rRNA sequencing was used to analyze 340 samples from yak, cattle, yak-cattle hybrids, and Tibetan sheep, which lived in a shared environment from 4 eco-regions of the QTPA during the same season, and aimed to investigate the fecal microbiota community composition, diversity, and potential function. All samples were clustered into 2 enterotypes, which were derived from the genera Ruminococcaceae UCG-005 and Acinetobacter, respectively. Environment, human activity, species, and parasitization all affected the fecal microbiota. By assessing the relationship between the fecal microbiota and the above variables, we identified a scattered pattern of fecal microbiota dissimilarity based more significantly on diet over other factors. Additionally, gastrointestinal nematode infection could reduce the capacity of the bacterial community for biosynthesis of other secondary metabolites, carbohydrate metabolism, and nucleotide metabolism. Ultimately, this study provided a fecal microbiota profile for ruminants living in 4 eco-regions of the QTPA and its potential future applications in developing animal husbandry regimes.IMPORTANCE Cattle, yak, and sheep reside as the main ruminants distributed throughout most regions of Qinghai-Tibetan Plateau Area (QTPA) in China. However, there is a lack of large-scale research in the QTPA on their fecal microbiota, which can regulate and reflect host health as an internalized “microbial organ.” Our study depicted the fecal microbiota community composition and diversity of yak, cattle, yak-cattle hybrids, and Tibetan sheep from 4 eco-regions of the QTPA. Additionally, our results demonstrated here that the ruminant samples could be clustered into 2 enterotypes and that diet outweighed other factors in shaping fecal microbiota in the QTPA. This study provided a basis for understanding the microbiota characteristic of ruminants and its possible applications for livestock production in the QTPA.

Effect of precision air supply cooling system with different cooling air speed on reproductive performance, stress status, immunoglobulin and fecal microbiota of lactating sows

This study investigated the precision air supply cooling system with different cooling air speed on reproductive performance, stress status, immunity and intestinal microbiota of sows. A total of 36 sows were randomly assigned into three groups: control group (CON, n = 12) without cooling system, low cooling air speed (2.24 ± 0.11 m/s) group (LCAS, n = 12) with precision air supply cooling system, high cooling air speed (3.33 ± 0.11 m/s) group (HCAS, n = 12) with precision air supply cooling system. The average daily ambient temperature and relative humidity in experimental farrowing rooms were 28 °C–32 °C and 65%–90%, respectively, during daytime (8:00–20:00). The reproductive performance, respiratory rate (RR), body surface temperature (BST), rectal temperature (RT) salivary parameters and fecal microbiota of lactating sows were measured. The results showed that compared with CON group, average daily feed intake of sows and average daily gain of piglets were increased (P < 0.05) in LCAS and HCAS groups. The RR, BST and RT were decreased (P < 0.05) in LCAS and HCAS groups in wk 1 before parturition and wk 2 after parturition. The salivary cortisol and alpha amylase level of LCAS and HCAS sows were decreased (P < 0.05) on d 14 after parturition, while the salivary immunoglobulin A and immunoglobulin G level of LCAS and HCAS sows were increased (P < 0.05) on d 7 after parturition. The LCAS and HCAS sows showed higher relative abundance of Clostridium_sensu_stricto_1 in feces, which was positively associated with immunoglobulin A (P < 0.01). In conclusion, both low and high cooling air speed improved reproductive performance, alleviated stress status, and enhanced salivary immunoglobulins and beneficial fecal microbiota community in lactating sows, which indicated that precision air supply cooling system could be an effective cooling strategy for lactating sows in high ambient temperature.

Exploration of the correlation between intestinal flora and peritoneal dialysis-related peritonitis.

Peritonitis is a serious complication of peritoneal dialysis (PD). Gut microbiota alterations occur in end-stage renal disease (ESRD) patients. The relationship between the gut microbiota and PD-related peritonitis (PRP) is still poorly understood. It is unclear whether the intestinal flora is involved in the pathogenesis of PRP. We collected fecal samples from PRP patients and normal group (NG) PD patients. 16S rRNA sequencing was used to analyze the gut microbiota of PRP and NG patients while also comparing the gram-positive peritonitis (GPP), Escherichia coli peritonitis (EP) and culture-negative peritonitis (CNP) groups in the subgroup analysis. The demographic data and clinical indicators of all patients were collected. Seventeen PRP patients and 28 NG patients were recruited for this study. The analysis of fecal community diversity with 16S rDNA sequencing showed an obvious change in the microbial structure of PRP patients, where Bacteroidetes and Synergistetes were upregulated at different levels, while Bacilli and Lactobacillus were downregulated at different levels compared to levels in the NG group. In the subgroup analysis, Saccharimonadaceae was significantly increased in the GPP group compared to the EP and CNP group. In addition, decreased gene function associated with metabolic pathways was observed in PRP patients. Bacteroidetes and Synergistetes were the dominant orders in PRP patients. The altered composition of the gut microbiota in PRP patients provided deeper insights into the pathogenesis of PRP, and these biomarkers might be established as potential therapeutic targets that deserve further exploration.

Effects of antibiotics consumption on the behavior of airborne antibiotic resistance genes in chicken farms

The antibiotics and antibiotic resistance genes (ARGs) have caused pollution of livestock farm environments. There are limited investigations about airborne ARGs and what role the antibiotics play remains largely unclear. The dynamics of various antibiotics were compared between feces samples from chicken fed a diet with and without antibiotics. In contrast to the farm with no antibiotics drugs, the hazard quotients (HQs) of OTC (24.8–205.4) and CTC (18.0–317.0) are particularly high in the farm with in-feed antibiotics drugs. The high ecological risks of antibiotics in chicken feces with in-feed antibiotic drugs were 100 % as determined. We quantified mobile genetic elements (MGEs) and ARGs and investigated bacterial communities in feces and air samples. The concentration of airborne ARG/MGE subtypes with in-feed antibiotic drugs is about two orders of magnitude higher than those without drugs. This study reveals that the indoor air of chicken farms is a reservoir of ARGs in the environment. Continuous feeding of antibiotics can change the intestinal microbial community structure of the chicken. The possibility of horizontal gene transfer of ARGs in air and feces samples might be increased by in-feed antibiotic drugs. The enrichment of ARGs in the chicken farm can be reduced by minimizing antibiotic use.

Enhancing Metabolic Efficiency through Optimizing Metabolizable Protein Profile in a Time Progressive Manner with Weaned Goats as a Model: Involvement of Gut Microbiota.

ABSTRACTFeeding a growing global population and lowering environmental pollution are the two biggest challenges facing ruminant livestock. Considering the significance of nitrogen metabolism in these challenges, a dietary intervention regarding metabolizable protein profiles with different rumen-undegradable protein (RUP) ratios (high RUP [HRUP] versus low RUP [LRUP]) was conducted in young ruminants with weaned goats as a model. Fecal samples were collected longitudinally for nine consecutive weeks to dissect the timing and duration of intervention, as well as its mechanism of action involving the gut microbiota. Results showed that at least 6 weeks of intervention were needed to distinguish the beneficial effects of HRUP, and HRUP intervention improved the metabolic efficiency of goats as evidenced by enhanced growth performance and nutrient-apparent digestibility at week 6 and week 8 after weaning. Integrated analysis of bacterial diversity, metabolites, and inferred function indicated that HRUP intervention promoted Eubacterium abundance, several pathways related to bacterial chemotaxis pathway, ABC transporters, and butanoate metabolism and thereafter elicited a shift from acetate production toward butyrate and branched-chain amino acid (BCAA) production. Meanwhile, three distinct phases of microbial progression were noted irrespective of dietary treatments, including the enrichment of fiber-degrading Ruminococcus, the enhancement of microbial cell motility, and the shift of fermentation type as weaned goats aged. The current report provides novel insights into early-life diet-microbiota axis triggered by metabolic protein intervention and puts high emphasis on the time window and duration of dietary intervention in modulating lifelong performance of ruminants.IMPORTANCE Precise dietary intervention in early-life gastrointestinal microbiota has significant implications in the long-life productivity and health of young ruminants, as well as in lowering their environmental footprint. Here, using weaned goats as a model, we report that animals adapted to high rumen-undegradable protein diet in a dynamic manner by enriching fecal community that could effectively move toward and scavenge nutrients such as glucose and amino acids and, thereafter, elicit butyrate and BCAA production. Meanwhile, the three dynamic assembly trajectories in fecal microbiota highlight the importance of taking microbiota dynamics into account. Our findings systematically reported when, which, and how the fecal microbiome responded to metabolizable protein profile intervention in young ruminants and laid a foundation for improving the productivity and health of livestock due to the host-microbiota interplay.

Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutrition.

Disrupted development of the gut microbiota is a contributing cause of childhood malnutrition. Bifidobacterium longum subspecies infantis is a prominent early colonizer of the infant gut that consumes human milk oligosaccharides (HMOs). We found that the absolute abundance of Bifidobacterium infantis is lower in 3- to 24-month-old Bangladeshi infants with severe acute malnutrition (SAM) compared to their healthy age-matched counterparts. A single-blind, placebo-controlled trial (SYNERGIE) was conducted in 2- to 6-month-old Bangladeshi infants with SAM. A commercial U.S. donor-derived B. infantis strain (EVC001) was administered daily with or without the HMO lacto-N-neotetraose for 28 days. This intervention increased fecal B. infantis abundance in infants with SAM, although to levels still 10- to 100-fold lower than in untreated healthy controls. EVC001 treatment promoted weight gain that was associated with reduced intestinal inflammation markers in infants with SAM. We cultured fecal B. infantis strains from Bangladeshi infants and colonized gnotobiotic mice with these cultured strains. The gnotobiotic mice were fed a diet representative of that consumed by 6-month-old Bangladeshi infants, with or without HMO supplementation. One B. infantis strain, Bg_2D9, expressing two gene clusters involved in uptake and utilization of N-glycans and plant-derived polysaccharides, exhibited superior fitness over EVC001. The fitness advantage of Bg_2D9 was confirmed in a gnotobiotic mouse model of mother-to-infant gut microbiota transmission where dams received a pretreatment fecal community from a SAM infant in the SYNERGIE trial. Whether Bg_2D9 is superior to EVC001 for treating malnourished infants who consume a diet with limited breastmilk requires further clinical testing.

181 Evaluation of the Fecal Microbiota in Commercial Sows with Variable Risk for Pelvic Organ Prolapse During Late Gestation

Abstract Sow mortality has increased during the last decade with a large portion due to pelvic organ prolapse (POP) manifesting during late gestation and early lactation. Approximately 21% of sow mortality is attributed to POP, creating a significant economic and animal welfare concern. The study objective was to identify differences in sow fecal microbiota associated with POP risk and to determine if fecal and vaginal microbial communities are correlated. Using an established perineal scoring (PS) system, 2,864 sows were assigned PS1 (low), PS2 (moderate), or PS3 (high) based on phenotypic observations and presumed POP risk during gestation week 15. Of those sows scored, 1.0%, 2.7%, and 23.4% of PS1, PS2, and PS3 assigned sows, respectively, subsequently experienced POP. At the time of scoring, fecal swabs were collected from sows (n = 213) and DNA was extracted for 16S rRNA gene Illumina MiSeq sequencing, and analyzed using mothur, phyloseq and SAS. Additionally, co-occurrence networks were constructed between fecal and vaginal microbial communities using CoNet (V1.1.1), to identify correlations in taxa abundance. Differences in fecal community composition (PERMANOVA; P &amp;lt; 0.05), structure (alpha diversity measurements; P &amp;lt; 0.05), and 13 individual operational taxonomic units (OTU; Q &amp;lt; 0.05) were detected between PS1 and PS3 sows. The abundance of several taxa were correlated across sample collection sites, suggesting the fecal and vaginal microbial communities may influence one another. Collectively, fewer differences exist in fecal microbiota in sows differing risk for POP than previously observed in vaginal microbiota, suggesting the vaginal microbial communities may be a better indicator of POP risk. Understanding correlations between the fecal and vaginal microbial communities may provide strategies or targets for combatting POP. This project was supported by the National Pork Board and the Foundation for Food and Agriculture Research.

Fungal communities in feces of the frugivorous bat Ectophylla alba and its highly specialized Ficus colubrinae diet

BackgroundBats are important long-distance dispersers of many tropical plants, yet, by consuming fruits, they may disperse not only the plant’s seeds, but also the mycobiota within those fruits. We characterized the culture-dependent and independent fungal communities in fruits of Ficus colubrinae and feces of Ectophylla alba to determine if passage through the digestive tract of bats affected the total mycobiota.ResultsUsing presence/absence and normalized abundance data from fruits and feces, we demonstrate that the fungal communities were significantly different, even though there was an overlap of ca. 38% of Amplicon Sequence Variants (ASVs). We show that some of the fungi from fruits were also present and grew from fecal samples. Fecal fungal communities were dominated by Agaricomycetes, followed by Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Malasseziomycetes, while fruit samples were dominated by Dothideomycetes, followed by Sordariomycetes, Agaricomycetes, Eurotiomycetes, and Laboulbeniomycetes. Linear discriminant analyses (LDA) show that, for bat feces, the indicator taxa include Basidiomycota (i.e., Agaricomycetes: Polyporales and Agaricales), and the ascomycetous class Eurotiomycetes (i.e., Eurotiales, Aspergillaceae). For fruits, indicator taxa are in the Ascomycota (i.e., Dothideomycetes: Botryosphaeriales; Laboulbeniomycetes: Pyxidiophorales; and Sordariomycetes: Glomerellales). In our study, the differences in fungal species composition between the two communities (fruits vs. feces) reflected on the changes in the functional diversity. For example, the core community in bat feces is constituted by saprobes and animal commensals, while that of fruits is composed mostly of phytopathogens and arthropod-associated fungi.ConclusionsOur study provides the groundwork to continue disentangling the direct and indirect symbiotic relationships in an ecological network that has not received enough attention: fungi-plants-bats. Findings also suggest that the role of frugivores in plant-animal mutualistic networks may extend beyond seed dispersal: they may also promote the dispersal of potentially beneficial microbial symbionts while, for example, hindering those that can cause plant disease.

Short-Chain Fatty Acids Modulate Healthy Gut Microbiota Composition and Functional Potential

Many studies have focused on the metabolic capacity of human gut microbiota to produce short-chain fatty acids and subsequent effects on host physiology. Given scarce data on how SCFAs produced by gut bacteria participate in cross-feeding to influence community structure and function, we evaluated the potential of SCFAs to modulate human gut microbiota in vitro. We employed anaerobic fecal cultivation in chemically defined medium supplemented with one of nine SCFAs to determine effects on both gut microbial community structure via 16S rRNA sequencing and function via genome reconstruction analysis. Each SCFA displayed significant and unique modulatory potential with respect to the relative abundance of bacterial taxa. Analysis of SCFA-supplemented communities revealed that alterations of individual closely related phylotypes displayed coherent changes, although exceptions were also observed which suggest strain-dependent differences in SCFA-induced changes. We used genome reconstruction to evaluate the functional implications of SCFA-mediated restructuring of fecal communities. We note that some SCFA-supplemented cultures displayed a reduction in the predicted abundance of SCFA producers, which suggests a possible undefined negative feedback mechanism. We conclude that SCFAs are not simply end-products of metabolism but also serve to modulate the gut microbiota through cross-feeding that alters the fitness of specified taxa. These results are important in the identification of prebiotics that elevate specific SCFAs for therapeutic benefit and highlight SCFA consumers as a salient part of the overall metabolic flux pertaining to bacterial fermentative processes.

Impact of wheat aleurone on biomarkers of cardiovascular disease, gut microbiota and metabolites in adults with high body mass index: a double-blind, placebo-controlled, randomized clinical trial

PurposeAleurone is a cereal bran fraction containing a variety of beneficial nutrients including polyphenols, fibers, minerals and vitamins. Animal and human studies support the beneficial role of aleurone consumption in reducing cardiovascular disease (CVD) risk. Gut microbiota fiber fermentation, polyphenol metabolism and betaine/choline metabolism may in part contribute to the physiological effects of aleurone. As primary objective, this study evaluated whether wheat aleurone supplemented foods could modify plasma homocysteine. Secondary objectives included changes in CVD biomarkers, fecal microbiota composition and plasma/urine metabolite profiles.MethodsA parallel double-blind, placebo-controlled and randomized trial was carried out in two groups of obese/overweight subjects, matched for age, BMI and gender, consuming foods supplemented with either aleurone (27 g/day) (AL, n = 34) or cellulose (placebo treatment, PL, n = 33) for 4 weeks.ResultsNo significant changes in plasma homocysteine or other clinical markers were observed with either treatment. Dietary fiber intake increased after AL and PL, animal protein intake increased after PL treatment. We observed a significant increase in fecal Bifidobacterium spp with AL and Lactobacillus spp with both AL and PL, but overall fecal microbiota community structure changed little according to 16S rRNA metataxonomics. Metabolomics implicated microbial metabolism of aleurone polyphenols and revealed distinctive biomarkers of AL treatment, including alkylresorcinol, cinnamic, benzoic and ferulic acids, folic acid, fatty acids, benzoxazinoid and roasted aroma related metabolites. Correlation analysis highlighted bacterial genera potentially linked to urinary compounds derived from aleurone metabolism and clinical parameters.ConclusionsAleurone has potential to modulate the gut microbial metabolic output and increase fecal bifidobacterial abundance. However, in this study, aleurone did not impact on plasma homocysteine or other CVD biomarkers.Trial RegistrationThe study was registered at ClinicalTrials.gov (NCT02067026) on the 17th February 2014.