Fecal Communities Research Articles

Fecal pollution mediates the dominance of stochastic assembly of antibiotic resistome in an urban lagoon (Yundang lagoon), China

Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P < 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.

Effect of Lactobacillus plantarum-fermented mulberry pomace on antioxidant properties and fecal microbial community

Rich in phenolic compounds and dietary fibers, mulberry pomace is a potential material for gut health. This study investigated the effect of the probiotic Lactobacillus plantarum on mulberry pomace. The antioxidant activity as well as the changes of fecal microbiota and short-chain fatty acids (SCFAs) were determined using chemical models, quantitative polymerase chain reaction (qPCR) and gas chromatography, respectively. Furthermore, the phenolic compounds were characterized by UPLC-MS. The results showed that the antioxidant activity was significantly improved in fermented mulberry pomace (FMP) samples. The fecal microbiota community was modulated by FMP through improving beneficial bacteria (Lactobacillus, Bifidobacterium, Ruminococcus, butyrate-producing bacteria and Akkermansia) and inhibiting pathogenic bacteria (Escherichia coli and Enterococcus). Moreover, FMP showed an increase in the production of SCFAs and lactic acid. The study identified that the corresponding glycosides of cyanidin and quercetin were released during Lactobacillus plantarum fermentation. A total of eighteen phenolic compounds were detected in samples and three compounds (p-hydroxybenzoic acid, catechin and gallocatechin) were only detected in FMP samples. The changes in phenolic compounds might explain the gut-improving functions. This study provided a suggestion that Lactobacillus plantarum fermentation was a potential way to utilize mulberry pomaces as a functional food.

Sex-based differences in fecal short-chain fatty acid and gut microbiota in irritable bowel syndrome patients.

ObjectiveTo explore alterations in fecal short‐chain fatty acids (SCFA) and gut microbiota in patients with diarrhea‐predominant irritable bowel disease (IBS‐D) and their relationships with clinical manifestations.MethodsWe recruited 162 patients with IBS‐D and 66 healthy controls (HC). Their manifestations and psychological status were evaluated using the IBS severity scoring system and the Hospital Anxiety and Depression Scale (HADS). Colorectal visceral sensitivity was evaluated using a barostat. Systemic inflammation was evaluated using plasma cytokine levels. Fecal SCFA were quantified using ultra‐performance liquid chromatography‐tandem mass spectrometry, and fecal microbiota communities were analyzed using 16S rRNA sequencing.ResultsMore men presented with IBS‐D than women in our patient cohort. Patients with IBS‐D had more severe manifestations, higher HADS score, and a higher rate of previous infectious enteritis than HC. Notably, female patients had significantly higher HADS scores than male patients. Male patients had significantly higher levels of plasma interleukin (IL)‐12, fecal propionate and colorectal visceral sensitivity than male HC, while no differences were observed between female patients and female HC. Fecal acetate, butyrate and valerate correlated with the initial visceral sensory threshold, stressors, and IL‐10 and IL‐12 levels. The propionate‐producing Prevotella 9 genus was significantly increased in male patients and positively correlated with fecal propionate.ConclusionDistinct sex‐based differences in clinical manifestations, fecal SCFA and microbiota richness are found in Chinese patients with IBS‐D, which may be used to diagnose dysbiosis in these patients.

23 Forced exercise on gut microbiota and cytokines in young horses

Exercise in young horses is common but impacts on gut microbial profiles and systemic cytokines are unknown. Quarter Horse yearlings (mean ± SEM; 496 ± 12 d of age; 343 ± 28 kg BW) were used to test the hypothesis that exercise would increase beneficial gut microbial profiles and decrease serum inflammatory cytokines. Horses were balanced by age, BW, and sex and randomly assigned to non-exercise control (CON; n = 10), dry treadmill exercise (DRY; n = 10), or aquatic treadmill exercise (H2O; n = 10; water at 60% wither height). Horses were stalled 12 h/d, 5 d/wk but otherwise housed in dry lots. Horses individually received 1.25% BW/d (as-fed) commercial concentrate and ad libitum Coastal bermudagrass hay. From d0 to 112, DRY and H2O walked on treadmills 30 min/d, 5 d/wk. Workload for DRY and H2O then increased to moderate intensity on a free-stall exerciser 5 d/wk to d140. Serum and fecal samples were collected on d0, 112, and 140. Serum was analyzed for interleukin (IL)-8, IL-10, IL-12, IL-13, growth related oncogene (GRO), and tumor necrosis factor α (TNFα) concentrations via commercial bead-based ELISA. The V4 region of 16S rRNA gene was amplified from fecal community DNA using universal primers. Resulting amplicons were sequenced (2 × 250bp PE) using Illumina's NovaSeq 6000, processed using DADA2 pipeline, and analyzed using R vegan package. Significant ( P < 0.05) differences between means were determined using linear models with repeated measures, main effects of time, treatment (trt), and trt × time, and a random effect of horse(trt). Microbiome richness was greater in exercised yearlings than CON ( P < 0.02). There was a trt × time interaction for richness ( P < 0.0001); CON decreased to d112 ( P = 0.003) but increased to d140 ( P = 0.01), H2O increased to d112 ( P < 0.0001) and decreased to d140 ( P < 0.0001), while DRY increased to d140 ( P = 0.0003). Microbiome diversity increased in all horses by d112 ( P < 0.0001) and tended to decrease to d140 ( P = 0.09) but was higher than d0 on 140 ( P < 0.0001). A trend for a trt × time interaction ( P = 0.06) indicated H2O horses had greater diversity on d112 than other groups ( P ≤ 0.01). Anti-inflammatory IL-10 declined ( P < 0.0001) from d0 to 140. In contrast, pro-inflammatory GRO, TNFα, and IL-8 increased from d0 to 112 ( P ≤ 0.008). From d112, GRO plateaued to d140 to remain greater than d0 at 140 ( P = 0.01), TNFα did not differ between d0 and 140, and IL-8 decreased to d140 ( P = 0.02). Cytokines did not differ by trt. Exercise improved microbial richness but did not impact microbial diversity or systemic cytokines. Future research should explore the effects of more intense exercise, diet, and environment on gut health and systemic cytokines in young horses.

Microbial community structure and composition is associated with host species and sex in Sigmodon cotton rats

BackgroundThe cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has not been explored in this model, partly due to the lack of a comprehensive characterization of microbial communities across different cotton rat species. Understanding the dynamics of their microbiome could significantly help to better understand its role when modeling viral infections in this animal model.ResultsWe examined the bacterial communities of the gut and three external sites (skin, ear, and nose) of two inbred species of cotton rats commonly used in research (S. hispidus and S. fulviventer) by using 16S rRNA gene sequencing, constituting the first comprehensive characterization of the cotton rat microbiome. We showed that S. fulviventer maintained higher alpha diversity and richness than S. hispidus at external sites (skin, ear, nose), but there were no differentially abundant genera. However, S. fulviventer and S. hispidus had distinct fecal microbiomes composed of several significantly differentially abundant genera. Whole metagenomic shotgun sequencing of fecal samples identified species-level differences between S. hispidus and S. fulviventer, as well as different metabolic pathway functions as a result of differential host microbiome contributions. Furthermore, the microbiome composition of the external sites showed significant sex-based differences while fecal communities were not largely different.ConclusionsOur study shows that host genetic background potentially exerts homeostatic pressures, resulting in distinct microbiomes for two different inbred cotton rat species. Because of the numerous studies that have uncovered strong relationships between host microbiome, viral infection outcomes, and immune responses, our findings represent a strong contribution for understanding the impact of different microbial communities on viral pathogenesis. Furthermore, we provide novel cotton rat microbiome data as a springboard to uncover the full therapeutic potential of the microbiome against viral infections.

Feeding dairy cows bakery by-products enhanced nutrient digestibility, but affected fecal microbial composition and pH in a dose-dependent manner

We reported recently that adding bakery by-products (BP) to the diets of dairy cows up to 30% improved performance and rumen pH, but caused major shifts in the nutrient profile and availability, likely modifying nutrient degradation patterns throughout the gastrointestinal tract. The aim of this study was to investigate the effects of the gradual replacement of cereals by BP on the apparent total-tract digestibility (ATTD), the fermentation patterns, and the microbial community in feces of dairy cows. Twenty-four mid-lactating Simmental cows (149 ± 22.3 days in milk, 756 ± 89.6 kg of initial body weight) were fed a total mixed ration ad libitum (fresh feed was offered twice per day) containing a 50:50 ratio of forage to concentrate (dry matter basis) throughout the experiment. The trial lasted 5 wk, whereby the first week was used for baseline measurements, in which all cows received the same diet, without BP. Cows were then randomly allocated into 3 groups differing in the BP content of diets (0% BP, 15% BP, and 30% BP on a DM basis) and fed for 4 wk. Fecal samples were taken for analysis of pH, volatile fatty acids (VFA), and 16S rRNA gene sequencing. The inclusion of BP resulted in an increase of ether extract and sugars, and a reduction of starch and neutral detergent fiber in the diet. Feeding BP linearly increased the ATTD of almost all nutrients resulting in up to 2 kg more digestible organic matter intake (DOMI). Increasing BP level up to 30% increased fecal total VFA concentration and decreased the pH. The proportion of butyrate in feces increased linearly, but the proportion of all other VFA was not affected by BP-feeding. The richness and diversity indices of the fecal microbiota linearly declined by the inclusion of BP. The cellulolytic phyla Fibrobacteres decreased, whereas amylolytic phyla, such as Proteobacteria, increased. Overall, results showed that feeding BP linearly increased ATTD and DOMI, but impaired fecal microbial diversity and pH. In the interest of the optimization of BP inclusion in the dairy cows' feeding, a dietary level between 15 to 30% of BP might be a better compromise than 30% in terms of an enhanced DOMI and performance with still lowered risk of hindgut dysbiosis, but this will require further investigations.

Faecal microbiota and antibiotic resistance genes in migratory waterbirds with contrasting habitat use

Migratory birds may have a vital role in the spread of antimicrobial resistance across habitats and regions, but empirical data remain scarce. We investigated differences in the gut microbiome composition and the abundance of antibiotic resistance genes (ARGs) in faeces from four migratory waterbirds wintering in South-West Spain that differ in their habitat use. The white stork Ciconia ciconia and lesser black-backed gull Larus fuscus are omnivorous and opportunistic birds that use highly anthropogenic habitats such as landfills and urban areas. The greylag goose Anser anser and common crane Grus grus are herbivores and use more natural habitats. Fresh faeces from 15 individuals of each species were analysed to assess the composition of bacterial communities using 16S rRNA amplicon-targeted sequencing, and to quantify the abundance of the Class I integron integrase gene (intI1) as well as genes encoding resistance to sulfonamides (sul1), beta-lactams (blaTEM, blaKPC and blaNDM), tetracyclines (tetW), fluoroquinolones (qnrS), and colistin (mcr-1) using qPCR. Bacterial communities in gull faeces were the richest and most diverse. Beta diversity analysis showed segregation in faecal communities between bird species, but those from storks and gulls were the most similar, these being the species that regularly feed in landfills. Potential bacterial pathogens identified in faeces differed significantly between bird species, with higher relative abundance in gulls. Faeces from birds that feed in landfills (stork and gull) contained a significantly higher abundance of ARGs (sul1, blaTEM, and tetW). Genes conferring resistance to last resort antibiotics such as carbapenems (blaKPC) and colistin (mcr-1) were only observed in faeces from gulls. These results show that these bird species are reservoirs of antimicrobial resistant bacteria and suggest that waterbirds may disseminate antibiotic resistance across environments (e.g., from landfills to ricefields or water supplies), and thus constitute a risk for their further spread to wildlife and humans.

Dynamics of bacterial communities in vaginas and feces between pre and postpartum of dairy cows

The reproductive tracts have an intimate relationship with reproduction because there are bacterial communities that can affect reproductive health. The differences in the bacterial community of periparturient dairy cows were investigated. Vaginal and fecal samples were collected seven days before and after calving, and DNA was extracted to sequence the V3-V4 regions of the 16S rRNA genes. In the postpartum vaginas, operational taxonomic units, Chao1, Shannon, and Simpson were decreased, and phyla Fusobacteria and Bacteroidetes were increased. In summary, bacterial abundance can affect the periparturient biological differences in dairy cows, suggesting a susceptibility to infection within one week after calving. Keywords: vagina, feces, microbiota, prepartum, postpartum

A postbiotic consisting of heat-treated lactobacilli has a bifidogenic effect in pure culture and in human fermented faecal communities.

The gut microbiota has a significant impact on host health. Dietary interventions using probiotics, prebiotics and postbiotics have the potential to alter microbiota composition and function. Other therapeutic interventions such as antibiotics and faecal microbiota transplantation have also been shown to significantly alter the microbiota and its metabolites. Supplementation of a faecal fermentation model of the human gut with a postbiotic product Lactobacillus LB led to changes in microbiome composition (i.e. increase in beneficial bifidobacteria) and associated metabolic changes (i.e. increased acid production). Lactobacillus LB is a heat-treated preparation of cellular biomass and a fermentate generated by Limosilactobacillus fermentum CNCM MA65/4E-1b (formerly known as Lactobacillus fermentum CNCM MA65/4E-1b) and Lactobacillus delbrueckii ssp. delbrueckii CNCM MA65/4E-2z, medically relevant strains used to produce antidiarrheal preparations. In pure culture, Lactobacillus LB also stimulates the growth of a range of bifidobacterial species and strains. Lactobacillus LB-like preparations generated using other Lactobacillaceae, including commercially available probiotic bacteria, did not have the same impact on a model strain (Bifidobacterium longum subsp. infantis ATCC 15697). This bifidogenic activity is heat- and enzyme-stable and cannot be attributed to lactose, which is a major constituent of Lactobacillus LB. L fermentum CNCM MA65/4E-1b is largely responsible for the observed activity and there is a clear role for compounds smaller than 1 kDa.Importance In general, disruptions to the gut microbiota are associated with multiple disorders in humans. The presence of high levels of Bifidobacterium spp. in the human gut is commonly considered to be beneficial. Bifidobacteria can be supplemented in the diet (as probiotics) or those bifidobacteria already present in the gut can be stimulated by the consumption of prebiotics such as inulin. We demonstrate that Lactobacillus LB (a product consisting of two heat-killed lactic acid bacteria and their metabolites) can stimulate the growth of bifidobacteria in human fermented faecal communities and in pure culture. Given the heat-treatment applied during the production process, there is no risk of the lactic acid bacteria colonising (or causing bacteraemia) in vulnerable consumers (infants, immunocompromised, etc). Lactobacillus LB has the potential to affect human health by selectively promoting the growth of beneficial bacteria.

Altered Gut Microbiota Related to Inflammatory Responses in Patients With Huntington's Disease.

Emerging evidence indicates that gut dysbiosis may play a regulatory role in the onset and progression of Huntington’s disease (HD). However, any alterations in the fecal microbiome of HD patients and its relation to the host cytokine response remain unknown. The present study investigated alterations and host cytokine responses in patients with HD. We enrolled 33 HD patients and 33 sex- and age- matched healthy controls. Fecal microbiota communities were determined through 16S ribosomal DNA gene sequencing, from which we analyzed fecal microbial richness, evenness, structure, and differential abundance of individual taxa between HD patients and healthy controls. HD patients were evaluated for their clinical characteristics, and the relationships of fecal microbiota with these clinical characteristics were analyzed. Plasma concentrations of interferon gamma (IFN-γ), interleukin 1 beta (IL-1β), IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-13, and tumor necrosis factor alpha were measured by Meso Scale Discovery (MSD) assays, and relationships between microbiota and cytokine levels were analyzed in the HD group. HD patients showed increased α-diversity (richness), β-diversity (structure), and altered relative abundances of several taxa compared to those in healthy controls. HD-associated clinical characteristics correlated with the abundances of components of fecal microbiota at the genus level. Genus Intestinimonas was correlated with total functional capacity scores and IL-4 levels. Our present study also revealed that genus Bilophila were negatively correlated with proinflammatory IL-6 levels. Taken together, our present study represents the first to demonstrate alterations in fecal microbiota and inflammatory cytokine responses in HD patients. Further elucidation of interactions between microbial and host immune responses may help to better understand the pathogenesis of HD.

Rubidium chloride modulated the fecal microbiota community in mice

BackgroundThe microbiota plays an important role in host health. Although rubidium (Rb) has been used to study its effects on depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated for their characteristics and bacterial microbiome changes.ResultsThe 16S ribosomal RNA gene sequencing of fecal microbiota showed that RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio, but significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. With regarding to the archaea, we only observed two less richness archaea Sulfolobus and Acidiplasma at the genus level.ConclusionsChanges of fecal microbes may in part contribute to the anticancer or anti-depressant effects of RbCl. These findings further validate that the microbiome could be a target for therapeutic intervention.

Viral communities associated with porcine diarrhoeal disease and genetic characterization of a bufavirus in Tibetan pigs in China

To investigate the viral communities in diarrhoeal faeces of Tibetan pigs, 146 diarrhoeic samples were collected from 16 pigs farms on the Tibetan plateau. Nineteen viruses belonging to eleven viral taxonomic families were identified in a pooled library. Metagenomics analysis revealed that the viruses were mainly small linear and circular DNA viruses. Furthermore, sequences of 10 NS1 genes and two complete genomes of PBuVs were obtained by PCR amplification. Sequence comparisons and phylogenetic analysis showed that the PBuVs from Tibetan pigs displayed more abundant genetic diversity than those from domestic pigs. This is the first description of the faecal viral community in Tibetan pigs associated with diarrhoea.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00705-020-04932-9.

Comparison of the Gut Microbiota in Patients with Benign and Malignant Breast Tumors: A Pilot Study.

The microbiome plays diverse roles in many diseases and can potentially contribute to cancer development. Breast cancer is the most commonly diagnosed cancer in women worldwide. Thus, we investigated whether the gut microbiota differs between patients with breast carcinoma and those with benign tumors. The DNA of the fecal microbiota community was detected by Illumina sequencing and the taxonomy of 16S rRNA genes. The α-diversity and β-diversity analyses were used to determine richness and evenness of the gut microbiota. Gene function prediction of the microbiota in patients with benign and malignant carcinoma was performed using PICRUSt. There was no significant difference in the α-diversity between patients with benign and malignant tumors (P = 3.15e−1 for the Chao index and P = 3.1e−1 for the ACE index). The microbiota composition was different between the 2 groups, although no statistical difference was observed in β-diversity. Of the 31 different genera compared between the 2 groups, level of only Citrobacter was significantly higher in the malignant tumor group than that in benign tumor group. The metabolic pathways of the gut microbiome in the malignant tumor group were significantly different from those in benign tumor group. Furthermore, the study establishes the distinct richness of the gut microbiome in patients with breast cancer with different clinicopathological factors, including ER, PR, Ki-67 level, Her2 status, and tumor grade. These findings suggest that the gut microbiome may be useful for the diagnosis and treatment of malignant breast carcinoma.

Dihydroquercetin supplement alleviates colonic inflammation potentially through improved gut microbiota community in mice.

The purpose of the current study was to investigate the effect of dietary dihydroquercetin (DHQ) supplementation on dextran sodium sulfate (DSS)-induced colitis in mice. Mice were given DHQ supplementation (3 g kg-1) throughout the study, starting 14 days prior to DSS treatment for 1 week followed by 2 days without DSS. The results showed that dietary DHQ supplementation restored DSS-induced disease activity index (DAI), colon length and histopathology scores of the colon tissue. Additionally, supplementation with DHQ reduced the pro-inflammatory cytokine levels, and enhanced the level of IL-10 in the serum. qPCR results indicated that DHQ supplementation significantly downregulated IL-1β, IL-6, and TNF-α, and upregulated IL-10 gene mRNA expression. Western blot results proved that DHQ supplementation upregulated ZO-1 and occludin levels. Using amplicon sequencing technology, 16S rRNA sequencing results showed that DHQ supplementation increased the fecal Firmicutes/Bacteroidetes ratio and the relative abundance of Lactobacillus and Dubosiella, and decreased the relative abundance of Bacteroidetes. Additionally, DHQ supplementation restored the decreased fecal acetic acid and butyric acid concentrations in DSS-induced colitis mice. Besides, Spearman's correlation analysis showed that Dubosiella was positively correlated with the butyric acid level and Bacteroidetes was positively correlated with the mRNA expression of IL-1β and IL-6. Both Lactobacillus and Dubosiella showed a negative correlation with the mRNA expression of IL-1β, IL-6, and TNF-α, and Dubosiella was positively correlated with IL-10. In summary, it was found that DHQ supplementation alleviated DSS-induced colitis which may be potentially associated with altered fecal microbiota communities in mice.

Impact of healthy aging on active bacterial assemblages throughout the gastrointestinal tract

ABSTRACT The adaption of gut microbiota (GM) throughout human life is a key factor in maintaining health. Interventions to restore a healthy GM composition may have the potential to improve health and disease outcomes in the elderly. We performed a comprehensive characterization of changes in the luminal and mucosa-associated microbiota composition in elderly compared with younger healthy individuals. Samples from saliva and feces, and biopsies from the upper and lower gastrointestinal tract (UGIT, LGIT), were collected from 59 asymptomatic individuals grouped by age: 40–55, 56–70, and 71–85 years). All underwent anthropometric, geriatric, and nutritional assessment. RNA was extracted and reverse-transcribed into complementary DNA; the V1–V2 regions of 16S ribosomal RNA genes were amplified and sequenced. Abundances of the taxa in all taxonomic ranks in each sample type were used to construct sample-similarity matrices by the Bray–Curtis algorithm. Significant differences between defined groups were assessed by analysis of similarity. The bacterial community showed strong interindividual variations and a clear distinction between samples from UGIT, LGIT, and feces. While in saliva some taxa were affected by aging, this number was considerably greater in UGIT and was subsequently higher in LGIT. Unexpectedly, aging scarcely influenced the bacterial community of feces over the age range of 40–85 years. The development of interventions to preserve and restore human health with increased age by establishing a healthy gut microbiome should not rely solely on data from fecal analysis, as the intestinal mucosa is affected by more significant changes, which differ from those observed in fecal analyses.

Profiling the Gastrointestinal Microbiota.

In this chapter, we provide a methodological description of the process to perform gastrointestinal (GIT) microbiota profiling on human stool samples. The process includes: (i) collection of feces, (ii) isolation of DNA from fecal community bacteria, (iii) selection of both 16S rDNA sequencing target and next-generation sequencing platform, and (iv) analysis and interpretation of sequence data. The process culminates into a comprehensive report on the GIT microbiota composition and structure that may translate into clinically actionable results.

1208. Development of a Novel Synthetic Glycan to Prevent Bacterial Infections and Ameliorate Respiratory Viral Infections

BackgroundThe prevention and treatment of bacterial infections is a human health challenge. A disadvantage of antibiotics is that they often kill beneficial commensal, bacteria in addition to, pathogenic bacteria. Indiscriminate killing disrupts the homeostasis between commensal bacteria and the host gut epithelium allowing colonization of the gut by pathogenic bacteria and increases susceptibility to infections. This research was done to develop a non-antibiotic modality to prevent bacterial infections by growing, rather than killing, commensal bacteria in the gut. Gut commensal bacteria grown on carbohydrates produce short-chain fatty acids (SCFAs) that support gut homeostasis maintenance and promote resistance to bacterial colonization. SCFAs have direct and indirect effects on the gut and lung mucosal immune system. They have also been linked to respiratory viral infection reduction and shown to influence macrophage function to mitigate pro-inflammatory neutrophil-mediated tissue damage.MethodsA library of over 1,500 synthetic proprietary glycans, termed Microbiome Metabolic Therapies (MMT™), was synthesized using different chemical and enzymatic approaches. An ex vivo platform using fecal bacterial communities from human subjects was devised to screen MMTs for their abilities to deplete pathogenic bacteria, and modulate multiple aspects of bacterial metabolism.ResultsKB109 was identified based on its ability to reduce the relative abundance of a diversity of pathogens including clinically relevant Gram-negative and Gram-positive bacteria in human fecal communities. KB109 also increased the relative abundance of prevalent commensal bacteria. Monoculture experiments demonstrated that KB109 promotes the growth of commensal bacteria, but not pathogens. Ex vivo screening revealed that KB109 consistently increased SFCA production across multiple fecal communities.ConclusionKB109 represents an appealing activity profile and offers an opportunity to prevent enteric and systemic bacterial infections by promoting gut homeostasis and colonization resistance, and ameliorating respiratory viral infections by stimulating immune homeostasis. KB109 is under evaluation in two COVID-19 clinical studies.DisclosuresJeffrey Meisner, PhD, Kaleido Biosciences (Employee, Shareholder) Jackson Lee, PhD, Kaleido Biosciences (Employee, Shareholder) Jonathan Lawrence, PhD, Kaleido Biosciences (Employee, Shareholder) Megan Roed, BA, Kaleido Biosciences (Employee, Shareholder) Johan van Hylckama Vlieg, PhD, Kaleido Biosciences (Employee, Shareholder)

Pollution characteristics of livestock faeces and the key driver of the spread of antibiotic resistance genes

The increasing prevalence of antibiotic resistance genes (ARGs) in livestock and poultry faeces has attracted considerable amounts of attention. However, in the actual breeding environment, the key driver of the spread of ARGs and which bacteria are involved remain unclear. This study investigated 19 antibiotics and 4 heavy metals in 147 animal faeces. The results showed that piglet faeces exhibited the highest levels of antibiotics and heavy metals. Twelve ARGs, 4 mobile genetic elements (MGEs) and bacterial communities of piglet faeces from 6 pig farms were further assessed to determine the key driver and relevant mechanism of the spread of ARGs. Sulphonamides (SAs) explained 36.5% of the variance (P < 0.05) of the bacterial community and were significantly related to 8 genes (P < 0.01), indicating that SAs dominated the spread of ARGs and should be tightly supervised. Structural equation modelling (SEM) indicated that SAs increased the abundance of ARGs via two pathways: horizontal transfer of ARGs (involving 10 genera) and vertical transfer of ARGs (involving 26 genera). These results improve our understanding of the potential hosts involved in the spread of ARGs, suggesting that monitoring of the above potential hosts is also important in animal feeding practice.

The Composition and Concordance of Lactobacillus Populations of Infant Gut and the Corresponding Breast-Milk and Maternal Gut.

The maternal gut is the principal source of commensal bacteria in the infant gut during the lactation stage, where breast milk acts as an intermediary for the transfer of potential probiotic bacteria consortia, including Lactobacillus. This study aimed to characterize the bacterial communities in human milk, maternal, and infant feces in a small yet very homogeneous cohort of 25 healthy mother–infant pairs in northwestern China (n = 25, infant age from 7 days to 2 years), with special emphasis on the cooccurrence and vertical transfer of Lactobacillus phylotypes at the species or strain level in mother-breast milk-infant triads. Accurate sequencing analysis revealed that among 73 Lactobacillus zero-radius operational classification units (ZOTUs) identified, 58 belonging to 18 recognized species or species groups were distributed in all three types of samples. Lactobacillus ruminis, L. mucosae and L. gasseri-johnsonii as true residents were the most represented in all three ecosystems, whereas the content of Lactobacillus phylotypes commonly developed as probiotics was not dominant. While the numbers of Lactobacillus species in breast milk and infant feces were greater than that in maternal feces, principal coordinates analysis (PCoA) based on beta diversity, coupled with the frequency of isolates determined by culture methods, showed that the Lactobacillus community in the infant gut was more similar to that in the maternal gut than to that in breast milk, suggesting that the gut is niche selective for Lactobacillus populations. In addition, identical strains of L. ruminis, L. paracasei, L. mucosae and L. salivarius were isolated from multiple mother–infant pairs, supporting the hypothesis that vertical transfer of bacteria via breastfeeding contributes to the initial establishment of the microbiota in the developing infant intestine.

Effects of Angiotensin (1-7) Expressing Lactobacillus and Exercise on Gut-Brain Axis in Aged Rats

Aging is associated with gut dysbiosis – a condition linked with altered central nervous system function (“gut-brain axis”). Age-related health benefits have been ascribed to the renin-angiotensin system, mediated partially via the angiotensin(1-7) axis. Research has shown exercise altering gut microbiota composition and function. This study explored the effects of a genetically modified probiotic expressing angiotensin (1-7) and exercise on the gut-brain axis. Sixty-two male F344/BN rats were randomized at 24-months-old to receive oral gavage of angiotensin (1-7) Lactobacillus paracasei (LP) or LP-A, wide-type LP, or control 3-times/week for 12 weeks; with or without exercise. Rats in exercise groups were walking on a treadmill 10-minutes/day for 5-days/week. Microbiome taxonomic analysis of fecal samples post intervention was performed via 16S-based PCR. A battery of behavior tests were performed before and after the intervention. PCoA revealed that groups differed in the overall fecal microbiota community structure by weighted UniFrac (p=0.034). Indices of alpha-diversity, including Shannon (p=0.02) and Simpson (p=0.019) indexes, displayed LP-A groups with more diverse microbiome than controls. Grip strength (p=0.042) and exercise tolerance (p<0.001) tests showed exercise groups had more muscle strength and aerobic capacity than the sedentary groups. Exercise groups had more lean mass (p=0.019); both LP-A and LP groups had lower fat mass compared to the controls in body composition measurement. LP-A travelled longer distance in the central area than the control in the open field test showing reduced anxiety (p=0.029). Therefore, we conclude LP-A and exercise have distinct and possibly overlapping beneficial effects on the gut-brain axis.