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PubMed1990

[The use of microbial and enzymatic function in organic synthesis. Total synthesis of the aglycone of venturicidins A and B].

The synthesis of chiral synthons by means of microbial and enzymatic function and its application to the synthesis of complex, bioactive substances, the aglycone of venturicidins A and B are reviewed. 1) The syntheses of chiral synthons having two chiral centers are described based on the microbial asymmetric reduction of alpha-methyl beta-keto esters or enzymatic asymmetric hydrolysis of alpha-methyl beta-acetoxy esters. 2) The new chiral synthons synthesized in 1) have been successfully applied for the total syntheses of oudemansins A and B. 3) Purification and properties of the asymmetric reduction enzyme of alpha-methyl beta-keto esters in Saccharomyces cerevisiae or Saccharomyces fermentati were investigated. 4) Formal total synthesis of (-)-indolmycin is described based on the asymmetric hydrolysis of alpha-acetoxy ester with lipases. 5) Enzymatic hydrolysis in organic solvents for kinetic resolution of water-insoluble alpha-acyloxy esters with immobilized lipases is described. 6) The first total synthesis of the aglycone of venturicidins A and B has been successfully achieved from the new chiral synthon based on the developed method in 1).

Esters↗
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↗
PubMed1992

Effect of microbial fermentation on functional specific gravity of small forage particles.

Two experiments were designed to determine the effect of gas production during in vitro digestion on functional specific gravity (FSG) of forage particles. In Exp. 1, FSG of ground alfalfa hay decreased from 1.123 to 1.049 between 3 and 9 h of incubation and increased thereafter to reach a plateau at 1.309 after 30 h of incubation. Gas production peaked at 6 h, but gas associated with particles increased until 9 h of incubation. Gas associated with solid residue was correlated to gas production (r = -.67) but also was influenced by gas holding capacity and rate of escape from the particles. In Exp. 2, measurements were performed on ground alfalfa hay, alfalfa silage, and bromegrass hay containing 42.6, 35, and 66.4% NDF, respectively. Gas production seemed to be related to the amount of readily available substrate. Although at 9 h of incubation more gas was produced by alfalfa silage (.235 mL.min-1.g of DM-1) than by bromegrass hay and alfalfa hay (.087 and .187 mL.min-1.g of DM-1, respectively), gas associated with particles was greater for alfalfa hay (.416 mL/g of DM) than for bromegrass hay and alfalfa silage (.256 and .281 mL/g of DM, respectively). The increase in FSG was more rapid for alfalfa silage than for the hays. After 27 h of digestion, gas associated with particles (milliliters per gram of DM) and FSG were .164, 1.226; .147, 1.235; and .001, 1.467 for bromegrass hay, alfalfa hay, and alfalfa silage, respectively. Gas produced during fermentation delayed the increase in specific gravity of forage particles.(ABSTRACT TRUNCATED AT 250 WORDS)

Animal Feed↗
PubMed1986

Ruminal evacuation's effect on microbial activity and ruminal function.

The influence of evacuating, mixing and returning ruminal contents on microbial populations, volatile fatty acid (VFA) concentrations and liquid flow rate was investigated with four ruminal-cannulated Hereford steers (247 kg avg wt). Ruminoreticular contents were sampled, then completely removed, mixed for 5 min and returned to the rumen. Subsequent samples were taken immediately, 1 h and 4 h later. Non-evacuated steers were sampled at identical time intervals either 1 d before or after evacuation. Averaged over time, there was no significant difference between evacuated and non-evacuated steers in total anaerobic, cellulolytic and facultative bacteria, protozoa, oxidation-reduction potential, VFA concentrations, and liquid flow rates. There were no treatment X time interactions and, except for holotrich protozoa and VFA, no differences from time of sampling. Ruminal evacuation does not appear disruptive to anaerobiosis or detrimental to ruminal microorganisms and digestive processes.

Animals↗
PubMed1987

Establishment of a biochemically active intestinal ecosystem in ex-germfree rats.

A time course study for the establishment of some biochemical microbial intestinal functions was undertaken in ex-germfree rats conventionalized, i.e., colonized with conventional flora, in three different ways: untreated (group 1); contact with visitor rats (group 2); inoculated with intestinal contents from conventional rats (group 3). The first two groups of rats were inoculated with the intestinal contents from conventional rats after being out of the germfree isolators for 4 weeks. The biochemical parameters studied were degradation of mucin, inactivation of tryptic activity, conversion of cholesterol to coprostanol and of bilirubin to urobilinogen, degradation of beta-aspartylglycine, and formation of short-chain fatty acids. The results showed that the way in which the microbes were introduced and the microbial biochemical functions themselves were of importance. In several cases, social contacts, i.e., contact with visitor rats, were just as effective for the functionally adequate establishment of microbial intestinal functions as was inoculation with intestinal contents from conventional rats. Some of the biochemical parameters studied were established after a few days, whereas the establishment of others was markedly delayed. When inoculated after 4 weeks, all rats in the first two groups were colonized with conventional flora within 1 week. The results indicate that the model system described is suitable when studying buildup mechanisms in intestinal ecosystem(s).

Animals↗
PubMed2026

Long-Term Warming Reduces Bacterial Diversity and Functional Potential in Temperate Forest Soil.

Soil microbes are key regulators of forest carbon cycling, yet how their diversity and functional potential respond to long-term warming remains poorly understood. Here, we report a five-year in situ warming experiment in a temperate forest, combining ten repeated measurements of microbial diversity and functional gene potential, as well as continuous monitoring of soil CO2 flux. We found that warming progressively reduced bacterial diversity and induced phylogenetically conserved community reorganization. Under warming, community composition shifted in a phylogenetically conserved manner. Warming generally reduced the abundance of microbial functional genes across most carbon-, nitrogen-, and phosphorus-cycling gene categories, except for genes associated with starch decomposition. Warming also altered the factors associated with soil CO2 flux: microbial diversity showed a stronger association with soil CO2 flux under long-term warming, whereas soil moisture was the dominant predictor in the control treatment. This warming-enhanced biodiversity control over soil CO2 flux was associated with shifts in microbial functional potential, particularly increases in starch-degrading genes and microbial biomass production potential. Together, our results suggest that warming can restructure microbial communities in ways that strengthen biodiversity-dependent regulation of soil carbon cycling, with implications for climate-carbon feedbacks.

Soil Microbiology↗
PubMed2026

Amplicon and metagenomic sequencing reveal thifluzamide drive rhizosphere microbial structural shifts and functional adaption.

Thifluzamide (TF) is a widely used phenyl urea fungicide in rice production; however, its impacts on the structural composition and functional dynamics of the rhizosphere microbiome remain poorly understood. Here, we systematically investigated the effects of TF on the structure, interactions, and functional potential of the rice (Oryza sativa L.) rhizosphere microbiome using integrated amplicon sequencing and metagenomic approaches. TF application significantly altered both bacterial and fungal community composition, bacterial diversity was markedly reduced, whereas fungal diversity increased. With bacterial diversity markedly reduced while fungal diversity increased. Beta-diversity analyses revealed strong treatment-driven community separation, indicating pronounced TF-induced microbial restructuring. Co-occurrence network analysis demonstrated reduced complexity and connectivity in bacterial networks but increased negative co-occurrence patterns within fungal communities, suggesting contrasting stability responses between microbial kingdoms. Metagenomic profiling further revealed substantial functional shifts, including the differential enrichment of KEGG and COG pathways associated with xenobiotic metabolism. Notably, while total ARG abundance remained stable, TF exposure altered the resistome profile by selectively enriching specific classes of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Strong positive correlations between MGEs and ARGs highlighted an elevated potential for horizontal gene transfer. Metagenome-assembled genome (MAG) analysis identified specific TF-enriched bacterial taxa, including Methylophilus, Sulfurospirillum, and Azospirillum, which harbored genes involved in pesticide degradation and xenobiotic transformation. Collectively, these findings demonstrate that TF profoundly reshapes the rice rhizosphere microbiome by altering microbial diversity, interaction networks, resistance gene profiles, and functional capacities. This study provides genomic insights into fungicide-microbiome interactions, underscoring the potential ecological implications associated with TF application, while identifying candidate microbial taxa that may contribute to pesticide degradation and rhizosphere microecology resilience.

Rhizosphere↗
PubMed2026

Unraveling critical role of photosynthetic bacteria in sustaining aquatic microbial community stability and function through large-scale genomic data analyses.

The application of photosynthetic bacteria (PB) in water remediation has demonstrated exceptional advantages in terms of high efficiency and low-carbon benefits. However, the limited understanding of PB across natural aquatic environments has constrained the rational development of this strategy. Here, we analyzed 3198 genomic sequencing samples from seven types of natural aquatic ecosystems to investigate the distribution and functions of 42 PB genera commonly used in water remediation. The results showed that the average abundance of the targeted PB reached 9.83 %, with the highest value of 14.93 % observed in River, while Lake harbored the greatest PB genus diversity. PB genera exhibited high sensitivity to salinity, with Rhodoferax dominating freshwater habitats, whereas Rhodovulum was predominant in marine environments. Notably, co-occurrence network analysis revealed that PB were closely associated with microbial community stability and optimized interspecific interactions. Aquatic microbial communities with high PB abundance were characterized by efficient division-of-labor modules, accompanied by enhanced PB-associated functional potential for carbon fixation, denitrification, and sulfur oxidation. In summary, this study systematically elucidates the regional biogeographical patterns and ecological roles of PB in natural aquatic environments, providing a comprehensive scientific basis and theoretical guidance for the development and practical application of PB-based water remediation technologies.

Bacteria↗
PubMed2026

Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.

Terrestrial Antarctica harbors compositionally diverse and functionally distinct microbial life. Yet the eco-evolutionary processes underlying adaptation to Antarctica's polyextreme conditions remain largely unknown. Here, we address how horizontal gene transfer (HGT) and de novo mutations influence microbial adaptation in 16 Antarctic soils using combined short- and long-read datasets. Phylogenetic reconciliation and mobile genetic element analysis of 676 metagenome-assembled genomes show frequent HGT across communities. While transferred genes span diverse functional categories, those involved in energy metabolism are exchanged at higher frequency. Genes for aerotrophy, i.e. the consumption of atmospheric trace gases to provide energy, carbon, and hydration, are among the most frequently disseminated. Approximately a quarter of carbon monoxide dehydrogenases and [NiFe]-hydrogenases are predicted to be horizontally acquired and are often associated with mobile genetic elements. Analysis of polymorphisms suggests widespread purifying selection, particularly for aerotrophy genes, providing further evidence that aerotrophy is critical for microbial survival in Antarctica. Genetic variation in hydrogenases is tightly associated with predicted protein structures, with intense selection acting on critical sites preserving stability and function. Together, these findings show that previously unrecognized eco-evolutionary dynamics shape the composition and function of Antarctic microbial communities, and confirm aerotrophy is a strongly selected and horizontally disseminated trait.

Antarctic Regions↗
PubMed2026

Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.

BACKGROUND: Decomposition of brine shrimp carcasses has a crucial role in carbon cycling of saline lakes, yet the microbial dynamics remain poorly understood. RESULTS: Here we integrated metagenomics, metatranscriptomics, culturomics, metabolomics, and microcosm experiments to investigate microbial community succession and function during brine shrimp (Artemia sp.) carcass decomposition in Barkol Lake, a hypersaline lake in China. A total of 149 metagenome-assembled genomes (MAGs) and 77 pure culture genomes were recovered across 33 phyla, with 72.12% genomes representing species-level novel lineages. Our results reveal diverse bacterial and archaeal taxa, including novel lineages from CG03, T1Sed10-126 and rare archaeal taxa (Asgardarchaeota, Thermoplasmatota, Nanoarchaeota, and Halobacteriota), involved in degradation of biomacromolecules-proteins, carbohydrates, lipids, and nucleic acids-via extracellular hydrolysis, nutrient transport, and intracellular catabolism. These taxa exhibit substrate preferences, rapidly responding to the breakdown of polysaccharides and proteins, followed by lipids and nucleic acids. Hydrolyzed oligomers are further oxidized by various microbes through fermentation, sulfate reduction, and methanogenesis via metabolic handoffs. Additionally, viral auxiliary metabolic genes (AMGs) further enhance microbial host functions, contributing to key ecological processes such as carbon cycling and stress response. A temporally structured microbial decomposer network (MDN) was observed, driving mineralization cascades from fermentation to sulfate reduction and methanogenesis. CONCLUSIONS: This study reveals microbial metabolic handoffs and virus-mediated modulation as critical mechanisms for organic matter turnover, expanding the known diversity and function of decomposers in saline ecosystems. Our findings offer new insights into biogeochemical processes in saline lakes and highlight a synergistic microbial decomposer network involving bacteria, archaea, and viruses that collectively drive nutrient cycling during brine shrimp carcass decomposition. Video Abstract.

Animals↗
PubMed2026

Increased precipitation decelerates temporal succession of grassland soil microbial communities.

Global precipitation regimes have been shifted in recent decades, imposing significant consequences in water-limited grassland ecosystems. However, the effects of increased precipitation on the succession of soil microbial communities remain unclear, mainly due to the scarcity of long-term experiments with time-series data. Here, we examined temporal succession of grassland soil microbial communities in a long-term increased precipitation experiment. Both soil microbial taxonomic and functional structures were significantly altered by increased precipitation. Increased precipitation significantly decelerated the succession rates of soil microbial functional structure (i.e. time-decay relationships). Consistent with the increased microbial decomposition and heterotrophic respiration, the abundances of soil microbial carbon decomposition genes were markedly enhanced by increased precipitation. Furthermore, increased precipitation stimulated genes involved in nutrient cycling processes, potentially promoting plant growth. Collectively, the contributions of stochastic processes in shaping microbial communities were increased under increased precipitation, suggesting that microbial successional trajectories may shift toward multiple alternative states characterized by greater stochasticity under future altered precipitation regimes.

Soil Microbiology↗
PubMed2026

Metagenomic insights into microbial drivers of organic micropollutant removal in wastewater-impacted riverbank filtration.

Organic micropollutants (OMPs) in wastewater treatment plant (WWTP) effluent pose persistent risks to aquatic ecosystems and drinking water sources. Riverbank filtration (RBF) is a nature-based treatment process, yet the compartment-specific roles of riverbed sediment and downstream soil in OMP attenuation remain poorly resolved under wastewater-impacted conditions. Here, we combined targeted chemical analysis, OMP property compilation, shotgun metagenomics, EnviPath-based biotransformation annotation, and exploratory network analysis to investigate OMP attenuation in a laboratory-scale RBF system treating real WWTP effluent for 10 months. Nineteen OMPs were monitored along a sequential sediment-soil filtration pathway. Sediment preferentially attenuated hydrophilic or charged compounds, including lidocaine, amantadine, and sotalol, whereas soil contributed more strongly to the attenuation of naproxen, atenolol, and losartan. Metagenomic profiling revealed distinct microbial communities and functional gene repertoires between sediment and soil after long-term operation. Sediment harbored higher relative abundances of genes associated with oxidative xenobiotic transformation, including cytochrome P450-related enzymes, demethylases, dehydrogenases, oxidases, and aromatic compound degradation pathways. An exploratory Spearman network further identified associations among microbial genera, EnviPath-annotated candidate biotransformation genes, and OMP removal rates, including 17 KO-OMP links supported by both correlation and pathway annotation. These findings indicate that sediment and soil develop complementary microbial functional potentials that may support compound-specific OMP attenuation. This study provides a mechanistic basis for optimizing sediment-soil configurations in wastewater-impacted RBF systems and for improving nature-based barriers against diverse OMP mixtures.

Wastewater↗
PubMed2026

Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.

Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.

Animals↗
PubMed1966

The enhancing effect of the microbial flora on macrophage function and the immune response. A study in germfree mice.

The immune response to bacteria and to a soluble protein was compared in germfree and conventionalized mice. Sixty germfree and 59 conventionalized mice received a suspension of killed Serratia marcescens into one front foot-pad and sterile horse ferritin into the other and were sacrificed in groups from 2 hr to 14 days after inoculation. All mice had no pre-existing antibody to either antigen and the flora of the conventionalized mice never contained Serratia. Lymphatic tissue changes and the fate of the antigens were followed in axillary lymph nodes and the spleens by histologic, fluorescent antibody, and autoradiographic techniques after tritiated thymidine injection. Individual serum antibody titers for both antigens were determined at each time period. The cellular and serologic responses were slightly delayed in the germfree mice but later equaled and sometimes exceeded those of the conventional animals. In all animals, lymph nodes draining the site of Serratia injection showed a more vigorous response than those on the ferritin-injected side but the reaction was qualitatively the same for both antigens. All lymph nodes contained the antigens by 2 hr after foot-pad injection. With time, both antigens lost their particulate nature sooner in conventionalized than in germfree macrophages. In the latter, both antigens persisted throughout the study while no longer demonstrable with fluoresceinated antiserum in conventional macrophages after the first week. While phagocytosis is equal in germfree and conventional mice, a greater digestive capacity of macrophages for antigens seems to result from the continuous exposure of conventional animals to the immunologic effects of the microbial flora. Conversely, the lack of substantial antigenic stimulation of lymphatic tissue in germfree animals fails to develop these macrophage functions beyond their basic ability to degrade foreign substances. Although the onset of the immune response is delayed in germfree mice, the relatively prolonged antigen digestion and the presumably slower release of immunogenic antigen fragments result in a more sustained and sometimes greater response than in conventional animals. This modifying effect of the microflora on the function of macrophages during the immune response is independent of previous experience with, or the nature of, the antigen.

Animals↗