Fecal Communities Research Articles

Anaerobic single-cell dispensing facilitates the cultivation of human gut bacteria.

Cultivation via classical agar plate (CAP) approaches is widely used to study microbial communities, but they are time-consuming. An alternative approach is the application of single-cell dispensing (SCD), which allows high-throughput, label-free sorting of microscopic particles. We aimed to develop a new anaerobic SCD workflow to cultivate human gut bacteria and compared it with CAP using faecal communities on three rich culture media. We found that the SCD approach significantly decreased the experimental time to obtain pure cultures from 17± 4 to 5± 0 days, while the isolate diversity and relative abundance coverage were comparable for both approaches. We further tested the total captured fraction by sequencing the sorted bacteria directly after growth as bulk biomass from 2400 dispensed single cells without downstream identification of individual strains. In this approach, the cultured fraction increased from 35.2% to 52.2% for SCD, highlighting the potential for deeper cultivation projects from single samples. SCD-based cultivation also captured species not detected by sequencing (16± 5 per sample, including seven novel taxa). From this work, 82 human gut bacterial species across five phyla (Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes and Proteobacteria) and 24 families were obtained, including the first cultured member of 11 novel genera and 10 novel species that were fully characterized taxonomically.

Analysis of the fecal and oral microbiota in chronic recurrent multifocal osteomyelitis

BackgroundChronic recurrent multifocal osteomyelitis (CRMO) is a rare autoinflammatory bone disease for which a lack of bacterial involvement is a key diagnostic feature to distinguish it from other symptomatically related diseases. However, the growing evidence suggesting an involvement of the host-associated microbiota in rheumatic disorders together with the now wide accessibility of modern culture-independent methods warrant a closer examination of CRMO.MethodsIn this study, we show through bacterial 16S rRNA gene profiling that numerous features of the oral- and fecal microbial communities differentiate children with and without CRMO.ResultsNotably, communities in diseased children are characterized by a lack of potential probiotic bacteria in the fecal community and an overabundance of known pathobionts in the oral microbial communities. Of special interest is the HACEK group, a set of commonly known oral pathogens that are implicated in the development of several acute and chronic diseases such as osteitis and rheumatoid arthritis. Furthermore, we observe that gut bacterial communities in the diseased children appear to reflect an altered host physiology more strongly than the oral community, which could suggest an oral disease origin followed by propagation and/or responses beyond the oral cavity.ConclusionsBacterial communities, in particular the oral microbiota, may serve as an indicator of underlying susceptibility to CRMO, or play a yet undefined role in its development.

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

BackgroundEscherichia coli peritonitis (EP) 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 is still poorly understood. It is unclear whether the intestinal flora is involved in the pathogenesis of EP.MethodsWe collected fecal samples from EP patients and normal group (NG) PD patients. 16S rRNA sequencing was used to analyze the gut microbiota of EP and NG patients. The demographic data and clinical indicators of all patients were collected.ResultsSix EP 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 EP patients, where Bacteroidetes and Synergistetes were upregulated at different levels, while Bacilli and Lactobacillus were downregulated at different levels compared to the NG group. Additionally, decreased gene function associated with metabolic pathways was observed in EP patients.ConclusionsThe altered composition of the gut microbiota in EP patients provided deeper insights into the pathogenesis of EP, and these biomarkers might be established as potential therapeutic targets that deserve further exploration.

Non-invasive monitoring of multiple wildlife health factors by fecal microbiome analysis.

Fecal microbial biomarkers represent a less invasive alternative for acquiring information on wildlife populations than many traditional sampling methodologies. Our goal was to evaluate linkages between fecal microbiome communities in Rocky Mountain elk (Cervus canadensis) and four host factors including sex, age, population, and physical condition (body‐fat). We paired a feature‐selection algorithm with an LDA‐classifier trained on elk differential bacterial abundance (16S‐rRNA amplicon survey) to predict host health factors from 104 elk microbiomes across four elk populations. We validated the accuracy of the various classifier predictions with leave‐one‐out cross‐validation using known measurements. We demonstrate that the elk fecal microbiome can predict the four host factors tested. Our results show that elk microbiomes respond to both the strong extrinsic factor of biogeography and simultaneously occurring, but more subtle, intrinsic forces of individual body‐fat, sex, and age‐class. Thus, we have developed and described herein a generalizable approach to disentangle microbiome responses attributed to multiple host factors of varying strength from the same bacterial sequence data set. Wildlife conservation and management presents many challenges, but we demonstrate that non‐invasive microbiome surveys from scat samples can provide alternative options for wildlife population monitoring. We believe that, with further validation, this method could be broadly applicable in other species and potentially predict other measurements. Our study can help guide the future development of microbiome‐based monitoring of wildlife populations and supports hypothetical expectations found in host‐microbiome theory.

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

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

Colonic Microbial Abundances Predict Adenoma Formers.

We aimed to examine associations between the oral, fecal, and mucosal microbiome communities and adenoma formation. Data are limited regarding the relationships between microbiota and preneoplastic colorectal lesions. Individuals undergoing screening colonoscopy were prospectively enrolled and divided into adenoma and nonadenoma formers. Oral, fecal, nonadenoma and adenoma-adjacent mucosa were collected along with clinical and dietary information. 16S rRNA gene libraries were generated using V4 primers. DADA2 processed sequence reads and custom R-scripts quantified microbial diversity. Linear regression identified differential taxonomy and diversity in microbial communities and machine learning identified adenoma former microbial signatures. One hundred four subjects were included, 46% with adenomas. Mucosal and fecal samples were dominated by Firmicutes and Bacteroidetes whereas Firmicutes and Proteobacteria were most abundant in oral communities. Mucosal communities harbored significant microbial diversity that was not observed in fecal or oral communities. Random forest classifiers predicted adenoma formation using fecal, oral, and mucosal amplicon sequence variant (ASV) abundances. The mucosal classifier reliably diagnosed adenoma formation with an area under the curve (AUC) = 0.993 and an out-of-bag (OOB) error of 3.2%. Mucosal classifier accuracy was strongly influenced by five taxa associated with the family Lachnospiraceae, genera Bacteroides and Marvinbryantia, and Blautia obeum. In contrast, classifiers built using fecal and oral samples manifested high OOB error rates (47.3% and 51.1%, respectively) and poor diagnostic abilities (fecal and oral AUC = 0.53). Normal mucosa microbial abundances of adenoma formers manifest unique patterns of microbial diversity that may be predictive of adenoma formation.

Comparison of Gut Microbiota between Gentoo and Adélie Penguins Breeding Sympatrically on Antarctic Ardley Island as Revealed by Fecal DNA Sequencing

There are two pygoscelid penguins, the Gentoo (Pygoscelis papua Forster, 1781) and Adélie (P. adeliae Hombron and Jacquinot, 1841) penguins, breeding sympatrically on Ardley Island, Fildes Peninsula region, South Shetlands, Antarctica. Whether the two closely related penguin species with similar dietary habits possess compositional similarity in gut microbiota remains unknown. DNA barcoding of feces is an emerging approach for gut microbiota analysis of protected animals. In the present study, the 16S rRNA gene from penguin feces was sequenced using the Illumina MiSeq platform to investigate the gut microbiota of the two pygoscelid penguin species. The fecal community of Gentoo penguins has higher diversity indices and OTU (operational taxonomic unit) richness compared to Adélie penguins. Besides unclassified bacteria, sequences fell into 22 major lineages of the domain Bacteria: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chlamydiae, Chloroflexi, Cloacimonetes, Cyanobacteria, Deinococcus-Thermus, Fibrobacteres, Firmicutes, Fusobacteria, Gemmatimonadetes, Ignavibacteriae, Planctomycetes, Proteobacteria, Tenericutes, Verrucomicrobia, and candidate divisions BRC1, SR1, WPS-2, and Saccharibacteria. Among these, Firmicutes (37.7%), Proteobacteria (23.1%, mainly Gamma- and Betaproteobacteria), Fusobacteria (14.3%), Bacteroidetes (7.9%), and Actinobacteria (6.6%) were dominant in the fecal microbiota of the two penguin species. At the same time, significantly higher abundances of Actinobacteria and Cyanobacteria were detected in Gentoo penguins than in Adélie penguins (p < 0.05). Overall, there was a clear difference in the composition of gut microbiota between the Adélie and Gentoo penguins. The results suggested that both the phylogeny of penguin species and the diet could be responsible for the differences in the gut microbiota of the two pygoscelid penguins breeding in the same area.

Mother's Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis.

The child microbiome, including gut and skin communities, is shaped by a multitude of factors, and breastfeeding is one of the most essential. Food allergy (FA) and atopic dermatitis (AD) are among the most common diseases in pediatrics, with the prevalence of each up to 6% and 20%, respectively. Therefore, we aimed at finding differences between the fecal and skin microbiomes of FA and AD patients in the context of breastfeeding, by means of the Illumina sequencing of 16S rRNA gene fragment libraries amplified from the total DNA isolated from samples collected from allergic and healthy infants. We also analyzed milk samples from the mothers of the examined children and searched for patterns of incidence suggesting milk influence on an infant’s allergy status. Here we show that a mother’s milk influences her child’s fecal and skin microbiomes and identify Acinetobacter as the taxon whose abundance is correlated with milk and child-derived samples. We demonstrate that breastfeeding makes allergic children's fecal and skin communities more similar to those of healthy infants than in the case of formula-feeding. We also identify signature taxa that might be important in maintaining health or allergy development.

Abundance, diversity and diffusion of antibiotic resistance genes in cat feces and dog feces

The ARG profiles in pet feces, such as cat and dog feces, and their potential threat to environmental safety are still unclear. In this study, ARGs in 45 cat and 28 dog fecal samples were detected, and a diffusion experiment was performed to assess the risk of ARGs diffusion into the air. The results showed that the abundances of ARGs in cat feces and dog feces were high, and the abundance in dog feces (0.89 ± 0.17 copies/bacterial cell) was significantly higher than that in cat feces (0.46 ± 0.09 copies/bacterial cell) (P < 0.05). The bacterial community, especially Firmicutes and Desulfobacterota in cat feces, and Proteobacteria in dog feces, was the main factor affecting the variation in the ARG profiles, contributing to 31.6% and 32.4% of the variation in cat feces and dog feces, respectively. Physicochemical factors (especially NH4+-N) and age also indirectly affected the variation in the ARG profiles by affecting the bacterial community. In addition, the ARGs in cat feces and dog feces diffused into the air, but there was no evidence that this diffusion posed a threat to environmental safety and human health. These results can provide reference data for healthy animal breeding and the prevention and control of ARG pollution.

Alteration of Gut Microbiota of a Food-Storing Hibernator, Siberian Chipmunk Tamias sibiricus.

Hibernation represents a state of fasting because hibernators cease eating in the torpid periods. Therefore, food deprivation during hibernation is expected to modify the gut microbiota of host. However, there are few reports of gut microbiota in food-storing hibernators that feed during the interbout arousals. Here we collected fecal samples of Siberian chipmunk T. sibiricus to character and examine changes in the gut microbiota at various stages relative to hibernation: pre-hibernation, early-hibernation, mid-hibernation, late-hibernation, and post-hibernation. Compared to the pre-hibernation state, alpha-diversity of gut microbiota was significantly increased during the interbout arousal periods. In addition, beta-diversity of the fecal communities from pre-hibernation and interbout arousal periods grouped together, and post-hibernation gut microbiota resembled the counterpart at late-hibernation. Hibernation significantly decreased the relative abundance of Firmicutes but increased Bacteroidetes, reflecting a shift of microbiota toward taxa in favor of host-derived substrates. The increased abundance of Ruminococcaceae_UCG-014, Lactobacillus, and Christensenellaceae_R-7_group in gut microbiota may help the chipmunks reduce intestinal inflammation and then maintain healthy bowel during hibernation. KEGG pathway indicated that hibernation altered the metabolic function of gut microflora of T. sibiricus.Our study provides evidence that the gut microbiota of food-storing hibernators, despite feeding during the interbout arousals, shows similar response to hibernation that has well documented in fat-storing counterparts, suggesting the potential for a core gut microbiota during hibernation of mammals. Importantly, these results will broaden our understanding of the effects of hibernation on gut microbiota of mammal hibernators.

Free Faecal Water: Analysis of Horse Faecal Microbiota and the Impact of Faecal Microbial Transplantation on Symptom Severity.

Simple SummaryFree faecal water (FFW) in equines causes soiling of the hindquarters and tail and may also include additional symptoms. The cause of FFW is unknown. In this study it was investigated whether the microbes present in the last part of the gut (i.e., the hindgut microbiota) may be involved. From the analysis of faecal samples, it was found that horses suffering from FFW had no differences in their hindgut microbiota compared to healthy horses stabled at the same location. However, subsequent treatment of the FFW horses with a faecal microbiota transplantation (FMT) from a healthy donor animal resulted in a decrease in FFW symptom severity. Nevertheless, animals did not respond uniformly to this treatment, with some only having temporary decreases in FFW symptom severity. No lasting changes in the hindgut microbiota of the FFW horses occurred as a result of the faecal transplant. The practical implication of these findings is that FMT can potentially be used to temporarily alleviate FFW symptom severity in horses, although future studies using controls are needed to confirm the effectiveness of FMT to treat FFW.Free faecal water (FFW) in equines results in pollution of the hindquarters and tail and can also involve clinical signs. Though the cause of FFW is unknown, it was hypothesized that it may involve the gut microbiota. This hypothesis was addressed as follows. First, the faecal prokaryotic community composition of horses suffering from FFW relative to healthy controls (n = 10) was compared. Second, FFW horses were treated with a standardised faecal microbiota transplantation (FMT) protocol (n = 10), followed by assessment of FFW symptom severity and faecal prokaryotic community composition over a follow-up period of 168 days. No significant differences were found in the faecal microbiota composition of FFW horses compared to healthy controls (p > 0.05). Relative to before FMT, FFW symptom severity decreased in affected horses 14 days after FMT (p = 0.02) and remained decreased for the remainder of the study (p < 0.02). However, individual animal responses to FMT varied. FMT had no effect on FFW horse faecal prokaryotic community composition in terms of alpha or beta diversity. Alpha diversity of the donor inocula used in the FMT was always lower than that of the faecal microbiota of the FFW treated horses (p < 0.001). In conclusion, whilst findings indicate FFW horses do not have an altered hindgut microbiota, some horses that received FMT had a temporary alleviation of FFW symptom severity without causing changes in the faecal microbiota. Future studies using controls are now needed to confirm the effectiveness of FMT to treat FFW.

The effect of sodium carboxymethyl starch with high degree of substitution on defecation.

Sodium carboxymethyl starch (CMS-Na), a kind of food additive with high degree of substitution, is also known as a prebiotic. The aim of this study was to determine the effect of CMS-Na on defecation. Constipated mouse model was prepared by loperamide. Normal rats were also used in the study. Short-chain fatty acids in rat feces were detected by gas chromatography. The bacterial communities in rat feces were identified by 16S rDNA gene sequencing. 5-hydroxytryptamine (5-HT) and tryptophan hydroxylase 1 (Tph1) were measured by ELISA. The results showed that CMS-Na increased the fecal granule counts and intestinal propulsion rate in constipated mice. The contents of water, acetic acid, propionic acid and n-butyrate in feces, Tph1 in colon and 5-HT in serum of rats were increased. In addition, CMS-Na shortened the colonic transport time in rats. The 16S rDNA gene sequencing results indicated that CMS-Na increased the relative abundance of Alloprevotella and decreased the proportion of Lactobacillus. However, the biodiversity of the normal intestinal flora was not altered. In conclusion, CMS-Na can promote defecation in constipated mice. The mechanism may be related to the regulation of Alloprevotella and Lactobacillus in colon, the increase of short-chain fatty acids, and the promotion of the synthesis of Tph1 and 5-HT.

Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis

BackgroundNecrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Bayesian regression was used to segregate cases from control samples using both microbial and clinical data.ResultsWe found that the infants suffering from NEC fell into two groups based on their microbiota; one with low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We propose that these two patterns represent the stimulation of a common pathway at extremes; the LPS-enriched microbiome suggesting overstimulation of TLR4, whilst a microbial community with low levels of CpG DNA suggests reduction of the counterbalance to TLR4 overstimulation.ConclusionsThe identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.

Alterations of gut microbiome and metabolite profiles in choledocholithiasis concurrent with cholangitis.

Gut microbiota and their metabolic products might play important roles in regulating the pathogenesis of choledocholithiasis concurrent with cholangitis (CC). The aim of this study was to explore the characteristic gut dysbiosis, metabolite profiles and the possible roles in patients with CC. A case-control study was carried out to analyze the alterations in the intestinal microbiota and their metabolites in patients with CC (n = 25) compared with healthy controls (HCs) (n = 25) by metagenomic sequencing to define the gut microbiota community and liquid chromatography/mass spectrometry (LC/MS) analysis to characterize the metabolite profiles. Significantly reduced Shannon diversity index (p = 0.043) and differential overall fecal microbiota community in CCs were observed. Twelve dominant altered species were identified and analyzed (LDA score > 3.0, p < 0.05) (Q value < 0.05), including unclassified_f_Enterobacteriaceae, Escherichia_coli, Roseburia_faecis and Eubacterium rectale. Moreover, the levels of KEGG pathways related to biofilm formation of Escherichia coli, lipopolysaccharide (LPS) biosynthesis, and the metabolism of propanoate and glutathione in CCs were significantly altered. Finally, 47 markedly changed metabolites (VIP > 1.0 and p < 0.05), including low level of kynurenic acid (KYNA) and high concentration of N-palmitoylsphingosine involving tryptophan metabolism and sphingolipid signaling pathways, were identified to validate aberrant metabolic patterns in CCs, and multiple correlated metabolic modules involving bile inflammation were altered in CCs. Our study provides novel insights into compositional and functional alterations in the gut microbiome and metabolite profiles in CC and the underlying mechanisms between gut microbiota and bile inflammation.

Chlortetracycline alters microbiota of gut or faeces in pigs and leads to accumulation and migration of antibiotic resistance genes

In this study, we investigated the effect of long-term use of chlortetracycline (CTC) on the gut microbiota composition and metabolism profiles in pigs, and the variation of antibiotic resistance genes (ARGs) and microbial communities in faeces and manure during aerobic composting (AC) and anaerobic digestion (AD). The pigs were fed the same basal diet supplemented with or without 75 mg/kg CTC, and fresh faeces of 30-, 60-, 90-, and 120-day-old pigs were collected from the CTC group. The results showed that CTC reduced the diversity of the gut microbiota significantly and changed its structure. Metabolomics analysis of intestinal contents revealed 23 differentially abundant metabolites, mainly organic acids, carbohydrates, and amino acids. Metabolic pathways, such as the TCA cycle, propionate metabolism, and pyruvate metabolism, were changed. From 30 to 120 days of age, the amount of CTC residues in faeces and the abundance of 3 tetracycline resistance genes increased significantly, and it was positively correlated with tetC, tetG, tetW, sul1 and intI2. CTC residue levels and ARGs abundance gradually decreased with fermentation time, and AC was better than AD at reducing ARGs abundance. The results suggest that in-feed CTC can reduce the diversity of the gut microbiota, change the structure, function and metabolism of the bacterial community, and increase the abundance of ARGs in faeces.

Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.

Synergistic effect of lotus seed resistant starch and short-chain fatty acids on mice fecal microbiota in vitro

This study aimed to investigate the synergistic effect of lotus seed resistant starch (LRS) and short-chain fatty acids (SCFAs) on mice fecal bacterial flora and the contents of SCFAs in vitro. Following 24 h of fermentation, 16S rRNA analysis revealed several differences in the fecal microbiota community structure among primal bacteria (PB), LRS and different SCFAs combined with LRS groups (SCFAs-LRS). The LRS group increased the relative abundance of Lactobacillus, Allobaculum, Clostridium, Bacteroides and Prevotella. Among the SCFAs-LRS group, AA-LRS increased the relative abundance of Prevotella, and Bacillus. PA-LRS increased abundance of Sphingomonas and the BA-LRS group significantly increased the relative abundance of Rhizobiales, Brucellaceae and Ochrobactrum. Meanwhile, propionic acid and BA productions significantly increased in the BA-LRS group. The SCFAs-LRS group elicited a beneficial effect on the fecal microbiota by increasing production of SCFAs. We highlight the fact that the combination of LRS and SCFA can increase the contents of SCFAs produced by mice fecal microbiota. In short, the combination of LRS and SCFA can influence intestinal flora by promoting the growth of beneficial bacteria and can serve as new prebiotics for promoting health and disease management.

Distinctive Microbiome Type Distribution in a Young Adult Balinese Cohort May Reflect Environmental Changes Associated with Modernization.

An important public health question is understanding how changes in human environments can drive changes in the gut microbiota that influence risks associated with human health and wellbeing. It is well-documented that the modernization of societies is strongly correlated with intergenerational change in the frequency of nutrition-related chronic diseases in which microbial dysbiosis is implicated. The population of Bali, Indonesia, is well-positioned to study the interconnection between a changing food environment and microbiome patterns in its early stages, because of a recent history of modernization. Here, we characterize the fecal microbiota and diet history of the young adult women in Bali, Indonesia (n = 41) in order to compare microbial patterns in this generation with those of other populations with different histories of a modern food environment (industrialized supply chain). We found strong support for two distinct fecal microbiota community types in our study cohort at similar frequency: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community (p < 0.001, analysis of similarity, Wilcoxon test). Although Type-P individuals had lower alpha diversity (p < 0.001, Shannon) and higher incidence of obesity, multivariate analyses with diet data showed that community types significantly influenced associations with BMI. In a multi-country dataset (n = 257), we confirmed that microbial beta diversity across subsistent and industrial populations was significantly associated with Prevotella and Bacteroides abundance (p < 0.001, generalized additive model) and that the prevalence of community types differs between societies. The young adult Balinese microbiota was distinctive in having an equal prevalence of two community types. Collectively, our study showed that the incorporation of community types as an explanatory factor into study design or modeling improved the ability to identify microbiome associations with diet and health metrics.

Investigating the effects of nitrogen deposition and substrates on the microbiome and mycobiome of the millipede Cherokia georgiana georgiana (Diplopoda: Polydesmida)

Millipedes are ubiquitous soil invertebrates that play major roles in physical and chemical processes in soil. Despite their importance to soil ecology and their presumed interactions with soil microorganisms, little is known about how millipedes influence and are influenced by soil microbes. Furthermore, it is not fully understood how these millipede-microbe interactions are influenced by available soil nitrogen, which is predicted to increase over the foreseeable future with increased anthropogenic production. Here, using the millipede Cherokia georgiana georgiana as a model and using a manipulative mesocosm and metabarcoding approach, we examine (1) the impacts of millipedes on soil microbial communities (fungi and bacteria) with varying nitrogen addition levels, and (2) the temporal impacts of nitrogen on millipede fecal communities (fungi and bacteria). This research demonstrates that millipede presence strongly alters soil communities and that alterations in nitrogen levels do not impact millipede gut communities. This work also provides the first evidence suggesting that millipede gut communities are predominantly derived from soils rather than leaf litter, though both contribute to gut composition. This work advances our current poor understanding of millipede-soil interactions and provides a framework for further investigations to disentangle the interactive effects of substrate, nitrogen, and time to better understand ecological impacts of these interactions.

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.