Gut Diversity Research Articles

Dynamic Spread of Antibiotic Resistance Determinants by Conjugation to a Human-Derived Gut Microbiota in a Transplanted Mouse Model

Background. Antibiotic-resistant (AR) bacteria pose an increasing threat to public health, but the dynamics of antibiotic resistance gene (ARG) spread in complex microbial communities are poorly understood. Conjugation is a predominant direct cell-to-cell mechanism for the horizontal gene transfer (HGT) of ARGs. We hypothesized that commensal Escherichia coli donor strains would mediate the conjugative transfer of ARGs to phylogenetically distinct bacteria without antibiotic selection pressure in gastrointestinal tracts of mice carrying a human-derived microbiota with undetectable levels of E. coli. Our objective was to identify a mouse model to study the factors regulating AR transfer by conjugation in the gut. Methods. Two donor E. coli strains were engineered to carry chromosomally encoded red fluorescent protein, and an ARG- and green fluorescent protein (GFP)-encoding broad host range RP4 conjugative plasmid. Mice were orally gavaged with two donor strains (1) E. coli MG1655 or (2) human-derived mouse-adapted E. coli LM715-1 and their colonization assessed by culture over time. Fluorescence-activated cell sorting (FACS) and 16S rDNA sequencing were performed to trace plasmid spread to the microbiota. Results. E. coli LM715-1 colonized mice for ten days, while E. coli MG1655 was not recovered after 72 h. Bacterial cells from fecal samples on days 1 and 3 post inoculation were sorted by FACS. Samples from mice given donor E. coli LM715-1 showed an increase in cells expressing green but not red fluorescence compared to pre-inoculation samples. 16S rRNA gene sequencing analysis of FACS GFP positive cells showed that bacterial families Lachnospiraceae, Clostridiaceae, Pseudomonadaceae, Rhodanobacteraceae, Erysipelotrichaceae, Oscillospiraceae, and Butyricicoccaceae were the primary recipients of the RP4 plasmid. Conclusions. Results show this ARG-bearing conjugative RP4 plasmid spread to diverse human gut bacterial taxa within a live animal where they persisted. These fluorescent marker strategies and human-derived microbiota transplanted mice provided a tractable model for investigating the dynamic spread of ARGs within gut microbiota and could be applied rigorously to varied microbiotas to understand conditions facilitating their spread.

The Influence of Maternal Diet on Gut Microbiota Diversity During Pregnancy: A Mini-Review

Background: The gut microbiota plays a critical role in maintaining health, influencing nutrient metabolism, immune function, and disease susceptibility. During pregnancy, maternal diet can significantly alter gut microbiota composition and diversity, potentially impacting maternal and fetal health. Methods: This mini-review aims to answer whether maternal diet during pregnancy is associated with the composition and diversity of maternal gut microbiota. A comprehensive literature search was conducted in Embase, Scopus, PubMed, Web of Science, and Cochrane databases in May 2024. A risk of bias assessment was done. Results: Twenty articles were selected, including randomized controlled trials, cohort, cross-sectional, and case-control studies. Which revealed that increased dietary fiber intake was consistently associated with higher gut microbiota richness and diversity. Conversely, high-fat diets were linked to reduced microbial diversity and pro-inflammatory profiles. Dietary interventions such as vegetarian and Mediterranean diets promoted a more diverse and beneficial gut microbiota composition. Conclusion: Maternal diet during pregnancy is closely associated with changes in gut microbiota composition and diversity. These findings underscore the importance of dietary interventions in managing gut microbiota and improving pregnancy outcomes. Future research should focus on personalized nutrition strategies to optimize maternal and fetal health. Key terms: Microbiome; Microbiota; Pregnant women; Diet; Dietary patterns.

Ketogenic diet in psychiatry: application in treating depression among athletes

Depression is a prevalent mental health challenge, particularly in athletes, where the interplay of high-performance demands, physical stress, and injury exacerbates psychological vulnerabilities. Emerging evidence suggests that the ketogenic diet (KD), a high-fat, moderate-protein, and low-carbohydrate dietary intervention, holds therapeutic potential for managing depression. KD induces ketosis, a metabolic state that enhances brain energy metabolism, reduces neuroinflammation, and stabilizes neurotransmitter function, all of which are implicated in the pathophysiology of depression. This review synthesizes findings from recent clinical trials, meta-analyses, and case studies focusing on KD's neurological and psychological effects. The results indicate significant improvements in depressive symptoms, mood stabilization, and mental resilience among individuals adhering to KD. Moreover, KD’s modulation of the gut-brain axis introduces an additional pathway for improving mental health by fostering a diverse gut microbiome and reducing systemic inflammation. For athletes, KD offers dual benefits: alleviating depressive symptoms while supporting cognitive function and recovery. However, adherence to the diet and potential side effects such as fatigue and gastrointestinal discomfort pose challenges. Current research is limited by a lack of large-scale, randomized controlled trials specifically targeting athletic populations. In conclusion, KD demonstrates promise as an adjunctive therapy for depression in athletes. Its multifaceted effects on brain health and performance metrics underscore its potential role in sports psychiatry. Further research is necessary to optimize KD protocols and establish evidence-based guidelines for its clinical application in athletic populations.

The Gut Microbiome in Hyperuricemia and Gout.

Humans develop hyperuricemia via decreased urate elimination and excess urate production, consequently promoting monosodium urate crystal deposition and incident gout. Normally, approximately two thirds of urate elimination is renal. However, chronic kidney disease (CKD) and other causes of decreased renal urate elimination drive hyperuricemia in most with gout. This places more demand on elimination of urate via the gut, where diet, purine metabolism and microbiota intersect. Heritable impairment of urate transport into the gut is common, and promotes hyperuricemia, renal urate overload, and early onset and palpable tophaceous gout phenotypes. Lactobacilli, by sequestering and modifying ambient purines, are being studied for the potential to suppress diet-induced urate generation and associated gout flares. Landmark preclinical studies recently revealed much higher-capacity urate-lowering effects of diverse, obligate and facultative anaerobic human and murine gut microbiota (predominantly of Bacillota phylum) termed purine-degrading bacteria (PDB). A conserved gene cluster in PDB drives urate conversion to lactate or anti-inflammatory short chain fatty acids (SCFA). When mice are rendered deficient in hepatic uricase to mimic human uricase absence, microbiota depletion rapidly elevates both cecal and serum urate, reversible by PDB administration. In healthy human volunteers with normal renal function, antibiotic-induced gut microbiota depletion, decreases the urate-lowering gene cluster unique to PDB and elevates fecal urate. Also, prior exposure to antibiotics with anaerobic coverage has been linked to heightened incident gout risk. Notably, intestinal dysbiosis that includes Bacillota depletion has been observed in gout cohorts. Therefore, the capacity of diverse gut bacterial strains to biochemically compensate for human limits in urate disposition suggests novel probiotic treatment approaches for gout with inadequate pharmacologic control of both flares and hyperuricemia. This is particularly so for severe CKD, which limits the options and maximal doses for use of conventional oral urate-lowering drugs.

Synergistic and off-target effects of bacteriocins in a simplified human intestinal microbiome: implications for Clostridioides difficile infection control

ABSTRACT Clostridioides difficile is a major cause of nosocomial diarrhea. As current antibiotic treatment failures and recurrence of infections are highly frequent, alternative strategies are needed for the treatment of this disease. This study explores the use of bacteriocins, specifically lacticin 3147 and pediocin PA-1, which have reported inhibitory activity against C. difficile. We engineered Lactococcus lactis strains to produce these bacteriocins individually or in combination, aiming to enhance their activity against C. difficile. Our results show that lacticin 3147 and pediocin PA-1 display synergy, resulting in higher anti-C. difficile activity. We then evaluated the effects of these L. lactis strains in a Simplified Human Intestinal Microbiome (SIHUMI-C) model, a bacterial consortium of eight diverse human gut species that includes C. difficile. After introducing the bacteriocin-producing L. lactis strains into SIHUMI-C, samples were collected over 24 hours, and the genome copies of each species were assessed using qPCR. Contrary to expectations, the combined bacteriocins increased C. difficile levels in the consortium despite showing synergy against C. difficile in agar-based screening. This can be rationally explained by antagonistic inter-species interactions within SIHUMI-C, providing new insights into how broad-spectrum antimicrobials might fail to control targeted species in complex gut microbial communities. These findings highlight the need to mitigate off-target effects in complex gut microbiomes when developing bacteriocin-based therapies with potential clinical implications for infectious disease treatment.

Identification of a secreted protease from Bacteroides fragilis that induces intestinal pain and inflammation by cleavage of PAR2.

Protease-activated receptor 2 (PAR2) is a central regulator of intestinal barrier function, inflammation and pain. Upregulated intestinal proteolysis and PAR2-signaling are implicated in inflammatory bowel diseases (IBDs) and irritable bowel syndrome (IBS). To identify potential bacterial regulators of PAR2 activity, we developed a functional assay for PAR2 processing and used it to screen conditioned media from a library of diverse gut commensal microbes. We found that multiple bacteria secrete proteases that cleave host PAR2. Using chemoproteomic profiling with a covalent irreversible inhibitor, we identified a previously uncharacterized Bacteroides fragilis serine protease Bfp1, and showed that it cleaves and activates PAR2 in multicellular and murine models. PAR2 cleavage by Bfp1 disrupts the intestinal barrier, sensitizes nociceptors, and triggers colonic inflammation and abdominal pain. Collectively, our findings uncover Bfp1-mediated PAR2-processing as a new axis of host-commensal-interaction in the gut that has the potential to be targeted for therapeutic intervention in IBD or IBS.

Benefits of a diverse gut microbiome in systemic anti-cancer therapy patients.

Benefits of a diverse gut microbiome in systemic anti-cancer therapy patients.

A gut instinct for childhood leukemia prevention: microbiome-targeting recommendations aimed at parents and caregivers.

Childhood leukemia accounts for 30% of all pediatric cancer cases with acute lymphoblastic leukemia (ALL) being the most common subtype. Involvement of the gut microbiome in ALL development has recently garnered interest due to an increasing recognition of the key contribution the microbiome plays in maintaining the immune system's homeostatic balance. Commensal gut microbiota provide a first line of defense against different pathogens and gut microbiome immaturity has been implicated in ALL pathogenesis. Several environmental factors such as nutrition, mode of delivery, breastfeeding and, early social or livestock contacts are known to alter the composition of the gut microbiota. Variations in these factors influence the risk of childhood leukemia onset. This review aims to elucidate the risk factors influencing microbial composition in the context of childhood ALL. The link between gut microbiome diversity and childhood ALL offers the opportunity to develop risk-reducing strategies that can be communicated to a broad target population of (future) parents and caregivers for childhood leukemia prevention. Here, we summarize evidence on how promoting a diverse gut microbiome in newborns through simple measures such as increasing social contacts early in life may decrease the risk of developing ALL in these children later on.

Artificial Intelligence-Based Target for Personalized Interventions of Atherosclerosis from Gut Microbiota Signature

Atherosclerosis remains a major driver for cardiovascular disease (CVD), despite advancements in traditional risk factor management therapies. Recent evidence emphasizes the crucial role of the gut microbiome in the progression of atherosclerosis and plaque rupture, highlighting a promising therapeutic avenue. This review focuses on the intertwined relationship between the gut microbiome, its metabolites, and atherosclerosis and CVD, also highlighting the potential therapeutic role of probiotics and prebiotics. Given the diverse and unique gut microbiota signatures among individuals, a one-size-fits-all therapeutic approach is unlikely to be effective. Personalized treatment strategies are therefore necessary. Here, we discussed how Artificial Intelligence (AI) can be leveraged to analyze individual gut microbiome profiles from microbiome sequencing, predict treatment response, and optimize therapeutic strategies based on individual patients, which would significantly improve outcomes of the treatment for atherosclerosis patients.

Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom.

The human gut microbiome contains many bacterial strains of the same species ("strain-level variants") that shape microbiome function. The tremendous scale and molecular resolution at which microbial communities are being interrogated motivates addressing how to describe strain-level variants. We introduce the "Spectral Tree"-an inferred tree of relatedness built from patterns of co-evolutionary constraint between greater than 7,000 diverse bacteria. Using the Spectral Tree to describe over 600 diverse gut commensal strains that we isolated, whole-genome sequenced, and metabolically profiled revealed (1) widespread phylogenetic structure among strain-level variants, (2) the origins of subspecies phylogeny as a shared history of phage infections across humans, and (3) the key role of inter-human strain variation in predicting strain-level metabolic qualities. Overall, our work demonstrates the existence and metabolic importance of structured phylogeny below the level of species for commensal gut bacteria, motivating a redefinition of individual strains according to their evolutionary context. A record of this paper's transparent peer review process is included in the supplemental information.

Can Gut Microbiota Analysis Reveal Clostridioides difficile Infection? Evidence from an Italian Cohort at Disease Onset.

A diverse and well-functioning gut microbiota normally serves as a protective shield against the invasion of harmful bacteria or the proliferation of opportunistic pathogens. Clostridioides difficile infection (CDI) is predominantly associated with the overuse of antibiotics, resulting in a significant alteration in the gut's microbial balance. Unfortunately, the lack of global standardization does not allow for the identification of a set of biomarkers associated with the onset and progression of this disease. In this study, we examined the composition of the gut microbiota in patients at the time of the initial detection of CDI compared to a control group of CDI-negative individuals, with a focus on identifying potential CDI biomarkers for diagnosis. While no significant differences in the alpha and beta diversity between CDI-negative and CDI-positive individuals were found, we found that certain genera (such as Clostridium XIVa and Clostridium XVIII) showed different abundance patterns in the two groups, indicating potential differences in gut microbiota balance. In conclusion, am enrichment in Clostridium XI and a decrease in Faecalibacterium emerged in the CDI-positive patients and following antibiotic treatment, indicating that changes in the Clostridium/Faecalibacterium ratio may be a promising biomarker that warrants further investigation for CDI diagnosis.

Disruption of the gut microbiota-inflammation-brain axis in unmedicated bipolar disorder II depression

The relationships of the gut microbiota-inflammation-brain axis in depressive bipolar disorder (BD) remains under-elaborated. Sixty-five unmedicated depressive patients with BD II and 58 controls (HCs) were prospectively enrolled. Resting-state functional MRI data of static and dynamic amplitude of low-frequency fluctuation (ALFF) was measured, and abnormal ALFF masks were subsequently set as regions of interest to calculate whole-brain static functional connectivity (sFC) and dynamic functional connectivity (dFC). Fecal samples were collected to assess gut diversity and enterotypes using 16S amplicon sequencing. Blood samples were also collected, serum was assayed for levels of cytokines (interleukin [IL]-2, IL-4, IL-6, IL-8, IL-10, tumor necrosis factor [TNF]-α). Patients with BD II exhibited decreased static ALFF values in the left cerebellum Crus II, and decreased cerebellar sFC and dFC to the right inferior parietal lobule and right superior frontal gyrus, respectively. Moreover, higher pro-inflammatory and anti-inflammatory cytokines levels, and increased proinflammatory bacteria and glutamate and gamma-aminobutyric acid metabolism related bacteria were identified in BD II. The interaction of Parabacteroides levels × IL-8 levels was an independent contributor to static ALFF in the left cerebellar Crus II. The findings bridged a gap in the underlying pathophysiological mechanism of the gut microbiota-inflammation-brain axis in BD II depression.

The Relationship Between Soil and Gut Microbiota Influences the Adaptive Strategies of Goitered Gazelles in the Qaidam Basin.

The gut microbiota is integral to the health and adaptability of wild herbivores. Interactions with soil microbiota can shape the composition and function of the gut microbiota, thereby influencing the hosts' adaptive strategies. As a result, soil microbiota plays a pivotal role in enabling wild herbivores to thrive in extreme environments. However, the influence of soil microbiota from distinct regions on host's gut microbiota has often been overlooked. We conducted the first comprehensive analysis of the composition and diversity of gut and soil microbiota in goitered gazelles across six regions in the Qaidam Basin, utilizing source tracking and ecological assembly process analyses. Significant differences were observed in the composition and diversity of soil and gut microbiota among the six groups. Source tracking analysis revealed that soil microbiota in the GangciGC (GC) group contributed the highest proportion to fecal microbiota (8.94%), while the Huaitoutala (HTTL) group contributed the lowest proportion (1.80%). The GC group also exhibited the lowest α-diversity in gut microbiota. The observed differences in gut microbial composition and diversity among goitered gazelles from six regions in the Qaidam Basin were closely tied to their adaptive strategies. Ecological assembly process analysis indicated that the gut microbiota were primarily influenced by stochastic processes, whereas deterministic processes dominated most soil microbial groups. Both the differences and commonalities in gut and soil microbiota play essential roles in enabling these gazelles to adapt to diverse environments. Notably, the utilization pattern of soil microbiota by gut microbiota did not align with regional trends in gut microbial α-diversity. This discrepancy may be attributed to variations in environmental pressures and the gut's filtering capacity, allowing gazelles to selectively acquire microbiota from soil to maintain homeostasis. This study highlights the significant regional variation in gut and soil microbiota diversity among goitered gazelle populations in the Qaidam Basin and underscores the critical role of soil-derived microbiota in their environmental adaptation.

Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.

The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where pediatric antibiotic consumption is exceptionally common. We characterized the effects of antibiotics commonly used by Peruvian children (i.e., amoxicillin, azithromycin, cefalexin, sulfa-trimethoprim) on gut diversity, genera, and antibiotic resistance gene (ARG) abundance from 3-16 months. This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-2019. Stool collected at 3, 6, 7, 9, 12, and 16 months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40,662 observations) to tabulate the number of antibiotic courses consumed in the 30 days prior to stool sampling. Using linear mixed models, the association of recent antibiotic use with species richness, diversity, gut genera, and ARG abundance over time was examined. Most children were vaginally delivered (73%), received breastmilk almost daily over the study period, and belonged to socioeconomically diverse households. Amoxicillin, azithromycin, cefalexin, and sulfa-trimethoprim did not impact gut diversity or genera abundance. Azithromycin use significantly impacted ARGs from the macrolide, aminoglycoside, and folate pathway antagonist classes. Amoxicillin use significantly increased total ARGs. Antibiotics' effects on ARGs appeared to be independent of gut microbiome changes. Common antibiotics like amoxicillin and azithromycin may be key drivers of the gut resistome but not the microbiome during early childhood in this setting with frequent breastfeeding.

Rurality and relative poverty drive acquisition of a stable and diverse gut microbiome in early childhood in a non-industrialized setting.

There are limited longitudinal data from non-industrialized settings on patterns and determinants of gut bacterial microbiota development in early childhood. We analysed epidemiological data and stool samples collected from 60 children followed from early infancy to 5 years of age in a rural tropical district in coastal Ecuador. Data were collected longitudinally on a wide variety of individual, maternal, and household exposures. Extracted DNA from stool samples were analyzed for bacterial microbiota using 16S rRNA gene sequencing. Both alpha and beta diversity indices suggested stable profiles towards 5 years of age. Greater alpha diversity and lower beta diversity were associated with factors typical of rural poverty including low household incomes, overcrowding, and greater agricultural and animal exposures, but not with birth mode or antibiotic exposures. Consumption of unpasteurized milk was consistently associated with greater alpha diversity indices. Infants living in a non-industrialized setting in conditions of greater poverty and typically rural exposures appeared to acquire more rapidly a stable and diverse gut bacterial microbiome during childhood.

Different artificial feeding strategies shape the diverse gut microbial communities and functions with the potential risk of pathogen transmission to captive Asian small-clawed otters (Aonyx cinereus).

Captive otters fed with different diets possessed distinct gut microbial communities and functions, with the enrichment of several pathogens and multiple resistance genes in their gut microbiota. The current artificial feeding strategies had the possibility to accelerate the colonization and proliferation of various pathogenic bacteria in the intestines of otters and the spread of resistance genes, increasing the risk of diseases. In addition, supplementation with commercial cat food had benefits for otters' intestinal fermentation and the metabolism of gut microbiota.

Lifestyle and the Gut-Brain Axis Insights into Mental Health and Microbiome Interactions

Introduction: The intricate relationship between lifestyle factors and gut health has become a focus of recent research, emphasizing the significant role of the gut-brain axis (GBA) in regulating both physical and emotional well- being. Unhealthy lifestyle choices, including a diet high in ultra-processed foods, irregular sleep patterns, physical inactivity, and substance abuse, have been closely associated with gut dysbiosis, leading to gastrointestinal (GI) symptoms and mood disturbances such as anxiety and depression. The gut microbiota, through the production of neurotransmitters like serotonin and dopamine, as well as short-chain fatty acids (SCFAs), influences mood and mental health via the GBA. Maintaining a healthy lifestyle, characterized by balanced nutrition, regular physical activity, and good sleep quality, is critical in fostering a diverse and stable gut microbiome, which in turn supports emotional stability.  Aim: This review aims to examine the existing literature on the impact of lifestyle factors, such as diet, physical activity, sleep, smoking, alcohol consumption, and stress management, on gut health and emotional well-being. The goal is to highlight the importance of gut microbiota in mental health and the potential therapeutic strategies to enhance gut health for improved emotional outcomes.  Methodology: A comprehensive search of peer-reviewed journal articles was conducted using databases such as PubMed, Google Scholar, and Web of Science. Keywords like "lifestyle," "gut health," "emotional well-being," "dietary habits," "physical activity," "sleep patterns," and "gut-brain axis" were used to identify relevant studies. Inclusion criteria focused on human clinical trials and observational studies published within the last 16 years. Studies involving animal subjects, non-peer- reviewed articles, and outdated research were excluded.  Results: The literature shows that diets high in fiber and low in processed foods support a healthier gut microbiome, while high consumption of ultra-processed foods disrupts gut bacteria, leading to GI symptoms and mood disorders. Regular physical activity was found to enhance gut microbiota diversity, contributing to better emotional well-being. Conversely, poor sleep quality and chronic stress were linked to gut dysbiosis, which exacerbated mood disturbances. Smoking and excessive alcohol consumption further damaged gut health, contributing to mood dysregulation. Probiotic and prebiotic interventions, particularly synbiotics, were found to restore gut balance and improve both GI and mental health outcomes.  Conclusion: This review underscores the pivotal role of lifestyle choices in shaping gut health and emotional well-being. A balanced diet, regular exercise, sufficient sleep, and stress management are essential for maintaining a healthy gut microbiome, which, in turn, supports emotional stability. Therapeutic strategies involving prebiotics, probiotics, and synbiotics offer promising avenues for improving both gut health and mood. Addressing lifestyle factors and promoting gut health can potentially serve as an effective approach for enhancing overall well-being and preventing mood disorders.

Stability in fecal metabolites amid a diverse gut microbiome composition: a one-month longitudinal study of variability in healthy individuals

ABSTRACT An extensive network of microbial-host interactions exists in the gut, making the gut microbiome a complex ecosystem to untangle. The microbial composition and the fecal metabolites are important readouts to investigate intricate microbiota-diet-host interplay. However, this ecosystem is dynamic, and it is of interest to understand the degree and timescale of changes occurring in the gut microbiota, during disease as well as in healthy individuals. Cross-sectional study design is often used to investigate the microbiome, but this design provides a static snapshot and cannot provide evidence on the dynamic nature of the gut microbiome. Longitudinal studies are better suited to extrapolate causation in a study or assess changes over time. This study investigates longitudinal change in the gut microbiome and fecal metabolites in 14 healthy individuals with weekly sampling over a period of one-month (four time points), to elucidate the temporal changes occurring in the gut microbiome composition and fecal metabolites. Utilizing 16S rRNA amplicon sequencing for microbiome analysis and NMR spectroscopy for fecal metabolite characterization, we assessed the stability of these two types of measurable parameters in fecal samples during the period of one month. Our results show that the gut microbiome display large variations between healthy individuals, but relatively lower within-individual variations, which makes it possible to uniquely identify individuals. The fecal metabolites showed higher stability over time compared to the microbiome and exhibited consistently smaller variations both within and between individuals. This relative higher stability of the fecal metabolites suggests a balanced, consistent output even amid individual’s differences in microbial composition and they can provide a viable complementary readout to better understand the microbiome activity.

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

Low-abundance members of microbial communities are difficult to study in their native habitats, including Escherichia coli, a minor but common inhabitant of the gastrointestinal tract, and key opportunistic pathogen of the urinary tract. While multi-omic analyses have detailed interactions between uropathogenic Escherichia coli (UPEC) and the bladder mediating urinary tract infection (UTI), little is known about UPEC in its pre-infection reservoir, the gastrointestinal tract, partly due to its low relative abundance (<1%). To sensitively explore the genomes and transcriptomes of diverse gut E. coli, we develop E. coli PanSelect, which uses probes designed to specifically capture E. coli’s broad pangenome. We demonstrate its ability to enrich diverse E. coli by orders of magnitude, in a mock community and in human stool from a study investigating recurrent UTI (rUTI). Comparisons of transcriptomes between gut E. coli of women with and without history of rUTI suggest rUTI gut E. coli are responding to increased oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of in vivo E. coli biology in other low-abundance environments, and the framework described here has broad applicability to other diverse, low-abundance organisms.

Comparative analysis of the intestinal microbiota diversity in wild and farmed Gryllus bimaculatus

Abstract This study aims to investigate the structure and diversity of the intestinal microbiome of Gryllus bimaculatus from wild and farmed environments. Additionally, we sought to identify the core microbes to get information on the microbial diversity of the gut microbiome to the farm condition. We analyzed the microbial community diversity in intestinal samples of both wild and farmed G. bimaculatus using high-throughput sequencing of 16S rRNA gene and ITS rRNA amplicons. Using the PICRUSt2 software, we predicted the functional capabilities of bacterial communities. The analysis indicated significant differences in the diversity of the microbial communities (bacteria) within the gut of crickets under farmed and wild conditions, with notably higher bacterial diversity observed in the gut of farmed crickets compared to those in the wild. The gut bacterial communities exhibited significant similarity across the two conditions, and the variations in diversity are primarily influenced by species with low abundance. Genus-level analysis revealed that the abundance of pathogens, including genera Listeria, Staphylococcus, and Candida, was significantly higher in the gut microbiota of farmed crickets than in the wild ones. By identifying core genera (present in over 80% of the samples), we discovered 19 bacterial genera and 1 fungal genus. The core bacterial genera constituted 60.35% and 87.10% of the cricket’s gut bacterial abundance in farmed and wild environments, respectively. The functional prediction analysis performed using PICRUSt2 identified a significant increase of pathways about “Terpenoids and polyketides metabolism”, and “Infectious disease: bacterial” in the farmed group; as well as a significant decrease in pathways about “Environmental adaptation”, “Development and regeneration”, and the “Nervous system”, compared to the wild group. In conclusion our results showed that the gut microbial community of the G. bimaculatus could be influenced by its environment and diet. However, this influence is primarily manifested in the variation of low-abundance genera, with the gut microbial community remains dominated by a few microbial groups. Therefore, it is speculated that the combination of core and edge species in the gut microbial community of the G. bimaculatus may constitute an effective strategy that not only maintains the core functions of the community but also adapts to environmental changes through the diversity of edge species. The high population density and excessive feeding in the farmed condition could have allowed for the creation of a more diverse gut microbiota for G. bimaculatus, including potential pathogens. Therefore, when breeding G. bimaculatus, the environmental hygiene management should be strengthened to reduce the carrying and transmission of pathogens.