Microbial communities | Nature Communications

Article
22 April 2024 | Open Access

LSD1 drives intestinal epithelial maturation and controls small intestinal immune cell composition independent of microbiota in a murine model

Post birth the gastrointestinal tract undergoes development including the establishment of the microbiome, establishment of tolerance and maturation of the epithelium. Here the authors show a histone demethylase LSD1 is required for postnatal intestinal epithelium maturation and how this impacts local immune cell composition and gut homeostasis.

Alberto Díez-Sánchez
, Håvard T. Lindholm
& Menno J. Oudhoff

Article
22 April 2024 | Open Access

Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer

The rising incidence of young-onset sporadic colorectal cancer (yCRC) is global concern. Here, leveraging a substantial number of deep sequencing metagenomes, the authors show striking similarities in gut microbial patterns at both the taxonomic and selected gene marker levels between yCRC and old-onset CRC.

Youwen Qin
, Xin Tong
& Pei-Rong Ding

Article
20 April 2024 | Open Access

Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Metagenomic taxonomic profiling usually relies either on reads or assembled contigs/MAGs. Here, authors present RAT, a tool that integrates taxonomic signals from reads, contigs, and MAGs into one profile with high precision and sensitivity. RAT provides a comprehensive view of the microbiome.

Ernestina Hauptfeld
, Nikolaos Pappas
& F. A. Bastiaan von Meijenfeldt

Article
17 April 2024 | Open Access

Survival and rapid resuscitation permit limited productivity in desert microbial communities

Prompt physiological reactivation after rainfall pulses may be key for microbial survival in arid ecosystems. Here, the authors use stable isotope tracers, single-cell NanoSIMS and metatranscriptomics to shed light on how desert biocrust microbial communities respond to rewetting.

Stefanie Imminger
, Dimitri V. Meier
& Dagmar Woebken

Comment
12 April 2024 | Open Access

All-inclusive nitrifiers in Antarctic soils

Multidisciplinary culture-dependent and -independent techniques elucidate the unique microbial nitrogen cycle in nutrient-poor coastal Antarctica soils and reveal the contribution of novel key microbes to their nitrogen budget.

Maximiliano Ortiz

Article
10 April 2024 | Open Access

Electrochemically coupled CH₄ and CO₂ consumption driven by microbial processes

The microbial valorisation of greenhouse gases could offer promising approaches climate change mitigation. Here, authors demonstrate the coupling of methane oxidation and carbon dioxide reduction by microbial consortia, facilitated by the redox cycling of iron minerals.

Yue Zheng
, Huan Wang
& Feng Zhao

Article
08 April 2024 | Open Access

Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach

Here, the authors employ multi-omics on a cohort comprising three generations of family members, showing that fecal microbiota populations, functions, and metabolome of infants vary greatly from their maternal lineage, exhibiting a less diverse microbiota and differences in various metabolite classes including short- and branched-chain fatty acids.

Tomás Clive Barker-Tejeda
, Elisa Zubeldia-Varela
& Alma Villaseñor

Article
08 April 2024 | Open Access

Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice

The microbial community in the intestine can affect other organs such as the skin but it is not clear if the opposite can occur. Here the authors show that skin wounding affects the microbial composition of the intestinal flora which then enhances DSS induced colitis and intestinal inflammation.

Tatsuya Dokoshi
, Yang Chen
& Richard L. Gallo

Article
04 April 2024 | Open Access

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience

This study provides insights into the functional roles of microbial symbionts within the reef-building coral Acropora kenti. The findings reveal molecular mechanisms underpinning coral health and adaptation to local environmental stressors, which may support host resilience in the face of anthropogenic climate change and pollution.

Lauren F. Messer
, David G. Bourne
& Gene W. Tyson

Article
04 April 2024 | Open Access

Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification

Sustainability in agriculture can be improved harnessing biological N₂ fixation in legumes. Here, the authors combine different crops with peanut plants finding that maize and oilseed rape are the most successful combinations which have potential to enhance rhizosphere microbiota N₂ fixation.

Mengjie Qiao
, Ruibo Sun
& Yan Chen

Article
28 March 2024 | Open Access

Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities

Identifying the metabolic interactions that underlie microbial communities is challenging. Here, the authors combine Tara Oceans -omics data with co-activity networks and genome-scale metabolic models to predict biotic interactions among planktonic prokaryotes in the upper ocean.

Nils Giordano
, Marinna Gaudin
& Samuel Chaffron

Article
26 March 2024 | Open Access

Profiling the colonic mucosal response to fecal microbiota transplantation identifies a role for GBP5 in colitis in humans and mice

Faecal microbiota transplantation (FMT) can be used to treat established colitis. Here the authors profile transcriptional changes in humans after FMT and how this relates to colitis remission identifying a role for GBP5, and this protein is validated in a loss-of-function mouse model.

Laurence D. W. Luu
, Abhimanu Pandey
& Nadeem O. Kaakoush

Article
23 March 2024 | Open Access

Multi-omic integration of microbiome data for identifying disease-associated modules

Here, Muller et al. introduce MintTea, a method for analyzing multi-omic microbiome data and identifying disease-associated modules comprising mixed sets of features that collectively shift in disease, offering insights into microbiome-disease interactions.

Efrat Muller
, Itamar Shiryan
& Elhanan Borenstein

Article
22 March 2024 | Open Access

Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions

Bioremediation via microbial inoculation often performs poorly in real-world conditions. Here, the authors show that bacterial inoculants may fail to establish in complex soil microbiomes because they open new niches that facilitate growth of resident microbes.

Senka Čaušević
, Manupriyam Dubey
& Jan Roelof van der Meer

Article
16 March 2024 | Open Access

Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus

The impact of other pathogens on disease outcome was studied in European infants with RSV infection. Additional viruses were commonly co-detected during infection but were weakly linked to severity. However, presence of Haemophilus bacteria strongly associated with severe cases.

Gu-Lung Lin
, Simon B. Drysdale
& Andrew J. Pollard

Article
16 March 2024 | Open Access

Data-driven prediction of colonization outcomes for complex microbial communities

Predicting the colonization of exogenous species in complex communities is a challenge in ecology. Here, the authors propose a data-driven approach to predict colonization outcomes and perform validation experiments in human gut microbial communities.

Lu Wu
, Xu-Wen Wang
& Lei Dai

Article
08 March 2024 | Open Access

The defensome of complex bacterial communities

Bacteria have evolved numerous innate and adaptive defence mechanisms. Here, Beavogui et al characterise the impact of biogeography, genetic mobility, and clustering in defense islands, on the defence systems of soil, marine, and human gut bacterial populations genomes.

Angelina Beavogui
, Auriane Lacroix
& Pedro H. Oliveira

Article
29 February 2024 | Open Access

A metagenomic catalog of the early-life human gut virome

Here, the authors present a metagenomic catalogue of the early-life human gut virome including 160,478 non-redundant DNA and RNA viral sequences from 8,130 gut virus-like particles enriched or bulk metagenomes in the first three years of life.

Shuqin Zeng
, Alexandre Almeida
& Shaopu Wang

Article
29 February 2024 | Open Access

Viral potential to modulate microbial methane metabolism varies by habitat

The role of viruses in environmental methane cycling is still largely unclear. Here, Zhong et al. analyse metagenomics data to identify auxiliary metabolic genes related to methane metabolism within viral contigs. They found that the potential viral impacts on methane production and oxidation varies by habitat.

Zhi-Ping Zhong
, Jingjie Du
& Matthew B. Sullivan

Article
24 February 2024 | Open Access

Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15

Several studies have shown that Fusobacterium nucleatum aggravates colorectal cancer (CRC) development and chemoresistance. Here the authors show that F. nucleatum is enriched preferentially in patients with KRAS p.G12D mutant CRC and that it promotes colorectal tumorigenesis in preclinical models by binding DHX15 on tumor cells.

Huiyuan Zhu
, Man Li
& Huanlong Qin

Article
23 February 2024 | Open Access

Dynamic root microbiome sustains soybean productivity under unbalanced fertilization

Root-associated microbiomes contribute to plant growth and health. Here, the authors unveil the quantitative development of the root microbiome under unbalanced fertilization and highlight a key microbial cluster for soybean productivity.

Mingxing Wang
, An-Hui Ge
& Ertao Wang

Article
23 February 2024 | Open Access

Enhancing phosphate-solubilising microbial communities through artificial selection

Phosphate-solubilising microorganisms can contribute to reduce the use of P fertiliser. Here, the authors use two artificial selection methods, environmental perturbation and propagation, to build phosphate-solubilising communities that retain P-solubilising capacity in hydroponic systems.

Lena Faller
, Marcio F. A. Leite
& Eiko E. Kuramae

Article
22 February 2024 | Open Access

Microbes translocation from oral cavity to nasopharyngeal carcinoma in patients

Oral microbes in non-oral locations are noted across various cancers. This study highlights the abnormal translocation of oral microbes to the nasopharynx, raising the risk of nasopharyngeal cancer by remodeling the tumor microenvironment and potentially influencing EBV infection.

Ying Liao
, Yan-Xia Wu
& Wei-Hua Jia

Article
21 February 2024 | Open Access

Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking

Here, the authors characterize the fine-scale dynamics of genome-wide insertion libraries across four human Bacteroides strains in gnotobiotic mice, revealing rapid adaptation and fitness tradeoffs when commensal gut bacteria adapt to a new host.

Daniel P. G. H. Wong
& Benjamin H. Good

Article
17 February 2024 | Open Access

Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea

Anaerobic methanotrophic (ANME) archaea are uncultivated microbes that oxidize the greenhouse gas methane and engage in extracellular electron transfer with other microbes, metal oxides, and electrodes. Here, Ouboter et al. observe strong methane-dependent current associated with high enrichment of ANME archaea on the anode, and provide insights into the mechanisms underlying extracellular electron transfer.

Heleen T. Ouboter
, Rob Mesman
& Cornelia U. Welte

Article
17 February 2024 | Open Access

Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease

Here, through parallel profiling of the mucosal transcriptome and microbiome of intestinal biopsies derived from patients with IBD and from non-IBD controls, the authors characterize interactions between gene expression and microbiota composition associated with traits of patients with inflammatory bowel diseases. Peer Review Information: Nature Communications thanks Robert Häsler, and the other, anonymous, reviewers for their contribution to the peer review of this work. A peer review file is available.

Shixian Hu
, Arno R. Bourgonje
& Rinse K. Weersma

Article
13 February 2024 | Open Access

Dubosiella newyorkensis modulates immune tolerance in colitis via the L-lysine-activated AhR-IDO1-Kyn pathway

Here, Zhang et al. identify a metabolic axis by which Lys-producing commensal bacterium Dubosiella newyorkensis mediates a Treg-mediated immunosuppressive microenvironment by activating AhR-IDO1-Kyn metabolic circuitry in dendritic cells.

Yanan Zhang
, Shuyu Tu
& Shu Jeffrey Zhu

Article
10 February 2024 | Open Access

Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations

The significance of gut phageome for wild animals with seasonal diets remains unexplored. Here, the authors use complementary metagenomics to analyze the phage-host dynamics and its implications for diet variations in wild skywalker hoolock gibbons.

Shao-Ming Gao
, Han-Lan Fei
& Peng-Fei Fan

Article
08 February 2024 | Open Access

Experimental warming accelerates positive soil priming in a temperate grassland ecosystem

Soil priming could release large amounts of soil C into the atmosphere. Here the authors show that experimental warming boosts soil priming and CO₂ emissions in grasslands potentially due to microbial changes. Model accuracy could be improved by incorporating these mechanisms.

Xuanyu Tao
, Zhifeng Yang
& Jizhong Zhou

Article
30 January 2024 | Open Access

Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition

Here, the authors develop a high-throughput method to quantify Bifidobacterium longum subsp. infantis (BL. infantis), a proficient HMO-utilizer, from metagenomic sequencing, and applied it to a longitudinal cohort consisting of 21 mother-infant dyads, suggesting BL. infantis colonization to start late in the breast-feeding period.

Dena Ennis
, Shimrit Shmorak
& Moran Yassour

Article
29 January 2024 | Open Access

A nanoparticle-based sonodynamic therapy reduces Helicobacter pylori infection in mouse without disrupting gut microbiota

Here, the authors develop a non-antibiotic approach using sonodynamic therapy mediated by a lecithin bilayer-coated poly(lactic-co-glycolic) nanoparticle preloaded with verteporfin, Ver-PLGA@Lecithin, to treat Helicobacter pylori.

Tao Liu
, Shuang Chai
& Lihua Yang

Article
27 January 2024 | Open Access

Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species

Combining theoretical derivation and numerical simulations, this study predicts an ecological mechanism for maintaining microbial coexistence via dynamic neutrality enabled by horizontal gene transfer. This mechanism allows the emergence of microbial diversity beyond the limit predicted by previous theories.

Shiben Zhu
, Juken Hong
& Teng Wang

Article
27 January 2024 | Open Access

Predatory protists reduce bacteria wilt disease incidence in tomato plants

Soil organisms are affected by the presence of predatory protists. Here, the authors predatory protists are negatively associated with bacteria wilt disease incidence in tomato plants and that fertilisation enhances the abundance of predatory protists

Sai Guo
, Zixuan Jiao
& Stefan Geisen

Article
26 January 2024 | Open Access

Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium

Synthetic microbial communities are suitable for mixed substrates fermentation and long metabolic pathway engineering. Here, the authors combine fermentation experiments with mathematical modeling to reveal the effect of compositional and temporal changes on division of labor in cellulosic ethanol production using two yeast strains.

Jonghyeok Shin
, Siqi Liao
& Yong-Su Jin

Article
26 January 2024 | Open Access

Microbial decomposition of biodegradable plastics on the deep-sea floor

It is unclear whether microbes can efficiently degrade biodegradable plastics in the extreme environmental conditions of the seafloor. Here, Omura et al. show that biodegradable plastics can be degraded by the action of microorganisms on the deep-sea floor, although with much less efficiency than in coastal settings.

Taku Omura
, Noriyuki Isobe
& Tadahisa Iwata

Article
17 January 2024 | Open Access

Effective binning of metagenomic contigs using contrastive multi-view representation learning

Here, the authors present COMEBin, a metagenomics binning method based on contrastive multi-view representation learning that uses data augmentation to generate multiple fragments (views) of each contig, resulting in high-quality embeddings of heterogeneous features. COMEBin outperforms state-of-the art binning methods, particularly in recovering near-complete genomes from real environmental samples.

Ziye Wang
, Ronghui You
& Shanfeng Zhu

Article
16 January 2024 | Open Access

Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes

Authors apply theory and microbial ecology modelling to a wastewater sample, and show that antimicrobial resistance carrying plasmids interact with a higher number and more diverse range of bacteria than plasmids that do not carry resistance genes.

Alice Risely
, Arthur Newbury
& Dirk Sanders

Article
16 January 2024 | Open Access

Towards estimating the number of strains that make up a natural bacterial population

What a microbial strain is and how many strains make up a natural bacterial population remain elusive concepts. Here, Viver et al. analyse Salinibacter ruber isolates and metagenomes from two solar salterns, revealing gaps within the species sequence space that they use to define and quantify sub-species categories, such as genomovars and strains, that co-exist in a saltern pond.

Tomeu Viver
, Roth E. Conrad
& Ramon Rossello-Mora

Article
10 January 2024 | Open Access

Defining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’

Given that the human body is composed of many microbial niches, and there have been few reports on the biogeography of the microbiome, the authors analyse the intra-individual inter-organ and intra-organ microbiome of seven surface organs of deceased individuals.

Jun-Jun She
, Wei-Xin Liu
& Jun Yu

Article
06 January 2024 | Open Access

Functional host-specific adaptation of the intestinal microbiome in hominids

Here, Rühlemann et al. analyze the gut microbiome of wild-living African great apes (Gorillas, Bonobos, Chimpanzees) in comparison to that of humans, identifying host specific patterns and shared evolutionary conserved traits disrupted in humans.

M. C. Rühlemann
, C. Bang
& A. Franke