Explore the vast range of titles available.

HMA mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effects of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, Microbial Ecosystem Therapeutic 4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbor a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.

While the gut microbiota is known to influence host physiology, the molecular mechanisms by which the host epigenetically regulates microbial composition remain largely unexplored. Our work reveals that the epigenetic enzyme Tet2 in intestinal epithelial cells acts as a master regulator of gut microbial ecology by modulating bile acid metabolism. The discovery that Tet2 deletion drives hyocholic acid (HCA) accumulation—which exerts age-dependent effects on Lactobacillus and Akkermansia —provides a novel principle for understanding host–microbe interactions across the lifespan. By linking epithelial DNA demethylation to bile acid transport and microbial phenotype, we establish a previously unrecognized Tet2-ASBT-HCA pathway that expands the conceptual framework for microbiota research. These insights open new avenues for therapeutic interventions aimed at reversing microbial dysbiosis through epigenetic or metabolic modulation.

In human-altered landscapes, animals face numerous threats to their survival, yet little is known about how rapid environmental change affects host–microbiome dynamics across generations. Microbial communities play critical roles in host nutrition, immunity, and overall fitness, and shifts in composition may alter an organism’s ability to adapt. We examined the gut microbiota of the endangered Pacific pocket mouse during the transition from wild to captive environments and across four descendant generations. We found that the microbiome did not immediately shift with captivity but instead stabilized into a distinct, captivity-associated state only after several generations. This study provides the first characterization of gut microbiota in pocket mice and is the first to show, at this resolution, how a wildlife species’ microbiome adapts to environmental change while tracking health and fitness across generations. Our findings highlight the need to incorporate microbiome dynamics into conservation breeding and management strategies.

The interplay between diet and the gut microbiome is fundamental to shaping host physiology and behavior; however, their interactions remain poorly understood. Most studies treat diet as a single-dimensional variable (e.g., high-fat or high-sugar), overlooking the complexity of nutrient balance and density. This oversimplification neglects how diet and microbes function as an integrated system. This study addresses this gap by testing 120 different nutrient-microbiome combinations in Drosophila melanogaster , systematically varying yeast and carbohydrate levels and microbiome configurations. Our results show that dietary nutrient composition drives body protein and fat storage, whereas the microbiome plays a notable role in glucose metabolism and buffers against excess fat accumulation. Microbial effects on reproduction, locomotion, and sleep depend on nutrient composition, and our model reveals specific diet-microbiome patterns driving these outcomes. By treating diet as a dynamic, multidimensional factor, we provide a novel, ecologically relevant framework for understanding how diet and microbiome shape host.

This study provides the first comprehensive analysis of gut microbiome development in Icelandic children, covering the time from before the introduction of solid foods to 5 years of age. Although the overall developmental patterns of the gut microbiome in Icelandic children were similar to what has been seen in other studies, interesting differences were observed, such as a higher abundance of Blautia at an earlier age compared to other study populations. Higher alpha diversity in archaeal-positive samples, both in mothers and in children at the ages of 2 and 5, compared with archaeal-negative samples seen in the present study, is worth further investigation. Additionally, the study suggests a potential role of maternal and perinatal factors, particularly GDM, which was not evident until the age of 5 years, emphasizing the necessity of long-term studies.

is among the most abundant bacterial genera in the healthy human colon, comprising approximately 10-15% of the total gut microbiota. Species within this genus ferment complex carbohydrates, including pectin, to produce butyrate, a short-chain fatty acid with anti-inflammatory and anti-carcinogenic properties. Butyrate is the primary energy source for colonocytes and in is synthesized via the butyryl-CoA:acetate CoA transferase pathway. Reduced levels of are often associated with increased abundance of and may be linked to early-onset colorectal cancer. Here, genomic analysis of strains revealed that several lack antibiotic resistance genes, suggesting a favorable safety profile. Additional genome mining revealed multiple biosynthetic gene clusters (BGCs) involved in the synthesis of secondary metabolites, including ranthipeptides, which may exhibit antimicrobial activity. Understanding the functional roles of these BGCs, particularly their potential to inhibit , is critical for advancing microbiome-based therapies. Moreover, developing effective delivery strategies to maintain populations in the colon is essential for promoting gut health and preventing disease.

The oral and gut microbiome develops from birth and plays important roles in health. This has been well studied in extremely preterm infants (EP; born <32 weeks gestation) and term infants (born >38 weeks gestation), but there is a paucity of research describing oral and gut microbiome development in late and moderate preterm infants (LMPT; 32 to 36 weeks gestation). Our study analyzed microbiome development in 160 LMPT infants from birth to 12 months corrected age. The results showed distinct microbial communities in stool and saliva, with increasing alpha diversity and niche specification over time. LMPT infants’ gut microbiome became dominated by Bifidobacterium by month 3, while the oral community was consistently dominated by Streptococcus . These results highlight that LMPT infants have gut and oral microbiome development that is more like term infants than EP infants, which has important implications for the care of LMPT infants.

Our findings suggest tailoring diet interventions to baseline microbiome types can promote metabolic health in Prevotella -rich/ Bacteroides -poor MSM, a significant portion of people living with HIV at risk for metabolic syndrome. This study was registered at NCT02610374 .

Microorganisms play a fundamental role in human health, contributing to digestion, immune regulation, and metabolic processes. While direct colonization by environmental microbes through ingestion, inhalation, and dermal contact has been documented, evidence suggests that multisensory interactions with nature-via visual, auditory, tactile, gustatory, and olfactory stimuli-also influence the gut microbiome through psychophysiological and immune-mediated pathways. Exposure to natural environments can regulate stress and immune responses, activate the parasympathetic nervous system, and modulate the hypothalamic-pituitary-adrenal and gut-brain axes, which in turn may alter gut microbiome composition and function. Furthermore, sensory interactions with nature may induce epigenetic changes that impact immune function and microbiome dynamics over time. Here, we review evidence for nature-based indirect shaping of the human microbiome (including multisensory and exposure-immunoregulation pathways) and suggest that after the early-life critical window of microbiome development (0-3 years), these indirect effects likely have a greater influence on gut microbiome dynamics than direct colonization by environmental microbiota (e.g., ingested directly from the air). However, this concept remains to be comprehensively tested. Therefore, understanding the relative contributions of direct microbial colonization versus indirect effects-such as multisensory stimulation and immune modulation-demands more integrated, transdisciplinary research. Integrating these insights into public health strategies, urban design, and nature-based interventions could promote microbiome eubiosis, ultimately improving human (and non-human animal) well-being in an era of increasing environmental and health challenges.

Abstract Microbial communities are not only shaped by the diversity of microorganisms and their individual metabolic potential, but also by the vast amount of intra- and interspecies interactions that can occur pairwise interactions among microorganisms, we suggest that more attention should be drawn towards the effects on the entire microbiome that emerge from individual interactions between community members. The production of certain metabolites that can be tied to a specific microbe-microbe interaction might subsequently influence the physicochemical parameters of the habitat, stimulate a change in the trophic network of the community or create new micro-habitats through the formation of biofilms, similar to the production of antimicrobial substances which might negatively affect only one microorganism but cause a ripple effect on the abundance of other community members. Here, we argue that combining established as well as innovative laboratory and computational methods is needed to predict novel interactions and assess their secondary effects. Such efforts will enable future microbiome studies to expand our knowledge on the dynamics of complex microbial communities. Microbiome studies need to consider not only interactions between individual microorganisms, but also the emerging effects that interactions have on the entire community.