Evolution of mammals and their gut microbes

Novel insight into the impact of black soldier fly larvae meal and protease on cecal microbiome, SCFAs, and excreta composition in laying hens

BACKGROUND

Insect farming represents a sustainable loop that recycles organic wastes back to the food chain while requiring minimal inputs such as land and water. Insect products are not only low in environment footprint, but also nutrient-dense and contain health-promoting bioactives. Black soldier fly larvae meal (BSFLM) stands out as an excellent source of protein and chitin, and the latter is a polysaccharide associated with promoting gut health. A 20-week feeding trial evaluated the effects of three dietary inclusion levels of BSFLM (0%, 6.5%, and 13%), with and without protease enzyme (Concentrase-P) supplementation, on two commercial laying hen strains: Lohmann Brown-Lite (brown hens) and Lohmann LSL-Lite White (white hens). The two strains of 52-week-old hens (mean weight = 2.2 kg) were housed in one production room, with each strain distributed across 36 conventional cages (5 birds per cage). Each treatment was randomly assigned to six cages (n = 6). At the end of the trial, cecal microbiome, SCFA production and excreta composition were studied.

RESULTS

White hens exhibited a distinct cecal microbiome compared to brown hens (p < 0.05), characterized by enhanced diversity, increased relative abundance of Actinobacteriota, and an altered cecal SCFA profile with increased butyric acid and reduced acetic acid levels (p < 0.05). Independent from strain, both 6.5% and 13% BSFLM inclusion promoted cecal microbial richness and evenness, shifting the community to produce more acetic acid and less butyric acid (p < 0.05). Excreta analysis showed significantly higher concentrations and daily excretion of nitrogen, ammoniacal nitrogen and non-ammoniacal nitrogen in both strains on the 13% BSFLM diet. Concentrase-P supplementation effectively ameliorated the elevated nitrogen and ammoniacal nitrogen excretion linked to the 13% BSFLM diet, despite having minimal effects on the cecal microbiome and SCFA production.

CONCLUSION

Our study provides a novel perspective on the enhanced cecal microbiome diversity in laying hens fed high levels of BSFLM, linking it to suboptimal protein digestion and an undesired increase in protein fermentation, which we have demonstrated can be partially addressed by protease supplementation. Our findings highlight the need to consider interactions between host nutrition, gut microbiome, and sustainability when evaluating novel feed ingredients.

Host-Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban-Rural Ecotone

Global change and urbanisation profoundly alter wildlife habitats, driving native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are shaped by host traits and environmental features, but little is known about their plasticity in co-occurring native and invasive species across urban-rural gradients. Here, we explored gut microbiomes of four sympatric small mammal species along an urban-rural ecotone in Borneo, one of the planet's oldest rainforest regions experiencing recent urban expansion. Host species identity was the strongest determinant of microbiome composition, while land use and spatial proximity shaped microbiome similarity within and among the three rat species. The urban-dwelling rat Rattus rattus had a microbiome composition more similar to that of the native, urban-adapted rat Sundamys muelleri (R. rattus' strongest environmental niche overlap), than to the closely related urban-dwelling R. norvegicus. The urban-dwelling shrew Suncus murinus presented the most distinct microbiome. The microbiome of R. norvegicus was the most sensitive to land use intensity, exhibiting significant alterations in composition and bacterial abundance across the ecotone. Our findings suggest that environmental niche overlap among native and invasive species promotes similar gut microbiomes. Even for omnivorous urban-dwellers with a worldwide distribution like R. norvegicus, gut microbiomes may change across fine-scale environmental gradients. Future research needs to confirm whether land use intensity can be a strong selective force on mammalian gut microbiomes, influencing the way in which native and invasive species are able to exploit novel environments.

Characteristic gene expression profile of intestinal mucosa early in life promotes bacterial colonization leading to healthy development of the intestinal environment

The gut microbiome early in life plays a crucial role in development of the host and affects health throughout life. The definition of a healthy microbiome early in life has not been established, and the underlying mechanism of how a young host selects appropriate microbes for colonization remains unclear. Understanding the mechanism may provide insights into novel preventive and therapeutic strategies by correcting dysbiosis early in life. We employed germ-free mice early in life (4 weeks of age) and later in life (10 weeks of age) for fecal microbiota transfer (FMT) from specific pathogen-free mice. We performed age-unmatched FMT between recipients early in life and donors early or later in life, in addition to common age-matched FMT. Age-matched FMT resulted in significantly different bacterial compositions between recipients early vs. later in life. When the gut microbiome from donors early or later in life was transferred to recipients early in life, bacterial compositions of recipients from donors later in life were similar to those of recipients from donors early in life. This finding suggests that the host early in life has mechanisms to select microbes appropriate for age from the exposed microbiome. We hypothesized that the age-specific intestinal environment promotes age-appropriate intestinal microbiome colonization and examined gene expression in the intestinal mucosa of germ-free mice. We observed that gene expression profiles were different between early vs. later in life. Correlation analysis demonstrated that genera Lachnospiraceae NK4A136 group and Roseburia were positively correlated to genes expressed predominantly early in life, but negatively with genes expressed predominantly later in life. We confirmed that the relative abundance of these genera was significantly higher in specific pathogen-free mice early in life compared with mice later in life. The characteristic gene expression of the intestinal mucosa early in life might play roles in selecting specific bacteria in the intestinal microbiome early in life.

High-fertility sows reshape gut microbiota: the rise of serotonin-related bacteria and its impact on sustaining reproductive performance

BACKGROUND

Compelling evidence has established a strong link between the gut microbiota and host reproductive health. However, the specific regulatory roles of individual bacterial species on reproductive performance are not well-understood. In the present study, Jinhua sows with varying reproductive performances under the same diet and management conditions were selected to explore potential mechanisms on the intricate relationship between the gut microbiome and host reproductive performance using 16S rRNA sequencing, metagenomics and serum metabolomics.

RESULTS

Our findings revealed that the KEGG pathways for base excision repair and DNA replication were enriched, along with gene-level enhancements in spore formation, in sows with higher reproductive performance, indicating that the gut microbiome experiences stress. Further analysis showed a positive correlation between these changes and litter size, indicating that the host acts as a stressor, reshaping the microbiome. This adaptation allows the intestinal microbes in sows with high reproductive performance to enrich specific serotonin-related bacteria, such as Oxalobacter formigenes, Ruminococcus sp. CAG 382, Clostridium leptum, and Clostridium botulinum. Subsequently, the enriched microbiota may promote host serotonin production, which is positively correlated with reproductive performance in our study, known to regulate follicle survival and oocyte maturation.

CONCLUSION

Our study provides a theoretical basis for understanding the interactions between gut microbes and the host. It highlights new insights into reassembling gut microbiota in sows with higher litter sizes and the role of serotonin-related microbiota and serotonin in fertility.

A relationship between body size and the gut microbiome suggests a conservation strategy

A key goal of conservation is to protect the biodiversity of wild species to support their continued evolution and survival. Conservation practice has long been guided by genetic, ecological, and demographic indicators of risk. Cope's rule suggests that species tend to evolve larger body sizes over time. Here, we provide strong evidence to support the inclusion of body size when formulating wildlife conservation strategies. The gut microbiome can mirror the physiological and environmental adaptation status of the host. This study established a connection between body size and the gut microbiome in the Felidae family using 70 fecal samples collected from 18 individuals through metagenomic data analysis and mining metagenome-assembled genomes (MAGs). Two enterotypes were identified in the Felidae gut: Bacteroides and Clostridium. Medium-sized felids predominantly harbored Clostridium, associated with pathogenicity, whereas large and small felids harbored both beneficial Bacteroides and pathogenic Clostridium. Species that evolved larger body sizes over time exhibited distinct changes in gut microbial communities, such as enhanced nutrient extraction and metabolic capabilities. Larger felids exhibited a more diverse, stable gut microbiome engaged in metabolic processes and extensive host interactions, indicating an evolved functional role in various biological processes. Conversely, that of smaller felids is less diverse, with more viruses and pathogenic elements primarily involved in chemical synthesis. These findings provide essential insights for developing conservation strategies that consider the nutritional needs of different-sized feline species, control the transmission of pathogens, and allocate resources based on their unique gut microbiome characteristics.IMPORTANCEBody size is a fundamental trait that varies greatly among taxa and has important implications for life history and ecology. Cope's rule suggests that species tend to evolve larger body sizes over time. However, its correlation to body size evolution remains unclear. This study aimed to establish a connection between body size and the gut microbiome in the Felidae family through metagenomic data analysis. Our results support Cope's rule, illustrating that increased body size correlates with shifts in the gut microbiome, enhancing survival and adaptability.

Differences in rectal fecal microbes among Hu sheep, Tibetan sheep, and their hybrid breeds and their relationship with growth traits

Variety and diversity serve as the foundation for animal husbandry development. Nowadays, heterosis is often used to improve animal performance and increase economic benefits. The intestine is an important organ for nutrient absorption and is also the largest immune organ in the body. Intestinal microorganisms can be influenced by various factors such as animal growth and development stages, gender, health status, feed nutrition level, and host genetic background, among others. In this study, three strains of male sheep, with no significant differences in initial weight at 6 months old, were raised under the same conditions until they reached 9 months of age. We collected the rectal feces of these 9-month-old sheep and compared the differences in rectal fecal microorganisms among the three strains using 16S rDNA sequencing technology. The permutational multivariate analysis of variance test revealed significant differences in microorganisms among different strains. Additionally, we identified six biomarkers in Tibetan sheep and Hu sheep, respectively. Functional enrichment analysis showed that microorganisms may affect the growth traits of sheep through lipid metabolism, and the functional differences among different strains were obvious. Therefore, we believe that crossbreeding can result in the offspring obtaining intestinal microorganisms from their parents to varying degrees, and host heredity is the primary cause of the intestinal microorganism differences.

IMPORTANCE

In this study, we identified parental biomarkers by exploring the relationship between parental and hybrid offspring and concluded that these biomarkers may affect related growth traits through fat deposition or lipid metabolism pathways. We also found that hybrid sheep inherited rectal fecal microbes from their parents to varying degrees.

Beneficial effect of consuming milk containing only A2 beta-casein on gut microbiota: A single-center, randomized, double-blind, cross-over study

Cow milk contains essential nutrients, with β-casein existing in A1 and A2 forms. Studies suggest that A2 milk (containing only A2 β-casein) may offer gastrointestinal (GI) benefits compared to A1/A2 milk (containing both forms). This study investigated the effects of A2 milk consumption on the gut microbiota of South Korean cohort experiencing GI discomfort after consuming A1/A2 milk. Thirty-five participants with GI discomfort after milk consumption were included. Stool DNA was analyzed using 16S rRNA gene sequencing before and after consuming either A1/A2 or A2 milk. Beta diversity analysis using the generalized UniFrac distance method revealed a significant shift in gut microbiota composition after A2 milk consumption (p = 0.04), but no significant change after consuming A1/A2 milk. Significant differences in gut microbiota composition were found between A1/A2 and A2 milk drinkers after milk consumption (p = 0.031). Alpha diversity indices remained unchanged. Notable increases in beneficial microbes, including Bifidobacterium and Blautia, were observed after A2 milk intake. Linear discriminant analysis Effect Size (LEfSe) analysis identified significant enrichment of Actinobacteria, particularly Bifidobacterium longum and Blautia wexlerae, in the A2 group. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis highlighted enriched transport systems related to energy, peptides, sugars, and raffinose family oligosaccharides in the A2 group. Spearman correlation showed significant associations between Bifidobacterium, Blautia, and enhanced transport systems exclusively in the A2 group. Two weeks of A2 milk consumption led to significant alterations in gut microbiota, promoting beneficial microbes and related functions. A2 milk could be a suitable alternative for subjects who experience milk-intake-related GI discomfort.

Gut Microbiota: An Immersion in Dysbiosis, Associated Pathologies, and Probiotics

The importance of the microbiome, particularly the gut microbiota and its implications for health, is well established. However, an increasing number of studies further strengthen the link between an imbalanced gut microbiota and a greater predisposition to different diseases. The gut microbiota constitutes a fundamental ecosystem for maintaining human health. Its alteration, known as dysbiosis, is associated with a wide range of conditions, including intestinal, metabolic, immunological, or neurological pathologies, among others. In recent years, there has been a substantial increase in knowledge about probiotics-bacterial species that enhance health or address various diseases-with numerous studies reporting their benefits in preventing or improving these conditions. This review aims to analyze the most common pathologies resulting from an imbalance in the gut microbiota, as well as detail the most important and known gut probiotics, their functions, and mechanisms of action in relation to these conditions.

Investigation of the genetic diversity of gut mycobiota of the wild and laboratory mice

Mice are colonized by diverse gut fungi, known as the mycobiota, which have received much less attention than bacterial microbiota. Here, we studied the diversities and structures of cecal fungal communities in wild (Lasiopodomys brandtii, Apodemus agrarius, and Microtus fortis) vs laboratory C57BL/6J mice to disentangle the contributions of gut fungi to the adaptation of mice to genetic diversity. Using ITS1 gene sequencing, we obtained 2,912 amplicon sequence variants (ASVs) and characterized the composition and diversity of cecal mycobiota in mice. There were significant differences in the composition of cecal fungal communities between wild and C57BL/6J mice, with more species diversity and richness of fungi in wild mice than C57BL/6J mice. We cultured 428 fungal strains from the cecal mycobiota, sequenced the whole genome of 48 selected strains, and identified 500,849 genes. Functional annotation analysis revealed multiple pathways related to energy metabolism, carbohydrate metabolism, fatty acid metabolism, and enzymes involved in the degradation of polysaccharides, lipids, and proteins, and secondary metabolite biosynthesis. The functions and abundance of Hypocreales and Pleosporales, which included the majority of the crucial metabolic pathways, were significantly higher in wild mice than in C57BL/6J mice. The results suggest that variations in the fungal community composition may relate to the adaptability of mice to their environmental habitats.

IMPORTANCE

In this study, we analyzed the fungal microbiota of three wild mouse species alongside laboratory mice using ITS1 amplicon sequencing. By integrating whole-genome sequencing with culturomics, we sequenced the genomes of 48 fungi isolated from cultured strains and investigated their biological functions to understand the role of intestinal fungi in the environmental adaptability of wild mice. This investigation has expanded the functional gene repository of gut fungi and shed new light on the intricate interplay between mice and their gut fungal communities. The data offer valuable insight into the ecological adaptation in wild mice, emphasizing the complex and dynamic relationship between the murine hosts and their mycobiota.

Short-term effects of a synbiotic diet on thyroid and sex hormones in Sarabi Dogs

BACKGROUND

Synbiotic products are those Functional foods/feeds that contain both probiotic and prebiotic strains and have health-promoting effects beyond probiotics or prebiotics alone. This study aimed to investigate the effect of synbiotic feed containing the probiotic strain Lactobacillus acidophilus La5 (1012 cfu/g) and inulin (5%) on changes in Thyroid hormones (T3, T4), TSH, LH, FSH, and Testosterone in male dogs throughout 24 days.

MATERIALS AND METHODS

In addition to the basic feed, the dogs in the treatment group also received the synbiotic supplement at 5% in each of their three meals during 24 days. Then, the serum levels of LH, FSH, TSH, and Testosterone were measured with an ELISA kit and finally, the obtained data were statistically analyzed.

RESULTS

The results showed that the consumption of this formulated synbiotic feed had no negative effect on the profile of Thyroid hormones (T3: from 1.09 ± 0.51 to 0.95 ± 0.40 ng/ml [p > 0.05]; and T4: from 6.60 ± 4.33 to 4.70 ± 4.29 µg/dl [p > 0.05]) as well as TSH (from 0.07 ± 0.09 to 0.03 ± 0.00 mIU/L [p > 0.05]), Testosterone (from 1.56 ± 0.66 to 1.26 ± 0.93 ng/ml [p > 0.05]), FSH (from 4.72 ± 1.12 to 11.55 ± 3.42 mIU/ml [p = 0.008]), LH (from 0.56 ± 0.48 to 0.31 ± 0.15 mIU/ml [p > 0.05]), and the changes in the amounts of these hormones was in the normal range during 24 days.

CONCLUSION

It concluded that the consumption of synbiotic feed (L. acidophilus + inulin, at the rate of 5%) in male dogs has no significant adverse effects were observed within the study period on Thyroid, TSH, and sex hormones and it seems that it may be used for a long time to take health-promoting effects without harming hormonal activities.

Range-Wide Assessment of the Tasmanian Devil Gut Microbiome

The gut microbiome is an important component of host health and function and is influenced by internal and external factors such as host phylogeny, age, diet, and environment. Monitoring the gut microbiome has become an increasingly important management tool for wild populations of threatened species. The Tasmanian devil (Sarcophilus harrisii) is the largest extant carnivorous marsupial from the island state of Tasmania, Australia. Devils are currently endangered due to devil facial tumor disease. Previous assessments have shown differences between captive and wild devil gut microbiomes and changes during translocations. However, wild gut microbiome variability across Tasmania and the drivers of these differences are not well understood. We conducted a range-wide assessment of gut microbiomes at 10 locations across Tasmania, via 16S rRNA sequencing, and tested the influence of diet (12S vertebrate sequencing), location, sex, and cohort. We show that the five most abundant phyla and genera were consistent across all 10 locations. Location, cohort, and sex impacted bacterial richness, but location did not impact diversity. While there were differences in diet across the state, there was no strong evidence of differences between juveniles and adults, nor between males and females. Contrary to our hypothesis, the vertebrate diet explained a small amount of variation in microbial communities. We suspect that other variables, such as environmental factors and immune system development, may have a stronger influence on gut microbiome variability. Dietary components missed by our 12S primer, including invertebrates and plants, may also contribute to these patterns. Adjustments to dietary supplementation are not recommended when preparing devils for translocation to different sites. Future research should prioritize collecting environmental samples for microbial analysis and integrating metabolomics to elucidate functional differences associated with Tasmanian devil gut microbiome variability.

Intestinal luminal anion transporters and their interplay with gut microbiome and inflammation

The intestine, as a critical interface between the external environment and the internal body, plays a central role in nutrient absorption, immune regulation, and maintaining homeostasis. The intestinal epithelium, composed of specialized epithelial cells, harbors apical anion transporters that primarily mediate the transport of chloride and bicarbonate ions, essential for maintaining electrolyte balance, pH homeostasis, and fluid absorption/secretion. In addition, the intestine hosts a diverse population of gut microbiota that plays a pivotal role in various physiological processes including nutrient metabolism, immune regulation, and maintenance of intestinal barrier integrity, all of which are critical for host gut homeostasis and health. The anion transporters and gut microbiome are intricately interconnected, where alterations in one can trigger changes in the other, leading to compromised barrier integrity and increasing susceptibility to pathophysiological states including gut inflammation. This review focuses on the interplay of key apical anion transporters including Down-Regulated in Adenoma (DRA, SLC26A3), Putative Anion Transporter-1 (PAT1, SLC26A6), and Cystic Fibrosis Transmembrane Conductance Regulator [CFTR, ATP-binding cassette subfamily C member 7 (ABCC7)] with the gut microbiome, barrier integrity, and their relationship to gut inflammation.

Variable phylosymbiosis and cophylogeny patterns in wild fish gut microbiota of a large subtropical river

The persistence and specificity of fish host-microbial interaction during evolution is an important part of exploring the host-microbial symbiosis mechanism. However, it remains unclear how the environmental and host factors shape fish host-microbe symbiotic relationships in subtropical rivers with complex natural environments. Freshwater fish are important consumers in rivers and lakes and are considered keystone species in maintaining the stability of food webs there. In this study, patterns and mechanisms shaping gut microbiota community in 42 fish species from the Pearl River, in the subtropical zone of China, were investigated. The results showed that fish host specificity is a key driver of gut microbiota evolution and diversification. Different taxonomic levels of the host showed different degrees of contribution to gut microbiota variation. Geographical location and habitat type were the next most important factors in shaping gut microbiota across the 42 fishes, followed by diet and gut trait. Our results emphasized the contribution of stochastic processes (drift and homogenizing dispersal) in the gut microbial community assembly of freshwater fishes in the middle and lower reaches of the Pearl River. Phylosymbiosis is evident at both global and local levels, which are jointly shaped by complex factors including ecological or host physiological filtration and evolutionary processes. The core microbiota showed co-evolutionary relationships of varying degrees with different taxonomic groups. We speculate that host genetic isolation or habitat variation facilitates the heterogeneous selection (deterministic process), which occurs and results in different host-core bacterium specificity.

IMPORTANCE

Freshwater fish are regarded as the dominant consumers in rivers and lakes. Due to their diverse feeding modes, fish significantly enhance the trophic link and nutrient recycling/retention in aquatic habitats. For this, they are often considered keystone species in maintaining the stability of food webs in rivers and lakes. A significant part of fish nutrition is essentially mediated by their gut microbiota, which can enhance fish tolerance to fluctuations in external resources and improve the efficiency of nutrients extracted from various food sources. As gut bacterial symbionts have a profound impact on the nutrition and development of their hosts, as well as their overall fitness, it is critical to answer the question of how hosts maintain these benefits by procuring or inheriting these vital symbionts, which is still largely unanswered, especially for freshwater fish. Our study provides new insights into the co-evolutionary relationship between wild fish and their symbiotic microbiome, the hidden diversity of gut microbiome, and the ecological adaptation potential of wild freshwater fish.

Effects of Different Stages of Training on the Intestinal Microbes of Yili Horses Analyzed Using Metagenomics

Objectives: The aim of this study was to investigate the effects of different stages of training on the intestinal microbial abundance of Yili horses. Methods: Ten Yili horses, all aged 2 years old and weighing 305 ± 20 kg, were selected and divided into a training group and an untrained group. The training group performed riding training 6 days a week, and the untrained group moved freely in the activity circle every day. Fecal samples were collected on days 30 and 60, and the intestinal microorganisms were detected and analyzed using metagenomics. Results: Compared with the 30-day untrained group, the relative abundances of Bacteroidetes were significantly increased in the 30-day training group (p < 0.01). Conversely, the abundances of Clostridiaceae, Clostridium, and Ruminococcus were significantly decreased (p < 0.01), whereas those of Prevotella, Bacteroideaceae, and Bacteroidetes were significantly increased (p < 0.05). Additionally, the relative abundances of Firmicutes and Actinomycetes were significantly decreased (p < 0.05). Compared with the 60-day untrained group, no significant differences in the phyla Bacteriaceae and Bacteriae of the 60-day training group (p > 0.05) were observed. In the linear discriminant analysis effect size analysis, seven significantly different bacteria were detected in the fecal flora of horses in the 30-day training group versus the untrained 30-day group, but only one significantly different bacterium was detected after 60 days. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed genes were related to metabolism and the environmental information processing pathway, carbohydrate metabolism, and membrane transport pathways. Conclusions: Therefore, training seems to affect the diversity and composition of the gut microbiota of Yili horses, especially during the first 30 days of training.

Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing

The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.

Gut microbiota diversity among humans, elephants, livestock and wild herbivores in Chitwan National Park bears implications for conservation medicine

Gut microbiome influences host health and well-being. Co-occurring hosts may exchange disease-causing bacteria belonging to these microbial communities. Therefore, monitoring gut microbiota composition in wildlife and humans is paramount to prevent zoonotic diseases, thus protecting and strengthening public health. We characterized diversity and abundance of the gut microbiome bacterial component across mahouts (captive elephant trainers and handlers), their pachyderms, livestock and wild herbivores in and around Chitwan National Park (Nepal). Firmicutes and Bacteroidota were invariably the dominant phyla. In humans, the relative abundance of Firmicutes was higher, the alpha diversity lower and beta diversity different compared to other host categories. Livestock and wild herbivores displayed similar alpha and beta diversity due to the presence of Proteobacteria, Actinobacteriota and Verrucomicrobiota. Elephants had a higher alpha diversity, and a significant beta diversity compared to other mammals. Our results suggest that taxonomic affiliation and diet niche are the main drivers of gut microbiota composition. Nevertheless, Mycobacterium and other potentially pathogenic bacteria genera were detected in elephants and livestock other than wild herbivores. These findings shed light on microbiota sharing and interlinking in each environment, thereby highlighting the importance of conservation medicine to better our understanding of health in co-occurring host species.

Hydrodynamic confinement of bacteria within intestinal folds

The gut microbiota significantly influence host health by impacting metabolism, immune function and development. Understanding bacterial behaviours in intestinal folds is crucial owing to their role in biofilm formation, which protects bacteria from immune responses and antibiotics and is associated with colorectal cancer. In this study, we observed the behaviours of Escherichia coli bacteria in the intestinal folds of zebrafish larvae (Danio rerio). It is found that E. coli swims in the intestinal folds for extended periods and is confined in a groove on the wall. In order to clarify the mechanism of the confinement, we further performed numerical simulations using a boundary element method. Our simulations demonstrate that bacterial movement in the groove is constrained by hydrodynamic and steric forces. The groove configuration significantly influences bacterial confinement, with bacteria in a deep groove escaping more easily in the presence of background flow. Based on the aggregation rate of E. coli in the intestinal folds of zebrafish larvae, it is indicated that the groove trapping significantly reduces cell flux away from the wall. These findings enhance our understanding of bacterial accumulation and biofilm formation in the gut, with implications for other environments with geometric constraints.

Host trees partially explain the complex bacterial communities of two threatened saproxylic beetles

Microorganisms are integral to ecosystem functioning and host adaptation, yet the understanding of microbiomes in diverse beetle taxa remains limited. We conducted a comprehensive study to investigate the microbial composition of two red flat bark beetle species, Cucujus haematodes and C. cinnaberinus, and assessed the influence of host taxonomic relatedness and host tree species on their microbiomes. We sampled 67 larvae of two Cucujus taxa taken from 11 host tree species. 16S rRNA V4 fragment sequencing revealed distinct microbial communities associated with each Cucujus species, with host tree species significantly influencing microbiome composition. Alpha and beta diversity metrics indicated significant differences between microbial communities in both beetle and host tree species. Principal component analysis indicated distinct clustering based on host tree species but not for beetle species. This overlap could be attributed to the similar ecology of both Cucujus species. The detection of various bacteria, among which some have already been reported in saproxylophagous beetles, suggests that the red flat bark beetles ingest the bacteria via foraging on other wood-dwelling invertebrates. Our findings show the complex interplay between host taxonomy, microhabitat and microbial composition in Cucujus, providing insights into their ecological roles and conservation implications. This research helps to fill the gap in understanding the microbial dynamics of saproxylic beetles, sheds light on factors shaping their microbiomes and highlights the importance of considering both host species and environmental conditions when studying insect-microbe interactions in forest ecosystems.

Outer membrane vesicles in gram-negative bacteria and its correlation with pathogenesis

There is a widespread distribution of gram-negative bacteria worldwide, which are responsible for the deaths of numerous patients each year. The illnesses they cause can be localized and systemic, and these bacteria possess several key virulence factors that contribute to their pathogenicity. In recent years, several distinct mechanisms of pathogenesis have evolved that remain largely unknown to scientists and medical experts. Among these, outer membrane vesicles (OMVs) are undoubtedly one of the most significant factors influencing virulence. OMVs contain various bacterial compounds and can have diverse effects on host organisms and the immune system, potentially exacerbating disease and inflammation while evading immune responses. This review comprehensively examines the role of OMVs in bacterial pathogenesis, their interaction with host cells, and their potential biomedical applications. Understanding the molecular mechanisms governing OMV biogenesis and function could pave the way for novel antimicrobial strategies and therapeutic interventions.

Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices

Comparative approaches in animal gut microbiome research have revealed patterns of phylosymbiosis, dietary and physiological convergences, and environment-host interactions. However, most large-scale comparative studies, especially those that are highly cited, have focused on mammals, and efforts to integrate comparative approaches with existing ecological frameworks are lacking. While mammals serve as useful model organisms, developing generalised principles of how animal gut microbiomes are shaped and how these microbiomes interact bidirectionally with host ecology and evolution requires a more complete sampling of the animal kingdom. Here, we provide an overview of what past comparative studies have taught us about the gut microbiome, and how community ecology theory may help resolve certain contradictions in comparative gut microbiome research. We explore whether certain hypotheses are supported across clades, and how the disproportionate focus on mammals has introduced potential bias into gut microbiome theory. We then introduce a methodological solution by which public gut microbiome data of understudied hosts can be compiled and analysed in a comparative context. Our aggregation and analysis of 179 studies shows that generating data sets with rich host diversity is possible with public data and that key gut microbes associated with mammals are widespread across the animal kingdom. We also show the effects that sample size and taxonomic rank have on comparative gut microbiome studies and that results of multivariate analyses can vary significantly with these two parameters. While challenges remain in developing a universal model of the animal gut microbiome, we show that existing ecological frameworks can help bring us one step closer to integrating the gut microbiome into animal ecology and evolution.

Analysis of the microbial diversity in the fecal material of the critically endangered orangutan

The orangutan ( Pongo spp.) is a critically endangered species. Today, populations of these animals are rapidly declining by up to 75%. They are found in the tropical rainforests of Borneo and Sumatra. In this study, using a next generation sequencing approach, the bacterial and fungal diversity in the fecal material of orangutans living in the Racine Zoo were investigated. The most predominant bacterial phyla were the Bacillota along with Bacteroidota. The most predominant fungal phylum was Ascomycota. Finally, the various functions of the bacterial communities present in the fecal material were predicted with PICRUSt2 using the KEGG database.

Cultivation of anaerobic bacteria: Foundations and principles

A brief history of techniques in anaerobic microbiology are presented leading up to the incorporation of several improvements we have used over the years to improve our culture of anaerobic microorganisms of environmental, industrial and clinical importance. Two overriding aspects from our combined 90 years of experience here are: the better one's control of anaerobic conditions and gas phases, the better results are obtained; techniques can and should be targeted for individual microorganisms and accompanying experiments. Continued improvements in anaerobic microbiology are expected and encouraged for the future.

Human microbiome acquisition and transmission

As humans, we host personal microbiomes intricately connected to our biology and health. Far from being isolated entities, our microbiomes are dynamically shaped by microbial exchange with the surroundings, in lifelong microbiome acquisition and transmission processes. In this Review, we explore recent studies on how our microbiomes are transmitted, beginning at birth and during interactions with other humans and the environment. We also describe the key methodological aspects of transmission inference, based on the uniqueness of the building blocks of the microbiome - single microbial strains. A better understanding of human microbiome transmission will have implications for studies of microbial host regulation, of microbiome-associated diseases, and for effective microbiome-targeting strategies. Besides exchanging strains with other humans, there is also preliminary evidence we acquire microorganisms from animals and food, and thus a complete understanding of microbiome acquisition and transmission can only be attained by adopting a One Health perspective.

Gut microbiota signatures of the three Mexican primate species, including hybrid populations

Diversity of the gut microbiota has proven to be related with host physiology, health and behavior, influencing host ecology and evolution. Gut microbial community relationships often recapitulate primate phylogeny, suggesting phylosymbiotic associations. Howler monkeys (Alouatta) have been a model for the study of host-gut microbiota relationships, showing the influence of different host related and environmental factors. Differences in life-history traits and feeding behavior with other atelids, like spider monkeys, may reveal distinct patterns of bacterial gut communities, yet few wild populations have been studied; likewise, gut microbiota studies of hybrid populations are mostly lacking. We analyzed diversity and abundance patterns of the gut microbiota of wild populations of the three Mexican primates Ateles geoffroyi, Alouatta palliata and A. pigra from different regions across its distribution in the country, including sympatric localities and the Alouatta hybrid zone. Interspecific differences in gut microbial diversity were higher than intraspecific differences, concordant with phylosymbiosis. Ateles harbored the more differentiated diversity with a major presence of rare taxa, while differences were less strong between Alouatta species. Hybrids had a microbial diversity in-between their parental species, yet also showing unique microbe taxa. Genetic distances between Alouatta individuals correlated positively with their gut microbial dissimilarities. Results show that interspecific and intraspecific overall diversity, abundance and composition patterns are affected by environment, geographic distribution and host genetics. Our study provides the first comprehensive study of gut microbiota of the three Mexican primates and hybrid populations.

An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov

The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this is similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales and Chlamydiae). Here, we provide a detailed and comprehensive account on the current knowledge on the Holosporales. First, acknowledging the up-to-date phylogenetic reconstructions and recent nomenclatural proposals, we reevaluate their taxonomy, thus re-ranking them as a suborder, i.e. Holosporineae, within the order Rhodospirillales. Then, we examine the phylogenetic diversity of the Holosporineae, presenting the 20 described genera and many yet undescribed sub-lineages, as well as the variety of the respective environments of provenance and hosts, which belong to several different eukaryotic supergroups. Noteworthy representatives of the Holosporineae are the infectious intranuclear Holospora, the host manipulator 'Caedimonas', and the farmed shrimp pathogen 'Candidatus Hepatobacter'. Next, we put these bacteria in the broad context of the whole Holosporineae, by comparing with the available data on the least studied representatives, including genome sequences. Accordingly, we reason on the most probable evolutionary trajectories for host interactions, host specificity, and emergence of potential pathogens in aquaculture and possibly humans, as well as on future research directions to investigate those many open points on the Holosporineae.

The Microbiota and Evolution of Obesity

Obesity is a major global concern and is generally attributed to a combination of genetic and environmental factors. Several hypotheses have been proposed to explain the evolutionary origins of obesity epidemic, including thrifty and drifty genotypes, and changes in thermogenesis. Here, we put forward the hypothesis of metaflammation, which proposes that due to intense selection pressures exerted by environmental pathogens, specific genes that help develop a robust defense mechanism against infectious diseases have had evolutionary advantages and that this may contribute to obesity in modern times due to connections between the immune and energy storage systems. Indeed, incorporating the genetic variations of gut microbiota into the complex genetic framework of obesity makes it more polygenic than previously believed. Thus, uncovering the evolutionary origins of obesity requires a multifaceted approach that considers the complexity of human history, the unique genetic makeup of different populations, and the influence of gut microbiome on host genetics.

Differences and correlation analysis of feeding habits and intestinal microbiome in Schizopygopsis microcephalus and Ptychobarbus kaznakovi in the upper reaches of Yangtze River

Background

The intestinal microbiota has co-evolved with the host to establish a stable and adaptive microbial community that is essential for maintaining host health and facilitating food digestion. Food selection is a critical factor influencing variations in gut microbial composition, shaping gut microbiome communities, and determining the ecological niches of fish.

Methods

In this study, high-throughput amplicon sequencing of 16S rRNA and 18S rRNA was utilized to compare the dietary and gut microbial differences between Schizopygopsis microcephalus and Ptychobarbus kaznakovi, both collected from the same sites in the Tuotuo River and Tongtian River, which are tributaries of the Yangtze River. We compared the microbial community structure, diet composition, and diversity between the two fish species using various analytical methods, including LefSe, α-diversity and β-diversity analyses. Additionally, we constructed co-occurrence networks to determine their correlations.

Results and discussion

The alpha diversity results indicated that S. microcephalus exhibited higher intestinal microbiota and feeding diversity compared to P. kaznakovi. Furthermore, the beta diversity results revealed significant differences in both intestinal microbiota and eukaryotic communities between the two species. The dominant bacterial phyla in both S. microcephalus and P. kaznakovi included Proteobacteria, Firmicutes, Actinobacteriota, Chloroflexi, and Verrucomicrobiota; however, Firmicutes was significantly more abundant in P. kaznakovi (P = 0.006), while Actinobacteriota was significantly higher (P = 0.019) in S. microcephalus at the phylum level. The primary food sources for S. microcephalus and P. kaznakovi were identified as Streptophyta (54.41%, 77.50%) and Cercozoa (8.67%, 1.94%), with Bacillariophyta (25.65%) was also the main food of constituting a major component of the diet for S. microcephalus. These differences suggested that S. microcephalus and P. kaznakovi occupy distinct dietary niches. To further explore the relationship between gut microbiota and feeding habits, we identified significant correlations between various food components and the gut microbial community through co-occurrence networks. This study enhances our understanding of the co-evolution and co-adaptation between host gut microbiota and feeding behaviors in sympatric fish species.

Gut bacterial and fungal communities of François' langur (Trachypithecus francoisi) changed coordinate to different seasons

Introduction

François' langur (Trachypithecus francoisi), an endangered primate endemic to limestone forests in Vietnam and China, relies on gut microbiota to maintain gastrointestinal stability and adapt to dietary shifts. While gut microbial communities are dynamic and sensitive to seasonal and resource variations, their specific responses in François' langurs remain poorly characterized. This study investigates seasonal variations in the composition and diversity of gut bacterial and fungal communities in this species to enhance understanding of its ecological adaptations.

Methods

Fresh fecal samples from 22 François' langurs in Mayanghe National Nature Reserve, China, were collected across four seasons. Bacterial and fungal communities were analyzed using high-throughput sequencing to assess taxonomic composition and α-diversity. Statistical comparisons were conducted to evaluate seasonal differences at phylum and genus levels.

Results

Significant seasonal shifts occurred in both bacterial and fungal communities. Bacterial α-diversity peaked in warmer seasons, whereas fungal diversity was higher in colder months. At the genus level, Akkermansia (1.3% relative abundance in summer), a mucin-degrading bacterium linked to gut health, dominated warmer seasons. In contrast, the fungal genus Cercophora, associated with plant biomass degradation, was enriched during colder seasons. Seasonal factors strongly influenced microbial structure, with distinct community assemblages observed across all seasons.

Discussion

The inverse diversity patterns of bacterial and fungal communities suggest complementary roles in nutrient extraction under seasonal dietary constraints. Akkermansia's summer prevalence may reflect enhanced mucin utilization during fruit-rich periods, while Cercophora's cold-season dominance likely aids cellulose breakdown in leaf-heavy diets. These dynamics highlight the microbiota's role in optimizing energy harvest from seasonally variable diets. By elucidating microbial seasonal plasticity, this study provides critical insights for developing conservation strategies tailored to the nutritional ecology of François' langurs.

Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice

Laboratory mice (Mus musculus domesticus) harbor gut bacterial strains that are distinct from those of wild mice but whose evolutionary histories are unclear. Here, we show that laboratory mice have retained gut bacterial lineages that diversified in parallel (co-diversified) with rodent species for > 25 million years, but that laboratory-mouse gut microbiota (LGM) strains of these ancestral symbionts have experienced accelerated accumulation of genetic load during the past ~ 120 years of captivity. Compared to closely related wild-mouse gut microbiota (WGM) strains, co-diversified LGM strains displayed significantly faster genome-wide rates of nonsynonymous substitutions, indicating elevated genetic drift-a difference that was absent in non-co-diversified symbiont clades. Competition experiments in germ-free mice further indicated that LGM strains within co-diversified clades displayed significantly reduced fitness in vivo compared to WGM relatives to an extent not observed within non-co-diversified clades. Thus, stochastic processes (e.g., bottlenecks), not natural selection in the laboratory, have been the predominant evolutionary forces underlying divergence of co-diversified symbiont strains between laboratory and wild house mice. Our results show that gut bacterial lineages conserved in diverse rodent species have acquired novel mutational burdens in laboratory mice, providing an evolutionary rationale for restoring laboratory mice with wild gut bacterial strain diversity.

Integrated microbiome and metabolome analysis reveals altered gut microbial communities and metabolite profiles in dairy cows with subclinical mastitis

BACKGROUND

Dairy cow mastitis is a common and prevalent disease arose by various complicated pathogeny, which poses serious threat to the health of cows, safety of dairy product and economic benefits for pastures. Due to the high stealthiness and long incubation period, subclinical mastitis (SM) of cows causes enormous economic losses. Besides the infection by exogenous pathogenic microorganisms, previous studies demonstrated that gastrointestinal microbial dysbiosis is one of the crucial causes for occurrence and development of mastitis based on the theory of entero-mammary axis. Whereas, limited researches have been conducted on potential pathological metabolic mechanisms underlying the relationship between gut microbiota and SM in cows.

RESULTS

The differences in blood parameters, gut microbiome, plasma and fecal metabolome between healthy and SM cows were compared by performing 16 S rDNA sequencing and non-targeted metabolomic analysis in the current study. The content of total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and activity of catalase (CAT), total antioxidant capacity(T-AOC) were significantly decreased, while malondialdehyde (MDA) concentration was dramatically increased in serum of SM cows in comparison with healthy cows. The gut of cows with SM harbored more abundant Cyanobacteria, Proteobacteria, Succinivibrio and Lactobacillus_iners. Moreover, the abundance of Paraprevotella, Coprococcus, Succiniclasticum, Desulfovibrio and Bifidobacterium_pseudolongum were observably reduced in the gut of SM cows. Furthermore, higher abundance of pro-inflammatory metabolites were observed in feces (9(S)-HPODE, 25-hydroxycholesterol, dodecanedioic acid, etc.) and plasma (9-hydroxy-10,12-octadecadienoic acid, 13,14-dihydro PGF1α, 5,6-dehydro arachidonic acid, myristic acid, histamine, etc.) of SM cows. The abundance of certain metabolites with anti-inflammatory and antioxidant properties (mandelic acid, gamma-tocotrienol, deoxycholic acid, etc.) were notably decreased in feces or plasma of cows with SM.

CONCLUSIONS

The intestinal microbial composition and metabolic profiles of healthy and SM cows were significantly distinct, that were characterized by decreased abundance of intestinal symbiotic bacteria, potential probiotics and anti-inflammatory, antioxidant compounds, along with increased abundance of potential pro-inflammatory bacteria, lipid metabolites, and the occurrence of oxidative stress in cows suffered from SM. The results of this study further enriched our understanding of the correlations between gut microbiota and metabolic profiles and SM, which provided insight into the formulation of management strategies for SM in cows.

Targeting CD4+ T cells through gut microbiota: therapeutic potential of traditional Chinese medicine in inflammatory bowel disease

Inflammatory Bowel Disease (IBD) is an autoimmune disease characterized by chronic relapsing inflammation of the intestinal tract. Gut microbiota (GM) and CD4+T cells are important in the development of IBD. A lot of studies have shown that GM and their metabolites like short-chain fatty acids, bile acids and tryptophan can be involved in the differentiation of CD4+T cells through various mechanisms, which in turn regulate the immune homeostasis of the IBD patients. Therefore, regulating CD4+T cells through GM may be a potential therapeutic direction for the treatment of IBD. Many studies have shown that Traditional Chinese Medicine (TCM) formulas and some herbal extracts can affect CD4+T cell differentiation by regulating GM and its metabolites. In this review, we mainly focus on the role of GM and their metabolites in regulating the differentiation of CD4+T cells and their correlation with IBD. We also summarize the current research progress on the regulation of this process by TCM.

Effect of microcystin-LR on intestinal microbiota, metabolism, and health of zebrafish (Danio rerio)

Microcystin-LR (MC-LR) is typically produced along with the occurrence of cyanobacterial blooms, potentially exerting deleterious effects on intestinal microbiota and health in aquatic animals. To date, the underlying mechanism by which MC-LR affects intestinal health remains elusive. In this study, adult male zebrafish were exposed to MC-LR to assess its impact on the microbiome and metabolome. Histopathological and biochemical results indicated that MC-LR damaged intestinal villi and epithelial cells, induced intestinal barrier injury and inflammatory response. Metabolomics results revealed that MC-LR induced amino acid, carbohydrate, lipid, energy metabolisms dysbiosis, and specifically promoted glycine, serine and threonine metabolism. Metagenomics results demonstrated that MC-LR altered the composition of intestinal microbiota, and microbial function prediction suggested that MC-LR promoted the functions associated with amino acid, lipid, carbohydrate and energy metabolisms. Multiomics and Metorigin analyses jointly confirmed that glycine, serine and threonine metabolism was predominantly regulated by dominant Proteobacteria, Firmicutes, Fusobacteriota and Bacteroidota under MC-LR stress. This study offers a comprehensive perspective on the toxicity of microbiota and microbiota-derived metabolism in fish intestines induced by MC-LR and deepens our comprehension of the disruptive influence of MC-LR on intestinal homeostasis in organisms.

Comprehensive cultivation of the broiler gut microbiota guides bacterial isolation from chickens

Chicken gut microbiota plays an important role in maintaining their physiological health. However, the cultivability of chicken gut microbiota is not well understood, limiting the exploration of certain key gut bacteria in regulating intestinal health and nutritional metabolism. This study aimed to examine the cultivability of chicken cecal microbiota and to provide guidance for future chicken gut microbiota cultivation. A total of 58 different culture conditions were applied to culture broiler cecal microbiota, and the culture-dependent (CD; pooled colonies form each plate) and culture-independent (CI; broiler cecal contents) samples were collected for 16S rRNA gene sequencing and microbial analysis. The CD methods detected higher microbial richness (3,636 vs 2,331 OTUs) than CI methods, and the recovery rates of bacterial OTUs and genera reached 43.6% and 68.9%, respectively. The genera of Bacteroides (19.9%), Alistipes (11.0%) and Barnesiella (10.7%) were highly abundant detected by CI methods, however, there occupied a small proportion (<1.0%) of total cultured microbiota in CD methods. We then developed reference figures and tables showing optimal cultivation conditions for different gut bacteria taxa. Moreover, 81 different lactic acid bacteria strains covering 5 genera were isolated, and 15 strains had less than 97.0% similarity to known bacteria in the national center for biotechnology information (NCBI) online database. Overall, this study provides preliminary guidance in culturing specific gut microbiota from chickens, which will contribute to future studies to characterize the biological functions of key microbes in chicken nutritional metabolism and health.

Study of the Effect of Synbiotic Diet on Haematological and Oxidative Indexes Changes in Male Dogs

BACKGROUND

Synbiotic products are functional foods/feeds that contain both probiotic and prebiotic strains and have health-promoting effects beyond those of probiotics or prebiotics alone.

OBJECTIVES

This study aimed to investigate the effect of synbiotic feed containing the probiotic strain Lactobacillus acidophilus La5 (1012 cfu/g) and inulin (5%) on changes in haematological and oxidative serum indices in male dogs.

METHODS

Twelve male dogs in two groups of six were included in the study. In addition to the basic feed, the dogs in the treatment group also received the synbiotic supplement at 5% in each of their three meals during 29 days. Then, on Day 0 and Day 29, the amount of malondialdehyde was measured based on thiobarbituric acid, and glutathione peroxidase activity and the amount of total serum antioxidants was also measured with the Randox kit; the obtained data were statistically analysed.

RESULTS

The results showed that white blood cells increased (from 10.28 ± 2.89 to 16.48 ± 7.59 [p = 0.138]) and red blood cells decreased (from 6.492 ± 0.64 to 5.92 ± 1.14 [p = 0.461]) in the treatment group, but these changes were not significant. In the treatment group, it was found that synbiotic food has a significant effect on the increase of MCH (from 24.32 ± 0.93 to 26.30 ± 1.04 pg [p = 0.003]) and MCHC (from 33.24 ± 0.32 to 36.58 ± 0.72 g/dL [p < 0.001]), but it does not have a significant effect on the decrease or increase of other haematological factors. Also, significant reductions in the amount of malondialdehyde (from 3.2 ± 1.05 to 1.35 ± 1.05 µmol/L [p = 0.015]) and increases in the number of total serum antioxidants (from 0.27 ± 0.06 to 0.42 ± 0.09 mmol/L [p = 0.035]) were obtained in the treatment group.

CONCLUSION

It concluded that the consumption of synbiotic feed (L. acidophilus + inulin, at the rate of 5%) in male dogs may reduce and prevent oxidative stress, adjust side effects and prevent some disorders. In any case, many studies are needed to definitively prove these results.

Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential

Akkermansia muciniphila is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of A. muciniphila as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host-microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made A. muciniphila a subject of enormous attention from multiple research fields. A. muciniphila is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of A. muciniphila and Akkermansia genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of A. muciniphila for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.

Anthropogenic reverberations on the gut microbiome of dwarf chameleons (Bradypodion)

Exploration of the microbiome has been referred to as a final frontier in biological research. This is due to its precedence for generating insights on the holistic functioning of organismal biology by exploring the interactions between hosts and their associated symbiotic organisms. The microbiomes of many vertebrate groups still require exploration to advance current knowledge and fill previous knowledge gaps. This study generated initial descriptions of the bacterial microbiomes of three species of dwarf chameleon (Bradypodion) from the 16S rRNA gene region targeting the V3 and V4 hypervariable regions. This led to the successful identification of 1,073 and 4,502 independent amplicon sequence variants from buccal swab and faecal material samples, respectively. This newly acquired information is intended as a baseline for future work incorporating holobiont information. The diversity of microbial taxa suggests that the total dwarf chameleon microbiome is similar to other squamates investigated to date, as well as chelonians (Testudines). Microbial frequency differences were noted in comparison to crocodilians (Archosauria) and mammalian groups. Furthermore, this study aimed to examine the influence of habitat transformation on the composition of the microbiome in dwarf chameleons as each of the study species occupy both urban and natural habitats. Given that most urban habitats are highly transformed, the expectation was that microbial assemblages of the gastro-intestinal tracts of all three Bradypodion species would show significant differences between populations (i.e., natural, or urban). It was found, however, that the level of effect was contingent on species: B. melanocephalum populations showed noticeable microbiome differences between urban and natural populations; B. thamnobates showed variations in microbial community dispersions between populations; and B. setaroi showed no significant microbiome differences based on diversity metrics although some frequency differences, in microbiome composition, were observed between populations. We suggest that the magnitude of difference between the habitats occupied by the populations is a factor, given the apparent disparity between the natural and urban habitats for B. melanocephalum as compared to the other two species.

The Gut Microbiota of the Greater Horseshoe Bat Confers Rapidly Corresponding Immune Cells in Mice

BACKGROUND

Emerging infectious diseases threaten human and animal health, with most pathogens originating from wildlife. Bats are natural hosts for many infectious agents. Previous studies have demonstrated that changes in some specific genes in bats may contribute to resistance to viral infections, but they have mostly overlooked the immune function of the bat gut microbiota.

AIMS

In this study, we used fecal transplants to transfer the gut microbiota from the Greater Horseshoe Bat (Rhinolophus ferrumequinum) into mice treated with antibiotics. The gut microbiota changes in mice were detected using 16S rRNA high-throughput sequencing technology. Flow cytometry was used to detect changes in associated immune cells in the spleen and mesenteric lymph nodes of the mice.

RESULTS

The results showed that the gut microbiota of mice showed characteristics of some bat gut microbiota. The Greater Horseshoe Bat's gut microbiota changed some immune cells' composition in the spleen and mesenteric lymph nodes of mice and also conferred a faster and higher proportion of natural killer cell activation.

CONCLUSION

This result provides new evidence for the regulatory immune function of bat gut microbiota and contributes to a deeper insight into the unique immune system of bats.

Effects of partial silage replacement with corn stover pellets on the rumen microbiota and serum metabolome of breeding cows

Introduction

Straw pellet ration replacing part of silage is of great significance for farmers to save farming costs and solve the lack of feed resources. A comprehensive analysis of rumen microbial and serum metabolite compositions is conducted to promote the development of the modern breeding cows-feeding industry.

Methods

In this study, 18 healthy 2-year-old Simmental breeding cows weighing 550 ± 20 kg were selected and randomly divided into two groups. They were fed under the same feeding conditions for 70 days, of which 8 in the control (CON) group were fed 65% roughage (100% silage) + 35% concentrate, and 10 in the treatment (TRT) group were fed 65% roughage (50% corn stover pellets +50% silage) + 35% concentrate, and milk quality, serum immunity indexes, serum metabolomes, rumen fermentation parameters, rumen Microorganisms.

Results

The results showed that there was no significant difference in production performance between the two groups of breeding cows fed hay and Corn stover pellet feed (p < 0.05); Immunoglobulin A (IgA) was significantly higher in TRT compared to CON (p < 0.05), and there was no significant difference in Immunoglobulin G (IgG) and Immunoglobulin M (IgM) between the two groups (p > 0.05); a total of 92 differential metabolites were screened out in the serum metabolomics analysis, among them, L-valine, L-leucine, L-arginine, L-cysteine, L-tyrosine, and L-tryptophan were up-regulated; In rumen fermentation parameters there was no significant difference between CON and TRT in rumen pH, rumen ammonia nitrogen (NH3-N) content, rumen Acetic/Propionic concentration (p > 0.05), and the concentration of Acetic, Propionic, butyric and Total volatile fatty acids (TVFA) in CON was significantly lower than that in TRT (p < 0.05). Among the rumen microorganisms, the dominant groups were Thick-walled Firmicutes, Bacteroidota, Prevotella and Ruminalococcus. In the correlation analysis between rumen fermentation parameters and rumen microorganisms, Propionic and TVFA showed a significant positive correlation with Prevotella (p < 0.05), butyric showed a highly significant positive correlation with Prevotella (p < 0.01), and propionic butyric, and TVFA showed a positive correlation with Bacteroides (p < 0.05); L-cysteine was significantly positively correlated with Prevotella and Anaeroplasma (p < 0.05) and Eubaterium in rumen microbial-serum metabolite correlation analysis (p < 0.01).

Conclusion

The microbial and metabolomic analyses provide us with essential data support to further provide a scientific basis for breeding cows feeding through the feeding pattern of straw pellets instead of silage, which will help breeding cows farming in future research.

The Faecal Microbiome Analysed from Healthy, Free-Roaming Giraffes (Giraffa camelopardalis)

Similar to other herbivores, healthy giraffes (Giraffa camelopardalis) rely on a variety of symbiotic microorganisms in their digestive systems to break down cellulose and hemicellulose. In this study, we investigate the impact that external stimuli might have on the faecal prokaryote composition of healthy, free-roaming giraffes. Faecal samples were collected from six male and seven female giraffe individuals, over a 2-year period, during the wet and dry seasons, from six locations within the Free State Province, South Africa. Giraffe populations were exposed to one of two feeding practices which included provision of supplemental feed or only naturally available vegetation. Seventeen (17) different prokaryotic phyla, consisting of 8370 amplicon sequence variants (ASVs), were identified from the 13 healthy, adult, free-roaming giraffes included in the study. Overall, the bacterial phyla with the largest relative abundance included Fusobacteria (22%), followed by Lentisphaera (17%) and Cyanobacteria (16%), which included 21 dominant prokaryotic ASVs. The relative abundance of Ruminococcaceae UCG 014 and Treponema 2 were found to be significantly (P < 0.05) higher and Escherichia / Shigella, Romboutsia and Ruminococcus 1 significantly lower for giraffes receiving supplemental feed compared to natural available vegetation. This is the first study to investigate the composition of the faecal prokaryotic communities of healthy, free-roaming giraffes. The analysis of faecal prokaryotes contributes to the development of non-invasive methods for assessing the nutritional status and identifying health issues in giraffe populations. Ultimately, such advances are beneficial towards the larger-scale conservation, determining nutritional needs and management of other sensitive wildlife species, as well.

Bacteria invade the brain following intracortical microelectrode implantation, inducing gut-brain axis disruption and contributing to reduced microelectrode performance

Brain-machine interface performance can be affected by neuroinflammatory responses due to blood-brain barrier (BBB) damage following intracortical microelectrode implantation. Recent findings suggest that certain gut bacterial constituents might enter the brain through damaged BBB. Therefore, we hypothesized that damage to the BBB caused by microelectrode implantation could facilitate microbiome entry into the brain. In our study, we found bacterial sequences, including gut-related ones, in the brains of mice with implanted microelectrodes. These sequences changed over time. Mice treated with antibiotics showed a reduced presence of these bacteria and had a different inflammatory response, which temporarily improved microelectrode recording performance. However, long-term antibiotic use worsened performance and disrupted neurodegenerative pathways. Many bacterial sequences found were not present in the gut or in unimplanted brains. Together, the current study established a paradigm-shifting mechanism that may contribute to chronic intracortical microelectrode recording performance and affect overall brain health following intracortical microelectrode implantation.

Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats

Wild animals face numerous challenges in less ideal habitats, including the lack of food as well as changes in diet. Understanding how the gut microbiomes of wild animals adapt to changes in food resources within suboptimal habitats is critical for their survival. Therefore, we conducted a longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome assembly over one year. The three gibbon species exhibited significantly different gut microbial diversity and composition. N. hainanus showed the lowest alpha diversity and highest nestedness, suggesting a more specialized and potentially stable microbial community in terms of composition, while H. tianxing displayed high species turnover and low nestedness, reflecting a more dynamic microbial ecosystem, which may indicate greater sensitivity to environmental changes or a flexible response to habitat variability. The gut microbial community of N. concolor was influenced by homogeneous selection in the deterministic process, primarily driven by Prevotellaceae. In contrast, the gut microbial communities of H. tianxing and N. hainanus were influenced by dispersal limitation in the stochastic process, driven by Acholeplasmataceae and Fibrobacterota, respectively. Further, the microbial response patterns to leaf feeding in N. hainanus differed from those of the other two gibbon species. In conclusion, this first cross-species comparative study provides initial insights into the different ecological adaptive strategies of gut microbiomes from a point of community assembly, which could contribute to the long-term conservation of wild primates. In this study, we conducted longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome (composition, alpha diversity, beta diversity and assembly process) over one year.

Commensal acidification of specific gut regions produces a protective priority effect against enteropathogenic bacterial infection

The commensal microbiome has been shown to protect against newly introduced enteric pathogens in multiple host species, a phenomenon known as a priority effect. Multiple mechanisms can contribute to this protective priority effect, including antimicrobial compounds, nutrient competition, and pH changes. In Drosophila melanogaster , Lactiplantibacillus plantarum has been shown to protect against enteric pathogens. However, the strains of L. plantarum studied were derived from laboratory flies or non-fly environments and have been found to be unstable colonizers of the fly gut that mainly reside on the food. To study the priority effect using a naturally occurring microbial relationship, we isolated a wild-fly derived strain of L. plantarum that stably colonizes the fly gut in conjunction with a common enteric pathogen, Serratia marcescens . Flies stably associated with the L. plantarum strain were more resilient to oral Serratia marcescens infection as seen by longer lifespan and lower S. marcescens load in the gut. Through in vitro experiments, we found that L. plantarum inhibits S. marcescens growth due to acidification. We used gut imaging with pH-indicator dyes to show that L. plantarum reduces the gut pH to levels that restrict S. marcescens growth in vivo . In flies colonized with L. plantarum prior to S. marcescens infection, L. plantarum and S. marcescens are spatially segregated in the gut and S. marcescens is less abundant where L. plantarum heavily colonizes, indicating that acidification of specific gut regions is a mechanism of a protective priority effect.

Dynamic Impacts of Stock Enhancement on Kaluga Sturgeon (Huso dauricus): Novel Conservation Strategy Insights from the Gut Microbe Composition and Gene Expression Mode

The sturgeon population has experienced strict threats due to inordinate human activities in the last decade and has been classified into the Red List of Threatened Species in recent years. Stock enhancement is one effective practice for the conservation of wild sturgeons. However, the survival conditions for sturgeon were not satisfactory after they were directly restocked into their natural habitat. Huso dauricus is an important protected sturgeon species, and finding an appropriate conservation strategy for the wild population is urgent. To clarify the dynamic adaptability of Huso dauricus to its wild environment, 1000 individuals were released into a natural river. On the 0th, 7th, 14th, and 30th days, five recaptured individuals were used to evaluate the dynamic trends in biochemical biomarkers, intestinal histomorphology, gut microbe taxon composition, and transcription profile over 30 days of stock enhancement. Our results indicated that Huso dauricus individuals still had a physiological stress status on the seventh day and then gradually adapted to the wild habitat 14 days after reintroduction based on the serum cortisol level. Meanwhile, the feeding habitat, organ function indicators, and growth performance showed similar dynamic changes within 30 days. Interestingly, their gut bacterial diversity and taxon structure also fluctuated over the 30 days after restocking, and they were accompanied by dynamic changes in intestinal pathological injury and tight junction protein expression in this period. The transcriptome analysis revealed the dynamic adaptability of Huso dauricus to wild habitats associated with the expression modes of genes related to the FoxO family, immune system, cytochrome family, and ATP metabolism. Taken together, the findings of the present research demonstrated that artificial reintroduction had dynamic impacts on the health condition of Huso dauricus and that 14 days of wilderness training might be essential for sturgeon restocking practices. Our study revealed the adaption mechanism of Huso dauricus at the molecular level during the restocking period and shed light on the theoretical guidelines for wild sturgeon conservation.

Multi-omics unveils strain-specific neuroactive metabolite production linked to inflammation modulation by Bacteroides and their extracellular vesicles

Bacteroides species are key members of the human gut microbiome and play crucial roles in gut ecology, metabolism, and host-microbe interactions. This study investigated the strain-specific production of neuroactive metabolites by 18 Bacteroidetes (12 Bacteroides, 4 Phocaeicola, and 2 Parabacteroides) using multi-omics approaches. Genomic analysis revealed a significant potential for producing GABA, tryptophan, tyrosine, and histidine metabolism-linked neuroactive compounds. Using untargeted and targeted metabolomics, we identified key neurotransmitter-related or precursor metabolites, including GABA, l-tryptophan, 5-HTP, normelatonin, kynurenic acid, l-tyrosine, and norepinephrine, in a strain- and media-specific manner, with GABA (1-2 mM) being the most abundant. Additionally, extracellular vesicles (EVs) produced by Bacteroides harbor multiple neuroactive metabolites, mainly GABA, and related key enzymes. We used CRISPR/Cas12a-based gene engineering to create a knockout mutant lacking the glutamate decarboxylase gene (gadB) to demonstrate the specific contribution of Bacteroides finegoldii-derived GABA in modulating intestinal homeostasis. Cell-free supernatants from wild-type (WT, GABA+) and ΔgadB (GABA-) provided GABA-independent reinforcement of epithelial membrane integrity in LPS-treated Caco-2/HT29-MTX co-cultures. EVs from WT and ΔgadB attenuated inflammatory immune response of LPS-treated RAW264.7 macrophages, with reduced pro-inflammatory cytokines (IL-1β and IL-6), downregulation of TNF-α, and upregulation of IL-10 and TGF-β. GABA production by B. finegoldii had a limited impact on gut barrier integrity but a significant role in modulating inflammation. This study is the first to demonstrate the presence of a myriad of neuroactive metabolites produced by Bacteroides species in a strain- and media-specific manner in supernatant and EVs, with GABA being the most dominant metabolite and influencing immune responses.

Uropygial gland microbiota of nearctic-neotropical migrants vary with season and migration distance

Symbiotic microbiota are important drivers of host behaviour, health, and fitness. While most studies focus on humans, model organisms, and domestic or economically important species, research investigating the role of host microbiota in wild populations is rapidly accumulating. Most studies focus on the gut microbiota; however, skin and other glandular microbiota also play an important role in shaping traits that may impact host fitness. The uropygial gland is an important source of chemical cues and harbours diverse microbes that could mediate chemical communication in birds, so determining the factors most important in shaping host microbiota should improve our understanding of microbially-mediated chemical communication. Hypothesizing that temporal, geographic, and taxonomic effects influence host microbiota, we evaluated the effects of season, migration distance, and taxonomy on the uropygial gland microbiota of 18 passerine species from 11 families. By sampling 473 birds at a single stopover location during spring and fall migration and using 16S rRNA sequencing, we demonstrate that season, followed by migration distance, had the strongest influence on uropygial gland microbial community composition. While statistically significant, taxonomic family and species had only weak effects on gland microbiota. Given that temporal effects on gland microbiota were nearly ubiquitous among the species we tested, determining the consequences of and mechanisms driving this seasonal variation are important next steps.

Estradiol metabolism by gut microbiota in women's depression pathogenesis: inspiration from nature

The recurrence and treatment resistance of depression remain significant issues, primarily due to an inadequate understanding of its pathogenesis. Recent scientific evidence indicates that gut microbiota influence estradiol metabolism and are associated with the development of depression in nonpremenopausal women. Integrating existing studies on the regulation of estradiol metabolism by microorganisms in nature and the relevance of its degradation products to depression, recent scientific explorations have further elucidated the key mechanisms by which gut microbiota catabolize estradiol through specific metabolic pathways. These emerging scientific findings suggest that the unique metabolic effects of gut microbiota on estradiol may be one of the central drivers in the onset and course of depression in non-menopausal women.

Reciprocal translocation experiments reveal gut microbiome plasticity and host specificity in a Qinghai-Xizang Plateau lizard

Animal adaptation to environmental challenges is a complex process involving intricate interactions between the host genotype and gut microbiome composition. The gut microbiome, highly responsive to external environmental factors, plays a crucial role in host adaptability and may facilitate local adaptation within species. Concurrently, the genetic background of host populations influences gut microbiome composition, highlighting the bidirectional relationship between host and microbiome. Despite this, our understanding of gut microbiome plasticity and its role in host adaptability remains limited, particularly in reptiles. To clarify this issue, we conducted a reciprocal translocation experiment with gravid females of the Qinghai toad-headed lizards ( Phrynocephalus vlangalii) between high-altitude (2 600 m a.s.l.) and superhigh-altitude (3 600 m a.s.l.) environments on Dangjin Mountain of the Qinghai-Xizang Plateau, China. One year later, we assessed the phenotypes and gut microbiomes of their offspring. Results revealed significant plasticity in gut microbiome diversity and structure in response to contrasting elevations. High-altitude conditions increased diversity, and maternal effects appeared to enable high-altitude lizards to maintain elevated diversity when exposed to superhigh-altitude environments. Additionally, superhigh-altitude lizards displayed distinct gut microbiome structures with notable host specificity, potentially linked to their lower growth rates. Overall, these findings underscore the importance of the gut microbiome in facilitating reptilian adaptation to rapid environmental changes across altitudinal gradients. Furthermore, this study provides critical insights into microbial mechanisms underpinning local adaptation and adaptative plasticity, offering a foundation for future research on host-microbiome interactions in evolutionary and ecological contexts.

Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys

Donkeys, as single-stomach herbivores, have a complex and diverse microbial community in their digestive tracts. The intestinal bacterial community is crucial for maintaining intestinal homeostasis, as well as the host's overall nutrition and health. However, research on donkey gut microbes is relatively limited, particularly regarding the microbial colonization patterns in different intestinal segments of adult donkeys. Therefore, this study examined the abundance and function of microbiota across various sites of the intestinal tract (duodenum, jejunum, ileum, cecum, colon) and feces of healthy adult Dezhou male donkeys using 16S rRNA gene sequencing and PICRUSt analysis. The results indicate that donkeys have a rich gut microbial diversity and a large microbial population. No significant differences in the indices of alpha diversity were observed among the donkey's duodenum, jejunum, ileum, cecum, colon, and feces. A Venn diagram analysis revealed the presence of both unique (Duodenum: 4645; Jejunum: 3586; Ileum: 4904; Cecum: 4253; Colon: 6135; Feces: 4885) and shared (339) ASVs among the different sections. A principal coordinate analysis (PCoA) revealed significant differences (R2 = 0.2076, p < 0.007) across the six intestinal segments of the donkeys. At the phylum level, Firmicutes (63.64%), Bacteroidetes (20.72%), Verrucomicrobiota (9.16%), Patescibacteria (1.95%), Spirochaetota (1.87%), Actinobacteriota (1.13%), and Proteobacteria (0.42%) were the dominant bacteria in all samples. The Wilcoxon rank-sum test revealed significant differences in the proportions of genera among different intestinal segments. Specific genera were significantly enriched in various segments: Lachnospiraceae_UCG-008 and Sphaerochaeta in the duodenum; Christensenellaceae_R-7_group and Bacillus in the jejunum; NK4A214_group and Alloprevotella in the ileum; UCG-005 and Lactobacillus in the cecum; Clostridium_sensu_stricto_1 and Chlamydia in the colon; and Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-004 in the feces. A PICRUSt2 functional prediction analysis indicated that carbohydrate metabolism, prokaryotic cellular communities, antimicrobial drug resistance, immune diseases, membrane transport, signal transduction, and transcription exhibited significant differences among the different intestinal segments. This study provided critical primary data on the differences in donkey gut microbiota and the synergistic effects between gut microbiota and host functions. These findings can be used to assess donkey health status, improve breeding, and develop microbial additives.

Impacts of host phylogeny, diet, and geography on the gut microbiome of rodents

Mammalian gut microbial communities are thought to play a variety of important roles in health and fitness, including digestion, metabolism, nutrition, immune response, behavior, and pathogen protection. Gut microbiota diversity among hosts is strongly shaped by diet as well as phylogenetic relationships among hosts. Although various host factors may influence microbial community structure, the relative contribution may vary depending on several variables, such as taxonomic scales of the species studied, dietary patterns, geographic location, and gut physiology. The present study focused on 12 species of rodents representing 3 rodent families and 3 dietary guilds (herbivores, granivores, and omnivores) to evaluate the influence of host phylogeny, dietary guild and geography on microbial diversity and community composition. Colon samples were examined from rodents that were collected from 7 different localities in Texas and Oklahoma which were characterized using 16S rRNA gene amplicon sequencing targeting the V1-V3 variable regions. The microbiota of colon samples was largely dominated by the family Porphyromonadaceae (Parabacteriodes, Coprobacter) and herbivorous hosts harbored richer gut microbial communities than granivores and omnivores. Differential abundance analysis showed significant trends in the abundance of several bacterial families when comparing herbivores and granivores to omnivores, however, there were no significant differences observed between herbivores and granivores. The gut microbiotas displayed patterns consistent with phylosymbiosis as host phylogeny explained more variation in gut microbiotas (34%) than host dietary guilds (10%), and geography (3%). Overall, results indicate that among this rodent assemblage, evolutionary relatedness is the major determinant of microbiome compositional variation, but diet and to a lesser extent geographic provenance are also influential.

The Gut Microbiota-Related Antihyperglycemic Effect of Metformin

It is critical to sustain the diversity of the microbiota to maintain host homeostasis and health. Growing evidence indicates that changes in gut microbial biodiversity may be associated with the development of several pathologies, including type 2 diabetes mellitus (T2DM). Metformin is still the first-line drug for treatment of T2DM unless there are contra-indications. The drug primarily inhibits hepatic gluconeogenesis and increases the sensitivity of target cells (hepatocytes, adipocytes and myocytes) to insulin; however, increasing evidence suggests that it may also influence the gut. As T2DM patients exhibit gut dysbiosis, the intestinal microbiome has gained interest as a key target for metabolic diseases. Interestingly, changes in the gut microbiome were also observed in T2DM patients treated with metformin compared to those who were not. Therefore, the aim of this review is to present the current state of knowledge regarding the association of the gut microbiome with the antihyperglycemic effect of metformin. Numerous studies indicate that the reduction in glucose concentration observed in T2DM patients treated with metformin is due in part to changes in the biodiversity of the gut microbiota. These changes contribute to improved intestinal barrier integrity, increased production of short-chain fatty acids (SCFAs), regulation of bile acid metabolism, and enhanced glucose absorption. Therefore, in addition to the well-recognized reduction of gluconeogenesis, metformin also appears to exert its glucose-lowering effect by influencing gut microbiome biodiversity. However, we are only beginning to understand how metformin acts on specific microorganisms in the intestine, and further research is needed to understand its role in regulating glucose metabolism, including the impact of this remarkable drug on specific microorganisms in the gut.