Microbial communities articles within Nature Communications

Microsporidia parasitism affect honeybees health and has been implicated in colony losses. Here, the authors show that members of the honeybee gut microbiota inhibit microsporidia proliferation, and engineer a gut symbiont that protects against Nosema ceranae infection via inhibiting its redox system.

Sapoval et al. introduce QuaID, a bioinformatics tool for SARS-CoV-2 variant detection based on quasi-unique mutations. QuaID leverages all mutations, including insertions and deletions, and provides precise detection of variants early in their spread.

Here, Seelbinder et al. show high Candida levels in cancer patients’ stool to correlate with greater metabolically flexibility but less robust bacterial communities and, combined with machine learning models to predict Candida levels from bacterial data, suggest that lactate producing bacteria may fuel Candida overgrowth in the gut during dysbiosis.

Antibiotics impact the gut microbiota in complex ways. Here, employing ecological models of resource competition, Newton et al. elucidate species coexistence patterns under resource competition and species-specific death rates, providing a model to predict microbiota dynamics under deleterious perturbations.

Plasmid acquisition imposes a transient burden on bacterial hosts. Here, authors show this burden results in a tradeoff between growth and lag that dictates plasmid fate, favoring intermediate cost plasmids over both low and high cost counterparts.

Dudek et al. describe rectangular bacterial structures in the mouths of dolphins. Using various genomic and microscopy techniques, they show that the structures consist of bacterial cells that appear to divide along the longitudinal axis and display other unusual features.

Thiosulfate oxidation by microbes has a major impact on global sulfur cycling. Here, Ding et al. provide evidence that bacteria of the Roseobacter group are major thiosulfate-oxidizers in marine biofilms, where anaerobic thiosulfate metabolism is preferred.

This study offers molecular insight into the sialidase and fucosidase decapping apparatus that initiates growth on mucin and promotes nutrient sharing by the dedicated mucolytic symbiont Akkermansia muciniphila with the mucus-associated microbiota.

Parabacteroides distasonis (P. distasonis), part of the gut microbiome, was reported to play a role in diabetes, colorectal cancer and inflammatory bowel disease. Here the authors report that P. distasonis ameliorates liver fibrosis in studies with male mice, potentially via altered bile acid metabolism and hepatocyte pyroptosis.

Root exudates display a diurnal signature, change with growth environment, and can be divided into a core metabolome common to multiple plant species, and specialized exudates produced by distinct species.

Cable bacteria are centimeter-long filamentous microbes that conduct electrons via internal wires, thus coupling sulfide oxidation between sediment layers. Here, Bjerg et al. show that the anoxic part of oxygen-respiring cable bacteria attracts swarms of other bacteria, which appear to transfer electrons to cable bacteria via soluble metabolites.

Animal gut microbiomes are fairly stable over time despite large daily fluctuations in diet and introductions of environmental bacteria. Here the authors report that fruit flies maintain the stability of their microbiome in part through a physical niche in the esophagus.

This study investigates the average genome size of planktonic prokaryotes across tropical and polar oceans and down to the hadal realm. Using hundreds of metagenomes of marine microorganisms, genome size was found to be highest in the perennially cold polar ocean, suggesting that environmental factors influence genome size selection and the ecological strategies of marine microbes.

Here, the authors comparatively analyze the impact of three successful clinical preventive interventions against NEC in preterm, VLBW infants and demonstrate a major impact of especially probiotic-based strategies on the development and maturation of the gut microbiome.

Intrahepatic cholestasis of pregnancy (ICP) is a liver disease that sometimes develops during pregnancy and is characterized by increased serum bile acid levels. Here the authors report that the gut microbiome species B. fragilis is enriched in patients with ICP and promotes ICP development in mice via inhibition of signalling though the bile acid receptor FXR.

Here, the authors provide a longitudinal genetic surveillance of the antimicrobial resistance potential of the human oral microbiome in the first decade of life, revealing a dynamic environment altered by tooth decay with the increasing potential to mobilize genes as children grow.

Here, the authors study the population-level impact of antimicrobial resistance genes (ARGs). By analyzing 8972 metagenomes and 3,096 gut microbiomes from healthy individuals not taking antibiotics, they demonstrate significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Using a collection of 154,723 human-associated metagenome assembled genomes (MAGs) they link these ARGs to microbial taxa and horizontal gene transfer.

Temperature shapes the adaptation and composition of microbiomes, but whether their enzymes drive the thermal response remains unknown. Using an analysis of seven enzyme classes from worldwide marine microbiome data, this study shows that enzyme thermal properties explain microbial thermal plasticity and they are both finely tuned by the thermal variability of the environment.

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, Howe et al. use metagenomics and metatranscriptomics to study changes in the leaf microbiome of perennial crops over two growing seasons.

This study found that a prebiotic intervention was well-tolerated and safe, beneficially changed the microbiome, decreased inflammation and a marker of neurodegeneration, with possible clinical effects in Parkinson’s disease (PD) patients. This study offers the rationale for further investigations using prebiotic fibers in PD.

Here, using metagenomics, the authors show that the gut microbiome of rural Zimbabwean infants undergoes programmed maturation that is unresponsive to sanitation and nutrition interventions but is strongly associated with maternal HIV infection and can moderately predict linear growth.

In this study, 591 mice from an advanced-intercross mouse line were used to provide evidence that fungi are regulated by host genetics, while uncovering a regulatory role of diet on the composition of fungi in the murine gut.

Here, the authors characterise Acinetobacter baumanii and Klebsiella pneumoniae isolated from a single human lung infection and proceed to define their interactions to shed light on how this impacts their evolution, growth parameters, metabolism and antimicrobial responses.

Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds of biotechnological interest. Here, the authors use metagenomics and metatranscriptomics to identify diverse BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela.

The NLRP3 inflammasome plays a pivotal role in clearing viral respiratory infection, but the molecular mechanism is not fully known. Here authors show that acetate, produced by gut bacteria, may enhance NLRP3-mediated type I interferon production following influenza infection in mice.

Metagenomic Hi-C enables genome retrieval in microbial samples. Here, the authors develop an integrative method to recover complete viral genomes and detect virus-host pairs using metagenomic Hi-C data.

Silymarin has been used for improving hepatic damage and lipid disorders, but its action mechanism remains to be clarified. Here, the authors reveal a mechanism of action underpinning the lipid-lowering effect of silymarin via the gut microbiota and its vitamin B12 producing capabilities.

Here, in a randomized trial, the authors comparatively evaluate the effect of a copper intrauterine device versus other contraceptive options on the vaginal environment after one and six consecutive months of use, finding to exert changes on the vaginal microbiota that may potentially lead to detrimental sex and reproductive health.

Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial community, Ascensao et al. show how ecological and epistatic patterns combine to shape adaptive landscapes.

Familial dysautonomia is a rare genetic disease caused in part by neurodegeneration. Here, the authors show that the gut-metabolism axis is altered in both patients and transgenic mice and that disease pathology is ameliorated by controlling microbiome divergence.

Gut microbiome dysbiosis has been shown to alter the immune response to lung infection. Authors utilise a murine model to investigate if gut colonisation with carbapenemase-producing Enterobacterales altered the outcomes of Pseudomonas aeruginosa lung infection.

Rhizosphere microbiota can influence plant pathogen interactions. Here the authors use field- and lab-based approaches to show that rhizosphere bacteria and fungi of healthy tomatoes can enhance tomato resistance against Fusarium wilt disease and formulate synthetic microbial communities that could help to control soil-borne disease.

Allura Red AC is a dye used in food products. Here the authors report that chronic, long-term exposure to Allura Red AC increases susceptibility to experimental colitis in mice dependent on the serotonin biosynthetic enzyme TPH1, while intermittent exposure more typical for the human setting did not increase susceptibility to experimental colitis.

Bacteria can deliver toxic effector proteins into the cytosol of neighboring cells. Here, the authors show that Yersinia pseudotuberculosis secretes an effector that modulates gene expression in neighboring cells of the same species and inhibits the growth of other competitors.

Vancomycin-resistant Enterococcus (VRE) represents a major threat for patients’ health. Here, using a mouse model, the authors show that specific commensals restrict VRE gut colonization through depletion of fructose, a nutrient source that boosts VRE growth in vivo.

Our understanding of microbial diversity and physiology in marine sediments is limited. Here, Gong et al. analyze thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments, and identify MAGs belonging to new bacterial phyla that seem able to mediate key steps in sedimentary biogeochemistry.

Here, by studying a multi-ethnic cross-sectional urban cohort (N = 3211, 6 ethnic groups), the authors show that depressive symptom levels are related to the gut microbiota taxonomic characteristics but that these are largely invariant across ethnic groups.

Here, the authors analyze the relation of fecal microbiota diversity and composition with depressive symptoms in 1,054 participants from the Rotterdam Study cohort and in 1,539 subjects of the Amsterdam HELIUS cohort, finding associations with bacteria known to be involved in the synthesis of key neurotransmitters for depression.

Here, the authors characterize the microbiome and resistome in a longitudinal cohort of 159 international students visiting the Andean city of Cusco, Peru. They find that international travel associates with spread of antimicrobial resistance, and that travelers’ diarrhea increases a persons’ risk for acquiring antimicrobial-resistant pathogens, while a diverse, “healthy” microbiome can be protective against diarrhea.

Opportunistic bacterial pathogen species frequently colonise the human gut as a normal part of the ecosystem but strain-level colonisation and competition dynamics in healthy hosts is yet to be established. Authors seek to understand the relationship between colonisation potential and ecological factors modulating pathogen prevalence in disease in a longitudinal cohort.

Here, the authors compare 76 dental calculus oral microbiomes from Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers living in the same region of Italy. Integrating these data with archaeological data and dietary information, they find evidence of a gradual transition to agriculture.

Aryl hydrocarbon receptor (AHR) is a sensor of the chemical environment including pollutants, diet components and metabolites. Here, authors determine the structure of the indirubin-bound AHR cytosolic complex providing mechanistic insights into ligand-binding promiscuity and selectivity.

Here, the authors perform large-scale high-resolution Parkinson’s disease metagenomics analyses, revealing widespread dysbiosis characterized by overabundance of pathogens, immunogens, toxicants, and curli, reduction in neuroprotective and antiinflammatory molecules, and dysregulated neuroactive signaling.

The establishment and composition of the host microbiota is known to impact the function of the host immune response. Here the authors show that mode of delivery may impact the intestinal microbiota composition from birth and modulate the response to routine childhood vaccines.

Contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Here the authors describe Squeegee, a computational approach designed to detect microbial contamination within low microbial biomass microbiomes and identify microbial contaminants in publicly available datasets that lack negative controls.

Here, using fecal metagenomics data of 2,320 individuals, the authors develop a microbiome-based machine learning approach showing high accuracy for multi-class disease diagnosis, highlighting its potential application in improving noninvasive diagnostics and monitor responses to therapy.

Here, the authors show that SARS-CoV-2 infection causes gut microbiome dysbiosis and gut epithelial cell alterations in a mouse model, and correlate dysbiosis observed in COVID-19 patients with blood stream infections, matching reads of bacterial sequences from stool samples to organisms found in the blood.

The mechanisms underlying methane production in oxygenated waters of oceans and lakes are unclear. Here, Perez-Coronel and Beman show that aerobic methane production in freshwater incubation experiments is associated with (bacterio)chlorophyll metabolism and photosynthesis, and with Proteobacterial degradation of methylphosphonate.

Here, the authors construct 102 complete metagenome-assembled genomes (cMAGs) from Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing, showing as high nucleotide accuracy as reference genomes and revealing that regions hard to assemble by short-read sequencing comprise mostly of genomic islands and rRNAs.