Gastrointestinal Bacterial Community Research Articles

Ingesting Stellera chamaejasme Significantly Impacts the Gastrointestinal Tract Bacterial Community and Diversity in Plateau Zokors (Eospalax baileyi).

Intestinal bacteria are considered the "second genome" of the host, playing a crucial physiological role in assisting the host in degrading plant secondary compounds, nutrient absorption, immune regulation, and other aspects. To explore the effects of Stellera chamaejasme on the bacterial community of the gastrointestinal tract of plateau zokor, this study uses the 16S rRNA gene high-throughput sequencing technology, and the biodiversity and the community structure of gut bacteria in different gastrointestinal tract segments (the stomach and cecum) of plateau zokors. The results showed that at the phylum level, the dominant flora in the stomach and cecum of plateau zokors before and after ingesting Stellera chamaejasme were Firmicutes and Bacteroidetes. In plateau zokors that ingested Stellera chamaejasme, the relative abundance of Firmicutes in the stomach and cecum decreased, the relative abundance of Bacteroidetes increased, and the ratio of Firmicutes to Bacteroidetes decreased. After plateau zokors ingested Stellera chamaejasme, the ACE index demonstrated a significant reduction in the richness of the stomach bacterial community, while cecal bacterial community richness showed no significant change. Stellera chamaejasme exhibits significantly different effects on the bacterial communities in different segments of the gastrointestinal tract. Beta diversity analysis revealed that, after plateau zokors ingested Stellera chamaejasme, there were notable distinctions in the bacterial communities within both the stomach and cecum, alongside a marked reduction in the variability of the intestinal bacterial profiles across individuals. The results show that ingesting Stellera chamaejasme has a significant impact on the composition and structure of the gastrointestinal tract bacterial community in plateau zokors.

Characterization of the gastrointestinal microbiome of the Syrian hamster (Mesocricetus auratus) and comparison to data from mice.

Syrian hamsters (Mesocricetus auratus) have been increasingly used as rodent models in recent years, especially for SARS-CoV-2 since the pandemic. However, the physiology of this animal model is not yet well-understood, even less when considering the digestive tract. Generally, the gastrointestinal microbiome influences the immune system, drug metabolism, and vaccination efficacy. However, a detailed understanding of the gastrointestinal microbiome of hamsters is missing. Therefore, we analyzed 10 healthy 11-week-old RjHan:AURA hamsters fed a pelleted standard diet. Their gastrointestinal content was sampled (i.e., forestomach, glandular stomach, ileum, cecum, and colon) and analyzed using 16S rRNA gene amplicon sequencing. Results displayed a distinct difference in the bacterial community before and after the cecum, possibly due to the available nutrients and digestive functions. Next, we compared hamsters with the literature data of young-adult C57BL/6J mice, another important animal model. We sampled the same gastrointestinal regions and analyzed the differences in the microbiome between both rodents. Surprisingly, we found strong differences in their specific gastrointestinal bacterial communities. For instance, Lactobacillaceae were more abundant in hamsters' forestomach and ileum, while Muribaculaceae dominated in the mouse forestomach and ileum. Similarly, in mouse cecum and colon, Muribaculaceae were dominant, while in hamsters, Lachnospiraceae and Erysipelotrichaceae dominated the bacterial community. Molecular strains of Muribaculaceae in both rodent species displayed some species specificity. This comparison allows a better understanding of the suitability of the Syrian hamster as an animal model, especially regarding its comparability to other rodent models. Thereby, this work contributes to the characterization of the hamster model and allows better experimental planning.

Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water.

The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.

Influence of Compost Amendments on Soil and Human Gastrointestinal Bacterial Communities during a Single Gardening Season.

To measure associations between gardening with different compost amendments and the human gut microbiota composition, gardeners (n = 25) were provided with one of three types of compost: chicken manure (CM), dairy manure and plant material (DMP), or plant-based (P). Stool samples were collected before gardening (T1), after compost amendment (T2), and at peak garden harvest (T3). Compost and soil samples were collected. DNA was extracted, 16S rRNA libraries were established, and libraries were sequenced by Illumina MiSeq. Sequences were processed using mothur, and data were analyzed in R software version 4.2.2. Fast expectation-maximization microbial source tracking analysis was used to determine stool bacteria sources. At T2/T3, the gut microbiotas of P participants had the lowest Shannon alpha diversity, which was also the trend at T1. In stool from T2, Ruminococcus 1 were less abundant in the microbiotas of those using P compost as compared to those using CM or DMP. At T2, Prevotella 9 had the highest abundance in the microbiotas of those using CM compost. In participants who used CM compost to amend their gardening plots, a larger proportion of the human stool bacteria were sourced from CM compared to soil. Soil exposure through gardening was associated with a small but detectable change in the gardeners' gut microbiota composition. These results suggest that human interactions with soil through gardening could potentially impact health through alterations to the gut microbiota.

Beneficial effects of American ginseng (Panax quinquefolius L.) extract residue as a feed additive on production, health status, and gastrointestinal bacteria in sika deer (Cervus nippon).

American ginseng residue is an industrial by-product of ginseng saponin extraction, including polysaccharides and amino acids; however, it is often discarded into the natural environment, representing a waste of resources as well as an environmental issue. In this study, we examined the effects of adding American ginseng residue to the basal diet of sika deer. Twelve antler-bearing male sika deer were assigned randomly to groups fed a diet supplemented with 0% (CON), 1% (LGR), and 3% (HGR) American ginseng residue, respectively, (n = 4 per group) for 5 weeks. Supplementation with 3% American ginseng residue significantly increased antler production and feed utilization efficiency in antler-bearing sika deer (p < 0.05). There were no significant differences in serum biochemical indexes among the three groups, but serum immunoglobulin A and glutathione peroxidase levels were significantly increased in the LGR and HGR groups (p < 0.05). Supplementation with American ginseng residue affected rumen fermentation in sika deer, significantly increasing the rumen contents of acetic acid, propionic acid, and total volatile fatty acids, and decreasing rumen fluid pH (p < 0.05), but had no significant effect on microbial protein or ammoniacal nitrogen content. American ginseng residue also affected the rumen bacterial composition, with significant up-regulation of Bacteroidota abundance in the HGR group, significant increases in Fibrobacterota and Fibrobacter abundance in the LGR group, and a significant decrease in Oscillospiraceae_UCG-005. Supplementation with ginseng residue had no significant effect on volatile fatty acids in the feces of sika deer, but did affect the composition of fecal bacteria, with significant decreases in Desulfobacterota and Rikenellaceae_RC9_gut_group in the HGR group, and a significant increase in Ruminococcus in the LGR group (p < 0.05). In addition, the abundance of Paeniclostridium in the feces decreased linearly with increasing concentration of ginseng residue, with a significant difference among the groups (p < 0.05). This study comprehensively evaluated the effects of American ginseng residue as a potential feed additive on the production performance and gastrointestinal bacterial community in antler-bearing sika deer. The results indicated that ginseng residue was a suitable feed additive for improving production performance and health in sika deer.

Weaning transition, but not the administration of probiotic candidate Kazachstania slooffiae, shaped the gastrointestinal bacterial and fungal communities in nursery piglets.

As in-feed antibiotics are phased out of swine production, producers are seeking alternatives to facilitate improvements in growth typically seen from this previously common feed additive. Kazachstania slooffiae is a prominent commensal fungus in the swine gut that peaks in relative abundance shortly after weaning and has beneficial interactions with other bacteriome members important for piglet health. In this study, piglets were supplemented with K. slooffiae to characterize responses in piglet health as well as fungal and bacterial components of the microbiome both spatially (along the entire gastrointestinal tract and feces) and temporally (before, during, and after weaning). Litters were assigned to one of four treatments: no K. slooffiae (CONT); one dose of K. slooffiae 7 days before weaning (day 14; PRE); one dose of K. slooffiae at weaning (day 21; POST); or one dose of K. slooffiae 7 days before weaning and one dose at weaning (PREPOST). The bacteriome and mycobiome were analyzed from fecal samples collected from all piglets at day 14, day 21, and day 49, and from organ samples along the gastrointestinal (GI) tract at day 21 and day 49. Blood samples were taken at day 14 and day 49 for cytokine analysis, and fecal samples were assayed for antimicrobial resistance. While some regional shifts were seen in response to K. slooffiae administration in the mycobiome of the GI tract, no remarkable changes in weight gain or health of the animals were observed, and changes were more likely due to sow and the environment. Ultimately, the combined microbiome changed most considerably following the transition from suckling to nursery diets. This work describes the mycobiome along the piglet GI tract through the weaning transition for the first time. Based on these findings, K. slooffiae administered at this concentration may not be an effective tool to hasten colonization of K. slooffiae in the piglet GI tract around the weaning transition nor support piglet growth, microbial gut health, or immunity. However, diet and environment greatly influence microbial community development.

Culturomics: Bringing culture back to the forefront for effective gastrointestinal bacterial capture

Abstract The gastrointestinal microbiota plays a crucial role in host nutrition and health. While culture-independent techniques have advanced microbial research, they often overlook low-abundance bacteria in the microbial community. Furthermore, empirical studies and mechanistic research rely on bacterial isolates obtained through culturing. The introduction of culturomics in 2012 significantly advanced culture-dependent techniques, contributing to microbial research. However, these methods remain labor-intensive, time-consuming, and costly, similar to traditional culture methods. This review provides an overview of the contributions of culturomics, summarizes procedures for optimizing sample and culture processes, and offers guidance on utilizing metagenomic data to enhance culturomics workflows. By collating and synthesizing these developments, this review aims to provide valuable insights into improving the practicality and productivity of culturomics for capturing gastrointestinal bacterial communities.

Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection

ABSTRACT Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While a close correlation between chronic Helicobacter pylori infection and CRC has been reported, the role of the virome has been overlooked. Here, we infected Apc-mutant mouse models and C57BL/6 mice with H. pylori and conducted a comprehensive metagenomics analysis of H. pylori-induced changes in lower gastrointestinal tract bacterial and viral communities. We observed an expansion of temperate phages in H. pylori infected Apc +/1638N mice at the early stage of carcinogenesis. Some of the temperate phages were predicted to infect bacteria associated with CRC, including Enterococcus faecalis. We also observed a high prevalence of virulent genes, such as flgJ, cwlJ, and sleB, encoded by temperate phages. In addition, we identified phages associated with pre-onset and onset of H. pylori-promoted carcinogenesis. Through co-occurrence network analysis, we found strong associations between the viral and bacterial communities in infected mice before the onset of carcinogenesis. These findings suggest that the expansion of temperate phages, possibly caused by prophage induction triggered by H. pylori infection, may have contributed to the development of CRC in mice by interacting with the bacterial community.

Dynamic Variation of Camel Gastrointestinal Bacterial Communities Contributing to Benzo(a)pyrene Degradation

Dynamic Variation of Camel Gastrointestinal Bacterial Communities Contributing to Benzo(a)pyrene Degradation

Distinct stages of the intestinal bacterial community of Ampullaceana balthica after salinization.

Environmental disturbances influence bacterial community structure and functioning. To investigate the effect of environmental disturbance caused by changes in salinity on host-protected bacterial communities, we analyzed the microbiome within the gastrointestinal tract of Ampullaceana balthica in different salinities. A. balthica is a benthic gastropod found in fresh- and mesohaline waters. Whereas the total energy reserves of A. balthica were unaffected by an increase of salinity to 3, a high mortality rate was detected after a shift from freshwater to salinity 6 suggesting a major disruption of energy homeostasis. The shift to salinity 6 also caused a change in the gastrointestinal bacterial community composition. At salinity 3, the bacterial community composition of different host individuals was related either to the freshwater or salinity 6 gastrointestinal bacterial community, indicating an ambivalent nature of salinity 3. Since salinity 3 represents the range where aquatic gastropods are able to regulate their osmolarity, this may be an important tipping point during salinization. The change in the intestinal microbiome was uncoupled from the change in the water bacterial community and unrelated to the food source microbiome. Our study shows that environmental disturbance caused by salinity acts also on the host-protected microbiome. In light of the sea-level rise, our findings indicate that salinization of the near-shore freshwater bodies will cause changes in organisms’ intestinal microbiomes if a critical salinity threshold (presumably ∼3) is exceeded.

Impact of disturbance and dietary shift on gastrointestinal bacterial community and its invertebrate host system.

The gut microbiome is one of the most important sites of host-microbe interactions, however, mechanisms governing the responses of host-associated microbes to changing environmental conditions are poorly understood. To address this, we investigated individual and combined effects of dietary changes and increase in salinity (from freshwater to salinity 3) or antibiotic concentration on the gastrointestinal bacterial community of the aquatic snail Ampullaceana balthica. In parallel, the energy reserves of the host were quantified. A change of natural food source to biofilm forming green algae Scenedesmus obliquus as well as the combined treatment of salinity and S. obliquus decreased the richness and changed the composition of the A. balthica gastrointestinal bacterial community. In these treatments Pseudomonas became the dominant bacterium. However, energy reserves of the host were higher in these treatments compared to the reference aquaria specimens and the combined treatment of antibiotics with S. obliquus. The presence of antibiotics inhibited the dominance of Pseudomonas and resulted in lower energy reserves despite S. obliquus feeding. Therefore the host seems to be able to adapt and replace its bacterial community composition to respond to mild changes in salinity and food source. Antibiotics in the water can disturb this self-regulating mechanism. Our study underlines the ability of aquatic macroinvertebrates to respond to sudden changes in food source and mild shifts in salinity. Moreover, it emphasizes the strong impact of the food source on the gastrointestinal microbiome and the importance of generalists during disturbance.

Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México.

BackgroundThe gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities.MethodsWe employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses.ResultsAs hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6–V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6–V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.

Air Particulate Matter Significantly Alters Bacterial‐Derived Metabolites in APP/PS1 Mice

Alterations to gastrointestinal bacterial communities have been linked to the exacerbation of numerous diseases, including Alzheimer’s Disease (AD), via changes to bacterial‐derived metabolites. Community changes can result from antibiotic use, dietary changes, psychosocial stress, and possibly air particulate matter exposure. Previous studies from our group demonstrated that a transgenic mouse model predisposed to create amyloid‐β fibers similar to AD, namely APP/PS1 mice, exposed to air particulate matter (PM) led to significant increases in hippocampal amyloid‐β1‐40 (Aβ) and Aβ1‐42, as well as astrocytosis, microgliosis, and proinflammatory cytokines in the temporal cortex as compared to PM‐exposed non‐carrier mice. Such findings indicate the presence of PM2.5‐induced neuroinflammation in APP/PS1 mice; however, the mechanism by which this occurs is unknown. Recent data demonstrates PM‐induced alterations to the gut microbiome, prompting us to test the hypothesis that disruptions of microbial‐derived metabolites are present in PM‐exposed APP/PS1 mice. To test this hypothesis, APP/PS1 and non‐carrier, littermate wild type (WT) mice were exposed to filtered air (FA) or PM for 5 days/week, 6 hours/day, for 3 months. The average daily PM exposure is 90.0 μg/m3, which is a 5‐fold concentration above the ambient mean daily PM2.5 concentration (18.8 ±11.4 μg/m3) at the study site in Columbus, OH. At the end of the 3‐month exposure, fecal samples were collected to assess bacterial byproducts, i.e. short chain fatty acids (SCFAs), by gas chromatography/mass spectrometry. Serum samples were collected to characterize additional metabolites including the bacterial metabolite trimethylamine (TMA) by liquid chromatography/mass spectrometry. Results demonstrated that SCFA butyric acid was significantly reduced by PM‐exposure in both APP/PS1 and WT animals as compared to their FA‐exposed counterparts (p&lt;0.01) and propionic acid was significantly increased in FA‐exposed APP/PS1 mice as compared to their WT counterparts (p&lt;0.0001). Serum metabolite analyses revealed distinct principal component patterns among groups, demonstrating unique metabolic profiles associated with exposure and genotype. One such metabolite, TMA, was significantly increased by PM‐exposure (p&lt;0.05). Taken together, these findings indicate that airborne particulate matter exposure alters metabolic profiles in a transgenic mouse model of AD.

Role of the duodenal microbiota in functional dyspepsia.

Functional dyspepsia (FD) is a common and debilitating gastrointestinal disorder attributed to altered gut-brain interactions. While the etiology of FD remains unknown, emerging research suggests the mechanisms are likely multifactorial and heterogenous among patient subgroups. Small bowel motor disturbances, visceral hypersensitivity, chronic microinflammation, and increased intestinal tract permeability have all been linked to the pathogenesis of FD. Recently, alterations to the gut microbiome have also been implicated to play an important role in the disease. Changes to the duodenal microbiota may either trigger or be a consequence of immune and neuronal disturbances observed in the disease, but the mechanisms of influence of small intestinal flora on gastrointestinal function and symptomatology are unknown. This review summarizes and synthesizes the literature on the link between the microbiota, low-grade inflammatory changes in the duodenum and FD. This review is not intended to provide a complete overview of FD or the small intestinal microbiota, but instead outline some of the key conceptual advances in understanding the interactions between altered gastrointestinal bacterial communities; dietary factors; host immune activation; and stimulation of the gut-brain axes in patients with FD versus controls. Current and emerging treatment approaches such as dietary interventions and antibiotic or probiotic use that have demonstrated symptom benefits for patients are reviewed, and their role in modulating the host-microbiota is discussed. Finally, suggested opportunities for diagnostic and therapeutic improvements for patients with this condition are presented.

Microbiome composition of Anna's hummingbirds differs among regions of the gastrointestinal tract

The gastrointestinal (GI) microbiome is an important mediator and indicator of host physiology, health and fitness in many vertebrate systems, but sources of variation in microbiome composition within species are poorly understood, particularly in free‐ranging birds. Hummingbirds have GI anatomy and physiology similar to other avian species, but they have a relatively rapid gastrointestinal transit rate, which could affect microbiome structure. To date, it has not been elucidated if microbiomes isolated from feces and samples from sections of the GI tract differ in an avian organism that has a rapid gastrointestinal time. Here, we test the hypothesis that the microbiome in free‐ranging and wildlife rehabilitation‐sourced Anna's hummingbirds Calypte anna differ between fecal and samples from three sections of the GI tract and between birds that differ in sex, age and poxvirus infection status. We characterized bacterial composition in fecal and GI tract samples from Anna's hummingbirds by amplicon sequencing of the 16S rRNA gene. We found strong evidence of differentiation in bacterial composition among GI tract regions and compared it to fecal samples. Actinobacteria, primarily genus Corynebacterium, Firmicutes and Fusobacteria were abundant in bird samples from regions of the GI tract. In contrast, fecal bacterial communities were more diverse and variable compared to GI tract samples. Bacterial community composition differed between male and female hummingbirds and with bird age (hatch year vs after‐hatch year). Finally, birds with symptoms of avian poxvirus infection had a higher relative abundance of Staphylococcus spp. than birds with no symptoms of pox. Our results suggest that Anna's hummingbirds host differentiated microbiome among GI tract regions that is consistent among individual birds. The GI bacterial community also contained taxa not represented in fecal samples. This provides evidence for the possibility of a residential gut microbiome in Anna's hummingbirds, although functional significance of the bacterial microbiome remains unknown.

Fecal Bacterial Community of Allopatric Przewalski's Gazelles and Their Sympatric Relatives.

Mammal gastrointestinal tracts harbor diverse bacterial communities that play important roles in digestion, development, behavior, and immune function. Although, there is an increasing understanding of the factors that affect microbial community composition in laboratory populations, the impact of environment and host community composition on microbiomes in wild populations is less understood. Given that the composition of bacterial communities can be shaped by ecological factors, particularly exposure to the microbiome of other individuals, inter-specific interactions should impact on microbiome community composition. Here, we evaluated inter-population and inter-specific similarity in the fecal microbiota of Przewalski’s gazelle (Procapra przewalskii), an endangered endemic ruminant around Qinghai Lake in China. We compared the fecal bacterial communities of three Przewalski’s gazelle populations, with those of two sympatric ruminants, Tibetan gazelle (Procapra picticaudata) and Tibetan sheep (Ovis aries). The fecal bacterial community richness (Chao1, ACE) did not vary across the three Przewalski’s gazelle populations, nor did the composition vary between species. In contrast, the managed Przewalski’s gazelle population had higher bacterial diversity (Shannon and Simpson) and was more similar to its sympatric Tibetan sheep in beta diversity than the wild Przewalski’s gazelle populations. These results suggest that ecological factors like host community composition or diet affect Przewalski’s gazelle’s gastrointestinal bacterial community. The role of bacterial community composition in maintaining gastrointestinal health should be assessed to improve conservation management of endangered Przewalski’s gazelle. More broadly, captive breeding and reintroduction efforts may be impeded, where captive management results in dysbiosis and introduction of pathogenic bacteria. In free ranging populations, where wildlife and livestock co-occur, infection by domestic pathogens and diseases may be an underappreciated threat to wild animals.

Effect of Red Orange and Lemon Extract-Enriched Diet in Suckling Lambs’ Fecal Microbiota

Red orange and lemon extract (RLE) is an anthocyanins-rich dietary supplement that may influence gastrointestinal bacterial community in ruminants. The aim of the present study was to investigate the RLE effects on gut microbiota composition in lambs. Twenty-eight lambs were randomly divided into a control group (CON; n = 14) and an anthocyanin group (ANT; n = 14) and fed the same diet; additionally, only the ANT received 90 mg/kg live weight of RLE at day. After lamb slaughter (40 ± 1 days), fecal samples were collected from the rectum and stored at −20 °C until analysis. Analysis of fecal microbiome was carried out by metabarcoding analysis of 16S rRNA. After reads denoising, sequences were aligned against SILVA rRNA sequence database using MALT, and taxonomic binning was performed with MEGAN. A significant increase in Firmicutes and Bacteroidetes and a decrease in Proteobacteria and Actinobacteria was observed in ANT compared to CON. Moreover, an interesting increase of Lactobacillus and Bifidobacterium genera and a decrease in Escherichia coli and Salmonella species were detected in ANT compared to CON. Results recommend that anthocyanin supplementation in lamb diet is able to modulate positively gut microbiota and may inhibit the growth of some potential pathogenic microorganisms.

Proanthocyanidin-enriched cranberry extract induces resilient bacterial community dynamics in a gnotobiotic mouse model

Cranberry consumption has numerous health benefits, with experimental reports showing its anti-inflammatory and anti-tumor properties. Importantly, microbiome research has demonstrated that the gastrointestinal bacterial community modulates host immunity, raising the question of whether the cranberry-derived effect may be related to its ability to modulate the microbiome. Only a few studies have investigated the effect of cranberry products on the microbiome to date. Especially because cranberries are rich in dietary fibers, the extent of microbiome modulation by polyphenols, particularly proanthocyanidins (PACs), remains to be shown. Since previous work has only focused on long-term effects of cranberry extracts, in this study we investigated the effect of a water-soluble, PAC-rich cranberry juice extract (CJE) on the short-term dynamics of a human-derived bacterial community in a gnotobiotic mouse model. CJE characterization revealed a high enrichment in PACs (57%), the highest ever utilized in a microbiome study. In a 37-day experiment with a ten-day CJE intervention and 14-day recovery phase, we profiled the microbiota via 16S rRNA sequencing and applied diverse time-series analytics methods to identify individual bacterial responses. We show that daily administration of CJE induces distinct dynamic patterns in bacterial abundances during and after treatment, before recovering resiliently to pre-treatment levels. Specifically, we observed an increase of Akkermansia muciniphila and Clostridium hiranonis at the expense of Bacteroides ovatus after the offset of the selection pressure imposed by the PAC-rich CJE. This demonstrates that termination of an intervention with a cranberry product can induce changes of a magnitude as high as the intervention itself.

Comparative study of the bacterial communities throughout the gastrointestinal tract in two beef cattle breeds.

Investigation of the compositional and functional characteristics of the gastrointestinal bacterial community in beef cattle breeds can improve our understanding of the influence of gastrointestinal tract (GIT) regions and host breeds on the bacterial community. In this study, 16S ribosomal RNA (16S rRNA) gene amplicon sequencing was used to characterize the bacterial communities in the rumen, duodenum, jejunum, ileum, caecum, and colon of Xuanhan yellow cattle (XHC) and Simmental crossbred cattle (SXC). The results showed that the diversity of the bacterial population was different in GIT regions of XHC and SXC (P < 0.05). In total, ten bacterial phyla, sixteen bacterial genera, and nine metabolic pathways were identified in the core bacteria. The phyla Firmicutes, Bacteroidetes, and Proteobacteria were predominant, but their proportions were different in GIT regions (P < 0.05). The diversity, structure, and composition of the bacteria in the rumen were similar between the breeds (P > 0.05), and the indices in the intestine showed significant differences (P < 0.05). Moreover, the composition and structure of the bacterial communities in the rumen, small intestine, and large intestine were different regardless of the breed. Thus, the bacterial communities were different among the gastrointestinal regions in each breed, and the bacterial community in the rumen had more stable characteristics than that in the intestine between two breeds. Further studies may focus on the minor microbial communities and the functions of GIT bacteria to better understand gut-microbe interactions. KEY POINTS: • Differences in bacteria among gastrointestinal regions differ in cattle breeds. • Differences between the breeds in the ruminal bacteria are less pronounced than differences in the intestinal bacteria.

Impact of Salinity on the Gastrointestinal Bacterial Community of Theodoxus fluviatilis.

Differences in salinity are boundaries that act as barriers for the dispersal of most aquatic organisms. This creates distinctive biota in freshwater and brackish water (mesohaline) environments. To test how saline boundaries influence the diversity and composition of host-associated microbiota, we analyzed the microbiome within the digestive tract of Theodoxus fluviatilis, an organism able to cross the freshwater and mesohaline boundary. Alpha-diversity measures of the microbiome in freshwater and brackish water were not significantly different. However, the composition of the bacterial community within freshwater T. fluviatilis differed significantly compared with mesohaline T. fluviatilis and typical bacteria could be determined for the freshwater and the mesohaline digestive tract microbiome. An artificial increase in salinity surrounding these freshwater snails resulted in a strong change in the bacterial community and typical marine bacteria became more pronounced in the digestive tract microbiome of freshwater T. fluviatilis. However, the composition of the digestive tract microbiome in freshwater snails did not converge to that found within mesohaline snails. Within mesohaline snails, no cardinal change was found after either an increase or decrease in salinity. In all samples, Pseudomonas, Pirellula, Flavobacterium, Limnohabitans, and Acinetobacter were among the most abundant bacteria. These bacterial genera were largely unaffected by changes in environmental conditions. As permanent residents in T. fluviatilis, they may support the digestion of the algal food in the digestive tract. Our results show that freshwater and mesohaline water host-associated microbiomes respond differently to changes in salinity. Therefore, the salinization of coastal freshwater environments due to a rise in sea level can influence the gut microbiome and its functions with currently unknown consequences for, e.g., nutritional physiology of the host.