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PubMed1994

Abnormal colonic microbial function in patients with rheumatoid arthritis.

The aim of this study was to examine the microflora-associated characteristics (MACs) of faecal samples of patients with rheumatoid arthritis (RA) and to evaluate the actions of sulphasalazine (SASP) on these MACs. The conversion of cholesterol to coprostanol, the production of urobilinogen, the degradation of faecal tryptic activity (FTA) and of beta-aspartylglycine were measured in faecal samples from 19 patients treated with SASP and 21 patients not treated with this medication. A control group of 21 healthy subjects was sex- and age-matched with the untreated patients. The conversion of cholesterol to coprostanol showed a bimodal distribution. The frequency of high converters in patients without SASP treatment was higher than in healthy subjects (p < 0.05). Treatment with SASP markedly increased the FTA and reduced the urobilinogen values, as compared to the untreated patients (p < 0.05). Beta-aspartylglycine was not found in any faecal samples. The results indicate that patients with RA have an abnormal formation of coprostanol, which is ascribed to alterations in the function of the Eubacteria species. In patients with RA, SASP treatment induces disturbances in the metabolism of the microflora.

Aged↗
PubMed2025

Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.

Increasing evidence indicates that the loss of soil microbial &#x3b1;-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial &#x3b1;-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal &#x3b1;- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal &#x3b1;-diversity declined under high environmental stress across three soil layers (0-20&#x2009;cm, 20-40&#x2009;cm and 40-60&#x2009;cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.

Soil Microbiology↗
PubMed2002

Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function.

An ongoing challenge within microbial ecology is the development of methodologies that attribute microbial community functions to microbial diversity. One approach, involving the incorporation of stable isotopes from labelled tracer compounds into biological signature molecules (biomarkers), may overcome this current limitation. To examine the potential of RNA as the biomarker in stable isotope probing we have generated a series of atom % (13)C-enriched RNA samples through exploitation of the anabolic abilities of a phenol-degrading environmental isolate. Isotope ratio mass spectrometry was used to determine the atom % (13)C of each RNA sample (ca. 1-100%). The corresponding buoyant density (1.755-1.795 g mL(-1)) was determined by equilibrium density gradient centrifugation and agarose gel electrophoresis. This empirically defined relationship between the atom % (13)C of RNA and its buoyant density suggests ribonucleic acids with atom % (13)C enrichments greater than 10% can be isolated by equilibrium density centrifugation. The processing and analysis of isolated RNA by reverse transcription polymerase chain reaction, denaturing gradient gel electrophoresis, cloning and sequencing are discussed. The RNA-based stable isotope probing protocol presented here will find particular utility in assessing the roles of microbial community members in the biodegradation of natural and anthropogenic xenobiotic compounds.

Biomarkers↗
PubMed2005

A quantitative assay for linking microbial community function and structure of a naphthalene-degrading microbial consortium.

A comprehensive culture-independent assay, called Q-FAST, was developed for concurrent identification and quantification of active microorganisms involved a specific function in a given microbial community. The development of Q-FAST was achieved by integrating the concept of stable isotope probing technique into a new quantitative fingerprinting assay called real-time-t-RFLP for microbial community structure analysis. The Q-FAST was successfully validated by using a three-member artificial microbial community containing a known naphthalene-utilizing bacterium (Pseudomonas putida G7) and two nonnaphthalene-degrading bacteria (Escherichia coli and Bacillus thuringiensis). The application of Q-FAST to identify and quantify a guild of naphthalene-utilizing microorganisms in soils revealed the involvement of eight members, with six members relating to several phylogenetic groups of eubacteria (three in beta-proteobacteria, two in gamma-proteobacteria, and one in genera Intrasporangium of Gram-positive bacteria) and two members showing no close phylogenetic affiliation to any known bacterial sequences deposited in GenBank. The quantity of three members belonging to beta-proteobacteria accounted for 34% of total 16S rDNA copies measured from the "heavier" fraction of DNA that was contributed from the DNA of microorganisms capable of incorporating 13C-labeled naphthalene into their genetic biomarkers. The other five members composed 66% of total 16S rDNA copies of active naphthalene-utilizing populations measured. Offering a powerful tool for studying microbial ecology, Q-FAST thus opens a new avenue for deeper exploration of microbial-mediated processes, mainly the quantitative relationship between microbial diversity and microbial activity in a given environment.

Bacillus thuringiensis↗
PubMed2025

Gut microbial and functional alterations lead to metagenomic signatures for midgut neuroendocrine tumor patients and for carcinoid syndrome.

Midgut neuroendocrine tumors (NET) derive from enterochromaffin cells, which have a close interrelationship with intestinal microbiota. Recently, we have utilized 16S rRNA sequencing to uncover that midgut NET patients have a depleted gut microbiome and a specific fecal microbial signature. This study aims to validate these findings and to further characterize the role of microbes and microbial metabolic pathways in midgut NET patients with and without carcinoid syndrome (CS). Fecal samples from 60 midgut NET patients and 20 household-matched controls were subjected to whole metagenome sequencing. The gut microbial community composition of midgut NET patients differed from that of controls, with 2 genera, 17 species and 9 microbial pathways showing differential abundance (P < 0.001). No differences in the microbial composition were observed between midgut NET patients with and without CS (P > 0.05). However, we did observe changes in inter-genus correlations of Bacteroides, Odoribacter, Parasutterella, Klebsiella, Ruminococcus and Proteobacteria when comparing these two patient groups. A signature of 16 microbial species (area under the receiver operating characteristics (AUROC) curve 0.892) or 18 microbial pathways (AUROC 0.909) accurately predicted the presence of a midgut NET. Furthermore, a microbial signature consisting of 14 functional microbial pathways distinguished CS patients from non-CS patients (AUROC 0.807). Thus, this study confirms that the gut microbiome of midgut NET patients is altered at the metagenomic level, which is not related to the presence of CS. A fecal microbial signature could constitute a novel biomarker for the diagnosis of midgut NET or CS.

Aged↗
PubMed2006

Shifts in microbial community functions and nitrifying communities as a result of combined application of copper and mefenoxam.

In this microcosm study, we focused on the effect of a combined application of copper and mefenoxam on the functional diversity of soil microbial communities. Treatments with combined and separate applications of copper and mefenoxam were sampled at 24 and 60 days and control soil was sampled at 0, 24 and 60 days. Structural and metabolic profiling of microorganisms were performed by arbitrarily primed (AP) and RNA arbitrarily primed-PCR (RAP-PCR). Cluster analysis resulted in separate grouping of AP and RAP-PCR profiles, with differences between control and treatments being more pronounced with respect to RAP-PCR profiles. amoA, a functional molecular marker for beta-subgroup ammonia-oxidizing bacteria, could only be detected at day 60 in treatments of mefenoxam, and mefenoxam+copper, with higher gene copies in the latter. There was also an increase in potential nitrification activity on application of mefenoxam and mefenoxam+copper. Comparison of amoA diversity was performed by denaturing gradient gel electrophoresis followed by construction of a clone library of amoA fragments amplified from the mefenoxam+copper-treated sample. Analysis of clones was performed by restriction digestion and subsequent sequencing. Patterns 1 and 5 were seen in 93% of the clones and clustered together with amoA sequences of Nitrosospira, indicating that Nitrosospira-like organisms are the major nitrifiers under mefenoxam treatments.

Alanine↗
PubMed2026

Microbial diversity, functional activities, and safety risks in fermented tea: a comprehensive review.

Microbial fermented teas are gaining global popularity due to their unique sensory profiles and health benefits. The quality and safety of these products are governed by complex microbial ecosystems that orchestrate the biotransformation of tea leaf components. This review addresses a critical paradox in the field: the same microbial activities that generate desirable bioactive metabolites, such as theabrownins and organic acids, also create ecological niches for mycotoxigenic fungi, posing significant health risks from contaminants like ochratoxin A, citrinin, and aflatoxins. While extensive research has cataloged the microbial diversity in these systems, a comprehensive framework linking processing environments to microbial community assembly, functional outcomes, and quantifiable safety risks remains elusive. This review systematically bridges this gap by synthesizing current knowledge on the microbial consortia-dominated by Aspergillus, Penicillium, Bacillus, and Lactiplantibacillus species-that drive tea fermentation. We critically analyze their functional roles in enhancing flavor, bioactivity, and potential probiotic activity while simultaneously evaluating the mechanisms of mycotoxin production and accumulation. By integrating microbial ecology, biochemistry, and food safety, we propose a forward-looking perspective focused on transitioning the industry from traditional, spontaneous fermentation to modern, controlled biotechnological processes. This approach, centered on the use of defined starter cultures, predictive modeling, and active biocontrol strategies, provides a roadmap for ensuring the consistent quality and safety of fermented tea products, ultimately unlocking their full potential as high-quality functional foods.

Tea↗
PubMed2026

Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.

UNLABELLED: Metagenomics enables comprehensive exploration of microbial communities but is influenced by library preparation and sequencing technologies, affecting recovery of microbial genomes and proteins. Here, we benchmarked six Illumina-compatible short-read library preparation conditions in triplicate at 2 &#xd7; 150 bp and 2 &#xd7; 250 bp read lengths alongside PacBio HiFi long-read sequencing using a composite environmental sample of marine mangrove sediment and terrestrial palm tree soil. Longer short reads (2 &#xd7; 250 bp) combined with optimal library preparation approaches improved assembly quality, protein detection, and metagenome-assembled genome (MAG) recovery, achieving results approaching those of long-read sequencing. TruSeq libraries at 2 &#xd7; 250 bp recovered more than sevenfold more unique proteins than the same kit at 2 &#xd7; 150 bp (811,701 vs 110,108) using the same number of sequencing reads, while recovering a comparable number of high-quality MAGs to PacBio HiFi long-read sequencing (11 vs 18) and surpassing it in protein discovery by almost 10-fold (811,701 vs 87,745) at less than half of the sequencing cost. Furthermore, biosynthetic gene cluster analysis identified 46 biosynthetic gene clusters in TruSeq-250PE assemblies compared to 38 in PacBio HiFi, with several showing no close match in the MIBiG database. Although long reads yield more contiguity and complete genomes, longer short reads offer a cost-effective, scalable alternative for uncovering microbial and functional diversity. These findings provide critical guidance for metagenomic experimental design, demonstrating that strategic selection of library preparation chemistry and sequencing parameters can reveal more unknown microbial information in complex biomes without requiring additional sequencing depth. IMPORTANCE: Metagenomic outcomes are strongly influenced by library preparation and sequencing strategies, yet their combined effects in complex environmental samples remain poorly defined. Here, we provide the first direct comparison of Illumina NovaSeq short-read metagenomic sequencing at 2 &#xd7; 150 bp and 2 &#xd7; 250 bp across multiple library preparation kits, alongside PacBio HiFi long-read sequencing. We show that sequencing read length and library preparation critically shape assembly quality, protein recovery, and metagenome-assembled genome (MAG) reconstruction. These findings demonstrate that short-read sequencing at 2 &#xd7; 250 bp, with appropriate library preparation, can match long-read technologies in MAG recovery while substantially surpassing them in protein discovery. With less than half of the sequencing price and a 3.5-fold reduction in cost per gigabase of usable data, this method facilitates more accessible large-scale metagenomic analysis within complex environmental systems.

Metagenomics↗
PubMed2003

Influence of zinc bacitracin and Bacillus licheniformis on microbial intestinal functions in weaned piglets.

The influence of zinc bacitracin (ZB) and of Bacillus licheniformis on host microbial-related functions in young piglets was investigated by applying the concept of microflora-associated characteristics. Six biochemical parameters were determined before and after weaning in faecal samples from piglets in four litters having access to a diet containing ZB, to a diet containing B. licheniformis, to a diet with both additives, or to a diet with no additives, from 3 weeks of age. Statistically significant differences were found in three of the intestinal functions investigated: formation of short-chain fatty acids (at 7 and 10 weeks of age). degradation of mucin (at 7 and 10 weeks of age) and conversion of bilirubin to urobilins (at 7 weeks of age). We also found age-dependent influences on the formation of short-chain fatty acids, on conversion of cholesterol to coprostanol and on conversion of bilirubin to urobilins. We conclude that a functional approach is appropriate for measuring exogenous influence(s) on the microbial intestinal metabolisms in weaned piglets.

Animals↗
PubMed2026

Microbial and functional shifts between flare and remission in a single-center cohort of children with inflammatory bowel disease.

BACKGROUND: Gut microbial dysbiosis is central to the pathogenesis of inflammatory bowel disease (IBD). While gut microbiome differences between patients with and without IBD are well established, microbiome changes associated with disease activity and remission remain limited, particularly in paediatric populations. AIM: To examine intra-individual taxonomic and functional gut microbiome changes during transition from active flare to remission under maintenance immunosuppression in a pilot single-center Singapore cohort of children with IBD. METHODS: Paired stool samples and clinical data were collected from seven patients with paediatric IBD [5 Crohn's disease (CD), 2 ulcerative colitis; &#x2264; 18 years] during active disease/flare (visit 1; Pediatric CD Activity Index/Pediatric Ulcerative Colitis Activity Index &#x2265; 10) and subsequent clinical remission (visit 2; Pediatric CD Activity Index/Pediatric Ulcerative Colitis Activity Index < 10). Samples underwent shotgun metagenomic sequencing for high-resolution taxonomic profiling and functional annotation of Kyoto Encyclopaedia of Genes and Genomes pathways. RESULTS: Gut microbial diversity was reduced during flare compared to remission, with Actinobacteria abundance significantly higher in remission. Two distinct microbial clusters differentiated flare and remission states: The remission cluster was enriched with Bifidobacterium adolescentis, Bifidobacterium dentium, Lactobacillus gasseri, Faecalibacterium prausnitzii, while the flare state showed increased Klebsiella pneumoniae. Remission was further characterized by a downregulation of pathogenic microbes and an upregulation of beneficial microbes including a higher abundance of the butyrate producer Anaerostipes hadrus (P = 0.046). Microbial functional genes enriched in remission were predominantly associated with metabolic pathways including vitamin and cofactor biosynthesis, as well as carbohydrate, amino acid, and lipid metabolism. CONCLUSION: The transition from flare to remission in Singaporean children with IBD is characterized by functional remodeling of the gut microbiome, which may contribute to recovery processes related to intestinal barrier integrity, cellular maintenance, and tissue repair. Targeted modulation of the gut microbiome may help sustain remission in paediatric IBD.

Functional shift↗
PubMed2006

Microbial rhodopsins: functional versatility and genetic mobility.

The type 1 (microbial) rhodopsins are a diverse group of photochemically reactive proteins that span the three domains of life. Their broad phylogenetic distribution has motivated conjecture that rhodopsin-like functionality was present in the last common ancestor of all life. Here, we discuss the evolution of the type 1 microbial rhodopsins and document five cases of lateral gene transfer (LGT) between domains. We suggest that, thanks to the functional versatility of these retinylidene proteins and the relative ease with which they can complement the existing energy-generating or photosensory repertoires of many organisms, LGT is in fact the principal force that determines their broad but patchy distribution.

Evolution, Molecular↗
PubMed2002

Effects of resource supplies on the structure and function of microbial communities.

The supplies of nutrients, and their elemental stoichiometry, can have significant impacts upon the structure and function of microbial communities. This review focuses on the effects of nutrient supplies on the biodegradation of organic matter, and on the dynamics of host-pathogen interactions. Analyses of data from the literature suggest significant effects of nitrogen:phosphorus supply ratios on the microbial decomposition of organic matter, and it is argued that these stoichiometric effects may have important implications for the fate and fluxes of carbon in natural ecosystems. In addition, it is shown that the supplies of nitrogen and phosphorus to the host can strongly influence the outcome of infections in both terrestrial and aquatic plants, suggesting that resource availability and resource supply ratios potentially may have significant effects on the health of many plant communities.

Bacteria↗
PubMedDate not supplied

[Biological functions of microbial exopolysaccharides].

The review includes literature data and the author's experimental data concerning the role of microbial exopolysaccharides (EPS) in protection of the producer cells from different unfavourable factors (drying, effect of toxic metals, antibiotics, biocydes, etc), participation of EPS in trophic metabolism of microorganisms (use of EPS as a source of carbon supply, role in regulation of cell ion balance), as well as in interaction of producers with other microorganisms, macroorganisms, objects of inorganic nature (EPS as virulence factor, EPS participation in the processes of adhesion, sorption and aggregation, in formation of plant-bacterial symbioses). A question of interrelation of physico-chemical properties of microbial EPS and their biological functions as well as of these data use in biotechnology for production of polysaccharides with preset properties is discussed.

Bacteria↗
PubMed2002

RNA stable isotope probing, a novel means of linking microbial community function to phylogeny.

Identifying microorganisms responsible for recognized environmental processes remains a great challenge in contemporary microbial ecology. Only in the last few years have methodological innovations provided access to the relationship between the function of a microbial community and the phylogeny of the organisms accountable for it. In this study stable-isotope-labeled [13C]phenol was fed into a phenol-degrading community from an aerobic industrial bioreactor, and the 13C-labeled RNA produced was used to identify the bacteria responsible for the process. Stable-isotope-labeled RNA was analyzed by equilibrium density centrifugation in concert with reverse transcription-PCR and denaturing gradient gel electrophoresis. In contradiction with findings from conventional methodologies, this unique approach revealed that phenol degradation in the microbial community under investigation is dominated by a member of the Thauera genus. Our results suggest that this organism is important for the function of this bioreactor.

Carbon Isotopes↗
PubMedDate not supplied

[The molecular biological mechanisms of the functioning of microbial glycopolymers and carbohydrases].

Special attention has been paid to glycopolymers which perform various functions in the microbial cell, determine its interaction with the environment, possess a broad range of biological activity (antigenicity, cytotoxicity, immunomodulating properties, participation in the bean-rhizobial symbiosis). Composition and structure of the following polysaccharides, lipopolysaccharides and their components: O-polysaccharide, core oligosaccharide and lipid A from bacteria of genera Clavibacter, Ralstonia, Pseudomonas and Rhizobium, have been studied. Phenotypization of the studied strains has been carried out and chemotaxonomic criteria for creation of serological classification schemes have been proposed. Serogrouping of strains is determined by the availability and chemical nature of lateral substituents of the basic chain of O-specific polysaccharide. Interrelation between physico-chemical characteristics of the polysaccharide complex of rhizobia and formation of bean-rhizobial symbiotic structures has been shown. It is established that polysaccharides, lipo- and exopolysaccharides are efficient immunomodulators, manifest high antileucosis and antimetastasis activities. Physico-chemical properties, specificity, kinetics and action mechanism, structure of active and substrate-binding centres of bacterial and fungal enzymes: alpha-amylase, alpha-galactosidase, galactose oxidase. Data obtained permitted developing recommendations on enzymes application to some fields of the national economy.

Bacteria↗
PubMed1997

Comparison of mechanistic rumen models on mathematical formulation of extramicrobial and microbial processes.

This study investigated the consequences of differences in applied concepts and individual mathematical formulations on steady-state behavior of three important mechanistic rumen models. In the models of Baldwin et al. (2) and Danfaer (6), the formulation of passage rate, nondietary inputs, defined rumen substrate pools, absorption rates, degradation rates, molecular weights, parameterization of VFA production, and physical compartmentalization were sequentially exchanged for the formulation of the model of Dijkstra et al. (9). Most of these adaptations had a considerable influence on model behavior, indicating large qualitative differences in formulation and sensitivity to concept choice. Because microbial substrate environments were similar after all adaptations, the microbial mechanisms could be compared objectively without being concealed by differences in extramicrobial formulation. None of the microbial functions were altered except for substrate degradation, which gave rise to a similar rate of substrate entrance to soluble rumen pools that are available for microbial utilization. Large differences remained in microbial functions of substrate fermentation, substrate incorporation, and microbial synthesis. Differences in extramicrobial rumen functions and microbial mechanisms had important consequences for simulated nutrient outputs from the rumen, illustrating the necessity for further validation of individual formulations.

Absorption↗