Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “microbial physiology”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2026

Low-pH sulfate reduction in acid mine drainage treatment systems: implications for acidophilic and acid-tolerant sulfate-reducing bacteria - a systematic review.

Acid mine drainage (AMD) is characterized by persistent acidity, high sulfate and dissolved metal concentrations. Sulfate-reducing bacteria (SRB) are attractive candidates for AMD remediation because dissimilatory sulfate reduction generates alkalinity while producing sulfide that can facilitate metal removal through precipitation. Extending these processes to acidic conditions has increased interest in acidophilic and acid-tolerant SRB (aSRB and atSRB), yet evidence from cultivation, molecular surveys and treatment systems has often been interpreted separately. This systematic review synthesized 53 culture-dependent, culture-independent, and treatment system studies from 2014 to 2024 to examine relationships among taxonomic occurrence, physiological capability, demonstrated low-pH sulfate reduction and treatment performance. Phylogenetic analysis showed that low-pH sulfate-reducing phenotypes were distributed across multiple lineages and 16S rRNA relatedness alone did not predict acid tolerance. Desulfosporosinus was the most consistently represented genus across studies, although its recurrence was influenced by cultivation strategies. Sulfate reduction was demonstrated below pH 3, with sustained low-pH activity most strongly supported by controlled reactor studies; approximately pH 4.0-5.5 emerged as a comparatively well-supported range, while activity at lower pH was more dependent on microbial physiology and experimental conditions. Low-pH sulfate reduction also emerged as a community-level process shaped by electron-donor use, metabolite turnover and complementary microbial functions, while treatment performance additionally depended on biomass retention, hydraulic conditions and sulfide management. The reviewed studies support a distinction between taxonomic presence, demonstrated activity and treatment contribution. Future work should prioritize standardized reporting of active sulfate-reduction conditions, stronger taxon-function validation and long-term field testing of low-pH sulfidogenic systems.

Sulfates↗
PubMed2026

Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism.

Microbial metabolism is a complex, emergent system driven by the coordinated interplay of intricate and dynamic molecular processes. To elucidate cellular behavior and enable biotechnological applications, quantitative models that address the inherent complexity of metabolism have been developed from a resource allocation perspective. Here, we synthesize recent advances in coarse-grained resource allocation frameworks and their applications in understanding microbial physiology and guiding gene circuit design. These frameworks reveal global regulatory constraints and predict cellular adaptation to nutrient and environmental changes. In addition, they enable the quantification of metabolic costs, the dissection of circuit-host interactions, and the development of strategies for burden mitigation. Collectively, these modeling frameworks provide a powerful platform for uncovering quantitative principles of microbial growth and engineering robust synthetic biological systems.

coarse-grained modeling↗
PubMed2026

KG-Microbe: Building modular and scalable knowledge graphs for microbiome and microbial sciences.

BACKGROUND: The integration of many disparate forms of data is essential for understanding the microbial world and its interaction with the environment and human health. Doing so is particularly challenging in the context of microbe-host and microbe-microbe interactions that contribute to health or environmental outcomes. There are thousands of relevant microbial species, and millions of interactions among those microbes and with their environment or host. Integrated information (e.g., about host and microbial physiology, genetics, and metabolism) facilitates deeper understanding of complex mechanisms and helps interpret correlative results. RESULTS: The KG-Microbe construction framework is a novel approach to harmonizing bacterial and archaeal data in the form of a findable, accessible, interoperable, reusable and AI-ready knowledge graph (KG). Starting from a core KG with organismal traits, environments, and growth preferences and the integration of established ontologies, the framework generates a hierarchy of related KGs targeting specific use cases, including the human microbiome in the context of disease, or environmental microbiomes. The framework supports customizable taxa subsets representing communities or clades of interest. Evaluations of the KG-Microbe KGs through a series of competency questions demonstrate the accuracy and effectiveness of the data harmonization, and the utility of the resulting KGs in studies of inflammatory bowel disease and Parkinson's disease. Finally, the predictive and environmental capabilities of the KGs are demonstrated by predicting growth preferences using graph features. CONCLUSIONS: The KG-Microbe framework unifies microbial contexts in a single resource to support integrative analyses across biomedical, host, and environmental domains. KG-Microbe is a flexible, modular enabling technology for humans and machine learning methods to uncover candidate mechanistic explanations of microbial associations.

Microbiota↗
PubMed2025

Lanthanide-dependent isolation of phyllosphere methylotrophs selects for a phylogenetically conserved but metabolically diverse community.

Lanthanides have emerged as important metal cofactors for biological processes. Lanthanide-associated metabolisms are well-studied in leaf symbiont methylotrophic bacteria, which utilize reduced one-carbon compounds such as methanol for growth. Yet, the importance of lanthanides in plant-microbe interactions and on microbial physiology and colonization in plants remains poorly understood. To investigate this, 344 pink-pigmented facultative methylotrophs were isolated from soybean leaves by selecting for bacteria capable of methanol oxidation with lanthanide cofactors, but none were obligately lanthanide-dependent. Phylogenetic analyses revealed that all strains were nearly identical to each other and are part of the extorquens clade of Methylobacterium, despite variability in genome and plasmid sizes. Strain-specific identification was enabled by the higher resolution provided with rpoB compared to 16S rRNA as marker genes. Despite the low strain-level diversity, the metabolic capabilities of the collection diverged greatly. Strains encoding identical lanthanide-dependent alcohol dehydrogenases displayed significantly different growth rates and/or final ODs from each other on alcohols in the presence and absence of lanthanides. Several strains also lacked well-characterized lanthanide-associated genes thought to be important for phyllosphere colonization. Additionally, 3% of our isolates were capable of growth on sugars and 23% were capable of growth on aromatic acids, substantially expanding the range of substrates utilized by Methylobacterium extorquens in the phyllosphere. Our findings suggest that the expansion of metabolic capabilities, as well as differential usage of lanthanides and their influence on metabolism, among closely related strains point to evolution of niche partitioning strategies to promote colonization of the phyllosphere.

Journal Article↗
PubMedDate not supplied

Siderophores: diverse roles in microbial and human physiology.

Siderophores, defined as high affinity iron(III) ion transport agents, and their cognate membrane-bound receptor complexes, occur in the enteric bacteria Escherichia coli and Salmonella typhimurium. The total system is tightly regulated by iron repression. The transport properties of the specific siderophores enterobactin and ferrichrome (which is not made by these particular enteric bacteria) have been examined in detail. In E. coli the outer membrane receptor for ferrichrome is programmed by the tonA gene; the receptor also serves as the binding site for T1, T5, phi80, albomycin and colicin M. Similarly, in S. typhimurium phage ES18, ferrichrome and albomycin compete for the genetic equivalent of the tonA locus. The ability of ascorbic acid to protect against atherosclerosis as well as rhinovirus infection in humans may be related to the role of the vitamin in iron metabolism. Deferrisiderophores are clinically useful in the treatment of acute and chronic iron poisoning but, on the other hand, they could constitute a natural hazard by transporting actinides, such as 239Pu, through the food chain.

Arteriosclerosis↗
PubMed2026

Amino acid reprogramming and biofilm-specific tricarboxylate transporters in PET-degrading Piscinibacter sakaiensis.

Plastic-degrading bacteria predominantly colonize polymer surfaces as biofilms, yet it remains unclear whether the biofilm phenotype contributes to metabolism beyond retaining extracellular enzymes. Here, we combine population-level RNA-sequencing across three conditions-biofilm cells on polyethylene terephthalate (PET), planktonic cells incubated with PET, and planktonic cells on maltose-with single-cell Raman spectroscopy to characterize the PET response of Piscinibacter sakaiensis (formerly Ideonella sakaiensis). This integrated approach reveals two metabolically distinct response layers. A carbon-source-driven response shared by all PET-exposed cells is dominated by a broad amino acid reprogramming, led by upregulation of branched-chain amino acid transport genes, enhanced serine biosynthesis, and reduced chemotaxis. A biofilm-specific layer selectively induces tripartite tricarboxylate transporter genes from three distinct genomic loci. This transcriptional feature is accompanied by a single-cell phenotype consistent with a protein-rich and saturated membrane. These results suggest that biofilm formation is not limited to enzyme retention but is associated with selective activation of transport systems, consistent with a putative role in capturing PET-derived intermediates at the polymer interface. This two-layer model separates general metabolic adaptation to PET from biofilm-specific functions and provides a framework for understanding how surface-associated bacterial physiology contributes to plastic degradation.IMPORTANCEPolyethylene terephthalate (PET) degradation in natural and engineered environments is largely mediated by surface-attached microbial communities, yet the physiological role of biofilm state during plastic degradation remains poorly understood. Using the model PET degrader Piscinibacter sakaiensis, we show that biofilm-associated cells are not simply retained near the polymer surface but exhibit a distinct metabolic program characterized by selective induction of tripartite tricarboxylate transporters. In contrast, extensive amino acid reprogramming occurs in both biofilm and planktonic PET-exposed cells, indicating that it is driven by carbon source rather than surface attachment. These findings reveal that PET degradation involves two separable physiological layers: a general metabolic response to PET-derived carbon shared across cell phenotypes, and a biofilm-specific transport response potentially linked to substrate capture at the plastic interface. This work advances our understanding of how microbial physiology is organized during plastic biodegradation and identifies transport processes as previously unrecognized components of PET-degrading biofilms.

PET biodegradation↗
PubMed2026

Glutathione acts as an exometabolite that promotes growth recovery in fission yeast with defects in amino acid metabolism and cell polarity.

UNLABELLED: Microorganisms in nature form communities through diverse interactions, such as mutualism and competition, to adapt to their ecological environments. These interactions seem to be mediated by extracellular metabolites (exometabolites), yet the chemical and biological diversity underlying these processes remains largely unexplored. In this study, we examined the chemical basis of exometabolite-mediated interactions in the fission yeast Schizosaccharomyces pombe by a genome-wide screen employing 3,420 viable gene deletion mutants. We identified 37 strains that exhibited growth defects in monoculture on a minimal medium but exhibited growth recovery in the vicinity of wild-type colonies (co-culture), suggesting that exometabolites derived from wild-type cells compensated for the gene deletion. Both lipophilic and water-soluble fractions obtained by solvent partitioning of the wild-type culture supernatant promoted growth recovery. Among the 11 mutants rescued by the water-soluble fraction, 6 were cysteine auxotrophs, prompting analyses of thiol-containing metabolites by liquid chromatography-mass spectrometry (LC-MS), revealing the presence of glutathione (GSH) in the culture supernatant. GSH restored growth in most strains as a nutrient source. In contrast, GSH rescued cell morphology defects in the hob3∆ mutant, lacking the Bin/amphiphysin/Rvs (BAR) adaptor protein Hob3, through a mechanism independent of nutrition. This research advances understanding of exometabolite-mediated interactions in S. pombe by identifying GSH as an exometabolite that influences cellular processes and potentially shapes microbial communities. IMPORTANCE: Microorganisms secrete a wide range of metabolites that control microbial community behavior. These extracellular metabolites (exometabolites) include not only well-studied signaling molecules but also diverse primary and secondary metabolites, suggesting complex interactions among microbes. However, the molecular basis of these interactions remains poorly understood, partly due to challenges in detecting them experimentally. In this study, we surveyed exometabolites involved in cell-cell interactions in the model eukaryotic microorganism Schizosaccharomyces pombe. S. pombe releases a wide variety of metabolites outside the cells, including previously reported nitrogen signaling factors (NSFs) and glutathione (GSH) identified in this work. By analyzing gene deletion mutants whose growth is supported by extracellular GSH, we provide new insights into how secreted primary exometabolites compensate for specific genetic defects and influence cell physiology in microbial populations.

exometabolite↗
PubMed2026

Effects of acute hypoxia followed by reoxygenation on intestinal histomorphology, oxidative stress and hypoxia signaling biomarkers, and microbiota in pikeperch (Sander lucioperca).

In aquatic environments, natural and anthropogenic factors commonly reduce dissolved oxygen (DO) and trigger hypoxia, which threatens the health and survival of aquatic organisms. As an important economic fish species in China, pikeperch (Sander lucioperca) is extremely sensitive to hypoxia. However, there are relatively few reports on how hypoxia and reoxygenation affect its intestinal physiology and microbial community. Three treatment groups were set for pikeperch: normoxia (DO = 8.5 ± 0.5 mg/L), 48 h hypoxia (DO = 2.5 ± 0.1 mg/L), and reoxygenation (48 h hypoxia followed by 6 h reoxygenation at normal DO), to evaluate alterations in intestinal histopathology, tight junction gene expression, oxidative stress, hypoxia signaling molecules and intestinal microbiota composition. The results showed that hypoxia significantly decreased muscularis thickness by approximately 32.5% and reduced the expression of tight junction genes (Occludin, Claudin2, and ZO-2). Moreover, hypoxia significantly increased oxidative stress index levels (GSH-Px, CAT, and MDA), markedly upregulated the expression of Bax, Caspase3, and HIF-1α, while significantly downregulating the expression of Bcl-2, Egln1, and Egln2. Notably, reoxygenation elicited partial compensatory effects against these hypoxia-induced changes. 16S rRNA sequencing analysis revealed that hypoxic stress altered the intestinal microbial community composition of pikeperch and increased its diversity. In the hypoxia group, the abundance of the phylum Bacillota, along with the genera Halomonas and Acinetobacter, was significantly elevated, whereas in the reoxygenation group, the genus Lactobacillus increased approximately 180-fold. The results indicated that hypoxia caused intestinal oxidative damage, cell apoptosis, and intestinal microbiota dysbiosis in pikeperch, while short-term reoxygenation achieved partial recovery from these hypoxia-triggered intestinal injuries. The present research provides valuable references for in-depth exploration of the molecular mechanisms behind the response of pikeperch to acute hypoxia and reoxygenation stress, while also offering a novel perspective to understand the mechanism by which hypoxia impacts intestinal health in fish.

Animals↗
PubMed2026

Beyond survival: microbial dispersion via aerosolization as an evolutionary trait.

Airborne dispersion of microorganisms is a constant ecologically significant global process. However, the initial stage of this process, the uplift of microbes to the atmosphere, remains poorly understood as an ecological filter. Differential aerosolization could serve as a potent selector allowing a subset of microorganisms to disperse via air more efficiently, providing potential advantages in establishment in new environments. While traits associated with atmospheric survival and deposition are well documented, microbial aerosolization is still generally presumed to be stochastic, primarily due to the small size of microorganisms and their lack of active biological ejection mechanisms like those found in seeds and larger fungal spores. However, emerging evidence suggests that uplift into the atmosphere is a dynamic interaction between physical forces in the environment and specific biological traits. This review synthesizes observations from genomic source tracking studies and laboratory experiments that describe how preferential enrichment of certain taxa into the atmosphere is based on intrinsic properties including extracellular polymeric substance (EPS) mediated aggregation, cell surface hydrophobicity, surfactant production, and other potentially relevant microbial traits. Additional candidate traits that may contribute to enhanced aerosolization are identified along with the potential mechanistic basis by which they might influence uplift. Future work with controlled chamber studies on single organisms and integration of atmospheric flux measurements with trait-based microbial uplift can provide a mechanistic basis for more accurate models of bioaerosol flux. Improving our comprehension of bioaerosol aerosolization behavior and flux is critical to understanding the dispersal of microorganisms across diverse habitats and their subsequent impacts on ecosystems, global climate, and the spread of diseases.

atmospheric microbiology↗
PubMed2026

Microbial partnerships and molecular mechanisms in plant stress physiology for climate-resilient and sustainable farming.

Plant-microbial partnerships and their underlying molecular mechanisms are indispensable, natural drivers of improved nutrient acquisition and stress tolerance in the face of climate-driven environmental challenges. Modern multi-omics tools, when coupled with artificial intelligence and synthetic biology, enable the precise design of targeted bioinoculants and synthetic microbial consortia. Translating these advanced microbiome-based strategies into scalable, field-level agricultural applications provides a sustainable path toward securing global food production while maintaining soil health. Global climate change imposes multifaceted abiotic and biotic stresses on crops, disrupting physiological and molecular processes and threatening agricultural productivity. Plant-associated microbes represent an underexplored yet powerful ally in enhancing crop resilience. This review presents current knowledge of plant-microbe interactions and the molecular mechanisms governing plant stress physiology, with an emphasis on climate-resilient and sustainable farming. Hence, ever-changing environmental cues pose a significant burden on agricultural productivity, and plant-associated microbial communities modulate a cascade of physiological and molecular responses, including production of phytohormones, signaling, regulation of reactive oxygen species homeostasis, and activation of plant immune responses to help plants withstand stress and enhance productivity. Moreover, root exudates, phytohormones, and quorum sensing mediate the central communication networks, facilitating plant-microbe cross talk. Additionally, the advances in OMICs approaches aid in disentangling the molecular underpinnings of these interactions by providing mechanistic insights and potential candidate gene targets for crop improvement and stress resilience. In the post-genomic era, integrating artificial intelligence and big data analysis to optimize microbiome-based strategies for sustainable agriculture is a new frontier for disentangling plant-microbe symbiosis to improve soil health, enhance crop yields, and improve stress tolerance. Thus, by integrating the ecological, physiological, and molecular perspectives, this review highlights the transformative potential of harnessing plant-microbe symbiosis for climate-resilient and sustainable agriculture.

Stress, Physiological↗
PubMed2026

Diet change reveals asymmetric response in gene expression and microbial composition across the digestive tract of two closely related herbivores.

BACKGROUND: Understanding what shapes variation in organisms' capacity to utilize novel resources is essential to predicting how species will respond to environmental change. For herbivores, exposure to toxic phytochemicals in novel plants may limit persistence in new habitats. We investigated the behavioral, physiological, genetic, and microbial consequences of diet switching in two closely related species of rodent herbivores that each consume differentially toxic plants in their native habitat, and that maintain different dietary strategies (i.e., relative dietary specialist versus relative generalist). RESULTS: In reciprocal laboratory feeding trials, we exposed wild-caught woodrats (genus Neotoma) to toxins characteristic of either familiar or novel plant secondary compounds. We measured changes in food and water intake, locomotor activity, gut microbial composition, and gene expression across the digestive tract following feeding trials. The dietary generalist responded minimally, but the specialist responded strongly when exposed to the novel diet. This response included behavioral and genetic components including increased water intake, reduction in locomotor activity, increased differential expression of detoxification genes, and a greater shift in gut microbial composition. CONCLUSIONS: The dietary specialist exhibited a strong response to diet switching that corresponded with ecologically relevant shifts in behavior and physiology that would have negative fitness consequences. Although the dietary specialist had a strong genetic and microbial response to novel plant secondary compounds, this response would likely be insufficient to overcome the immediate challenge of exposure to novel dietary toxins in the wild. Our results underscore the link between feeding strategy and the capacity to shift to novel dietary resources in response to environmental change.

Animals↗
PubMed2026

Plant genetic and root-associated microbial diversity modulate Lactuca sativa responsiveness to a soil inoculum under phosphate deficiency.

Microbial-based approaches offer a promising strategy to decrease the use of chemical fertilizers in agriculture. Among them, arbuscular mycorrhizal fungi (AMF), which extend root surface area and enhance phosphate uptake, and phosphate-solubilizing bacteria (PSB) are particularly relevant. However, their effectiveness depends strongly on plant genetic diversity. To identify genetic markers underlying plant responses to beneficial soil microbes, we studied a panel of 128 fully sequenced Lactuca sativa varieties under controlled phosphate-starvation conditions and treated with AMF and PSB. Lettuce genetic variation showed a strong effect on physiological and morphological responses to microbial inoculation. Genome-wide association studies identified specific genomic regions associated with changes in leaf phosphate content and shoot biomass following treatment. Beyond genetic factors, we observed shifts in fungal β-diversity and increased bacterial α-diversity associated with phenotypic variation. We also identified 44 amplicon sequence variants associated with agriculturally relevant traits. Among these, six bacterial strains were experimentally validated through in vitro and pot experiments for their effects on leaf phosphate concentration and shoot biomass. Overall, we highlighted key genetic, microbial, and physiological mechanisms that may enhance microbial treatments for improved plant phosphate management in lettuce.

16S and ITS metabarcoding↗
PubMed1977

On the physiology and biochemistry of the scalp and hair lipids.

Analyses were made of the scalp and hair lipids of 67 test persons. These were the most important results: 1. Seborrhoea is caused on one hand by a high secretion performance of the sebaceous glands. A further cause is that a longer period of time passes before a constant lipid amount is established. 2. There was an average of 19.32% of free fatty acids in the scalp and hair lipids on the 1st day after the hair was washed, and 38.68% on the 10th day. These results allow an assessment of the physiological significance of microbial lipolysis outside the secretory ducts of the sebaceous glands. 3. On the hairy head the percentage of free fatty acids in the scalp and hair lipids is independent of the amount of lipids. Such a difference in the concentration of fatty acids as is found between seborrhoea oleosa and seborrhoea sicca on hairless skin can not be found on the hairy head.

Adolescent↗
PubMed2026

Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.

BACKGROUND: Feces represent a complex biological matrix that provides valuable information about intestinal physiology and gut microbial activity. Comprehensive fecal DNA sequencing is mostly utilized as a non-invasive way to profile the gut microbiome, and both clinical practice and research on inflammatory bowel diseases (IBD) would greatly benefit from accurate and non-invasive methods to monitor gut inflammation in IBD patients. In IBD, excessive immune cell recruitment and epithelial cell shedding in the gut increase the amount of human DNA in feces, making fecal DNA profiling a desirable approach to monitor gut inflammation dynamics. METHODS: We used a combination of sequencing techniques to comprehensively characterize the fecal DNA diversity in a newly established cohort of pediatric IBD patients and controls (Pediatric cohort, N = 134 children, Israel). We performed methylation-based human cell-specific profiling together with shotgun metagenomics to characterize the human and the microbial DNA content in feces, respectively. Moreover, we included a large complementary external cohort including adult IBD patients and controls (Adult cohort, N = 689 adults, the Netherlands), not only to compare microbial patterns across the age spectrum, but also to extend our findings from the methylation-based profiling to the more broadly-available quantification of human DNA in metagenomic sequencing. RESULTS: We found that neutrophil DNA dominates fecal human DNA content in IBD patients, and our measurements were highly correlated with fecal calprotectin levels. Combining neutrophil and other cell type DNA fractions in one metric was able to distinguish between remissive and active cases of IBD. Human reads percentage by metagenomics was well correlated with disease severity and species richness, which had distinct trends in CD and UC over time. We used a combination of species richness, human DNA percentage, and microbiome composition data to predict IBD and distinguish CD from UC in both adult and pediatric IBD cohorts. CONCLUSIONS: The comprehensive characterization of human and microbiome fecal DNA is a useful approach to track immune response level and investigate the interaction that the immune system has with gut microbiome richness and composition over time, enriching opportunities for better disease monitoring and thus better treatment of IBD patients. Video Abstract.

Humans↗
PubMedDate not supplied

[Morpho-physiological research on Schizomycetes. Morphogenesis and cytoarchitecture of the microbial colony. I: B. anthracis].

The cytoarchitecture of B. anthracis can be easily studied in serial sections both at the light and at the electron microscope. The morphogenesis of the colony makes clear the peculiar structure of B. anthracis which seems essentially due to the chemical and physical characteristics of the cell envelopes and to the incomplete division of daughter cells. Other factors such as surface tension, humidity, mechanical obstacles and regressive phenomena, seem to be active, in B. anthracis, only since the third day.

Bacillus anthracis↗
PubMed2026

[Intestinal microbiota alterations after digestive tract reconstruction surgery and their impacts on host physiology].

The gut microbiota, acknowledged as the human body's 'second genome', plays a pivotal role in maintaining health. Digestive tract reconstruction surgery profoundly alters the anatomical structure and physiological environment of the gastrointestinal tract, thereby inducing significant shifts in the intestinal microbiota. These microbial changes subsequently influence host physiological functions through metabolic, immune, neuroendocrine, and other pathways. For instance, Roux-en-Y gastric bypass surgery enriches short-chain fatty acid(SCFA)-producing Bacteroides, improving systemic insulin sensitivity. Conversely, pancreaticoduodenectomy leads to a marked enrichment of potential pathobionts such as Klebsiella and Clostridium, which may elevate the risk of infections and tumor recurrence. This review comprehensively summarizes the characteristic changes in the gut microbiota following various digestive tract reconstruction procedures and discusses their multifaceted impacts on host physiology, aiming to provide insights for future experimental research and clinical practice.

Humans↗
PubMed2026

Assessing the diversity and functional profile of the "microbial proteome" in fermented foods.

Fermented foods are staples in diets worldwide and are known for their health benefits. Microorganisms are the key to fermented food production as they convert raw substrates into digestible, nutritious, and health-promoting products. While microbes are essential for fermented food production, their contribution to the dietary protein profile of the final food product in terms of microbial biomass is largely unknown. We analyzed proteins from 17 fermented foods using metaproteomics to identify and quantify microbial and food-derived proteins. We found that microbial proteins contribute up to 11% of the total protein content in fermented foods and comprise as much as 60% of the total number of identified proteins. These microbial proteins included many for central functions in microbial cells, such as glycolysis enzymes, translation machinery, and chaperones, as well as proteins for specialized functions that are important for the ecological niches in food fermentation, such as carbohydrate degrading enzymes and proteases. Some of these microbial proteins, such as proteases, could impact gut physiology. These findings highlight the substantial contribution of microbial proteins to the nutritional and functional profile of fermented foods, which may have important implications for interactions with the gut microbiota and health outcomes.

Fermented Foods↗
PubMed2026

Multi-omics insights into the physiological mechanisms of bile acid accumulation in the gallbladder in brumation-like snakes.

Hibernation/brumation represents an important physiological adaptation for animals to cope with seasonal environmental changes. Field observations suggested increased gallbladder weight in the Five-pacer viper (Deinagkistrodon acutus) during brumation, and our quantitative measurements confirmed this increase together with bile acid accumulation. By integrating a multi-omic approach, this study elucidates the regulatory mechanisms of bile acid accumulation in the gallbladder during brumation. Results showed that taurocholic acid (TCA) and taurodeoxycholic acid (TDCA) were the major components in the gallbladder of the brumation-like group, with significantly elevated concentrations of bile acids, whereas bile acid concentrations in serum and intestinal contents were markedly reduced, indicating suppression of the enterohepatic circulation and consequent accumulation of bile acids in the gallbladder. Hepatic transcriptomic analysis revealed significant downregulation of bile acid synthesis and regulatory genes in brumation-like snakes. In contrast, the alternative synthesis pathway gene sterol 27-hydroxylase (CYP27A1) and some transporter genes were slightly upregulated. Further, some modification genes and regulatory genes showed no significant differences between active and brumation-like states. Gut microbiota analysis demonstrated Akkermansia muciniphila, Bacteroides fragilis, and Citrobacter freundii were more enriched in the active group, which were common microbes related to bile acid metabolism, and the correlation analysis confirmed this relationship. Taken together, these findings indicate that the "physiological bile acid accumulation" observed in snakes during brumation-like state is jointly driven by suppressed hepatic synthesis, reduced enterohepatic circulation, and remodeled microbial community structure. The study provides novel comparative physiological insights into extreme metabolic homeostasis in animals.

Animals↗