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| Open AccessIdentification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting
Here, Riva et al. employ a multi-modal approach to identify gut microbes stimulated by the popular dietary supplement inulin and reveal that inulin binding and metabolic stimulation are widespread in the microbiome, making the framework a suitable way to study key microbes that perform specific functions in the microbiome.
- Alessandra Riva
- , Hamid Rasoulimehrabani
- & David Berry
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Article
| Open AccessGenome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota
The identification of processes activated by specific microbes during microbiota colonization of plant roots is hampered by technical issues in metatranscriptomics. Here, Vannier et al. colonized germ-free plants with a defined root microbiota comprising over 100 microbial isolates, and addressed those issues in various ways to identify strain-specific processes as well as common gene sets activated by microbes during root colonization.
- Nathan Vannier
- , Fantin Mesny
- & Stéphane Hacquard
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Article
| Open AccessPhyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes
Nitrate ammonifiers are poorly known despite their importance for soil nitrogen retention. This study shows that they are phylogenetically diverse and globally distributed across terrestrial biomes and that the outcome of the competition with denitrifiers is controlled by soil nitrate.
- Aurélien Saghaï
- , Grace Pold
- & Sara Hallin
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Article
| Open AccessResin acids play key roles in shaping microbial communities during degradation of spruce bark
The bark is the outermost defense of trees against microbial attack, largely due to toxicity of extractive compounds. Here, Ristinmaa et al. study microbial community dynamics and chemical changes during degradation of spruce bark over six months, showing that the microbial degradation of extractive compounds, such as resin acids, has a major role in shaping the microbial community.
- Amanda Sörensen Ristinmaa
- , Albert Tafur Rangel
- & Johan Larsbrink
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Article
| Open AccessStrong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP
The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. Here, Clerc et al. show that marine bacteria are strongly attracted to algal polysaccharides, and this chemotactic behaviour is enhanced by dimethylsulfoniopropionate (DMSP), a ubiquitous algal metabolite.
- Estelle E. Clerc
- , Jean-Baptiste Raina
- & Roman Stocker
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Article
| Open AccessIdentifying microbiota community patterns important for plant protection using synthetic communities and machine learning
The authors investigate microbiota properties for plant protection using synthetic communities and machine learning approaches. They identify strains that reduce pathogen colonization despite variation in microbiota composition.
- Barbara Emmenegger
- , Julien Massoni
- & Julia A. Vorholt
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Article
| Open AccessHealth-related quality of life is linked to the gut microbiome in kidney transplant recipients
Here, Swarte et al. use metagenomics to investigate the association between the gut microbiome and Health-Related Quality of Life (HRQoL) in kidney transplant recipients, showing evidence for the association of multiple taxonomic, metabolic and neuroactive pathways (gut brain modules) with lower HRQoL, together suggesting potential modifiable gut microbial factors to improve HRQoL.
- J. Casper Swarte
- , Tim J. Knobbe
- & Rinse K. Weersma
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Article
| Open AccessXylose and shikimate transporters facilitates microbial consortium as a chassis for benzylisoquinoline alkaloid production
It’s challenging to produce natural products using single strains of engineered microbes fed by renewable carbon sources. Here, the authors assemble a microbial consortium consisting of engineered S. stipitis and S. cerevisiae for streamlined production of (S)-norcoclaurine from glucose and xylose simultaneously.
- Meirong Gao
- , Yuxin Zhao
- & Zengyi Shao
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Article
| Open AccessMetagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface
The authors study microbial communities in hydrothermally heated, subseafloor sediment layers. They find that microbial abundance and diversity decrease with sediment depth and temperature, and provide evidence for the existence of a specialized deep, hot biosphere.
- Paraskevi Mara
- , David Geller-McGrath
- & Andreas Teske
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Article
| Open AccessRNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms
The roles of extracellular RNAs present in bacterial biofilms are poorly understood. Here, Mugunthan et al. show that specific mRNAs associate with extracellular DNA in the matrix of bacterial biofilms, facilitating the formation of viscoelastic networks.
- Sudarsan Mugunthan
- , Lan Li Wong
- & Thomas Seviour
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Article
| Open AccessParabacteroides distasonis ameliorates insulin resistance via activation of intestinal GPR109a
Here, the authors show that the gut commensal Parabacteroides distasonis alleviates insulin resistance via nicotinic acid-intestinal GPR109a axis activation, a process promoted by Dendrobium officinale polysaccharide.
- Yonggan Sun
- , Qixing Nie
- & Shaoping Nie
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Article
| Open AccessIdentification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius
Here, by characterizing 477 genomes from cultivated bacteria and metagenome-assembled genomes of the bee gut microbiota, the authors uncover uncharacterized biosynthetic gene clusters encoding small molecules with potential antimicrobial activity against bee pathogens, shedding light on the role of microbiome in honeybee health.
- Haoyu Lang
- , Yuwen Liu
- & Hao Zheng
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Article
| Open AccessExperimental mining plumes and ocean warming trigger stress in a deep pelagic jellyfish
The deep ocean is increasingly subjected to human-induced environmental change, but little is known about species-specific responses to stressors, including those from deep sea mining. This study shows that elevated temperatures and simulated sediment plumes cause physiological stress in a cosmopolitan deep-sea jellyfish, confirming the detrimental impact of seabed mining.
- Vanessa I. Stenvers
- , Helena Hauss
- & Henk-Jan T. Hoving
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Article
| Open AccessDirect comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities
The bacterium Bacillus subtilis can form various types of surface-associated communities, such as colonies, pellicles and submerged biofilms. Here, Dergham et al. provide a direct comparison of spatial transcriptional heterogeneity across the three types of surface-associated communities, revealing mosaic expression patterns for genes involved in various pathways.
- Yasmine Dergham
- , Dominique Le Coq
- & Romain Briandet
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Article
| Open AccessBacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient
Bacterial functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, Wang et al. investigate bacterial communities along a natural pH gradient in forest soils, and find that average genome size and functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral.
- Cong Wang
- , Qing-Yi Yu
- & Cheng Gao
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Article
| Open AccessInfant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species
Here, Lou et al. apply metagenomics and microbiome cultivation to infant fecal samples and uncover co-existing members encoding extracellular fucosidases that initiate 2’-fucosyllactose (2’FL) breakdown and can promote extensive growth of Bifidobacterium breve.
- Yue Clare Lou
- , Benjamin E. Rubin
- & Jillian F. Banfield
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Article
| Open AccessMicrobial methane cycling in a landfill on a decadal time scale
Microbial degradation of organic matter in landfills generates methane, a potent greenhouse gas. Here, Grégoire et al. use metagenomic approaches to study microbial methane cycling in waste landfilled over 39 years, highlighting the importance of specific microbial lineages and methane oxidation in the absence of oxygen.
- Daniel S. Grégoire
- , Nikhil A. George
- & Laura A. Hug
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Article
| Open AccessClinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide
Antimicrobial resistance genes (ARGs) in commensal gut bacteria may act as a reservoir for acquisition by pathogens. Here, the authors assess the distribution and transfer potential of ARGs in gut microbiomes and find that clinically important ARGs are taxonomically restricted despite being associated with mobile plasmids
- Peter J. Diebold
- , Matthew W. Rhee
- & Ilana L. Brito
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Article
| Open AccessA genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources
Soil conceals a vast realm of unexplored microbes, often referred to as the “microbial dark matter.” This hidden universe boasts a rich tapestry of microbial and genetic biodiversity. Here, the authors introduce the SMAG catalogue, comprising of 40,039 metagenome-assembled genomes from 3304 soil metagenomes, and uncovering 21,077 species-level genome bins.
- Bin Ma
- , Caiyu Lu
- & Jianming Xu
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Article
| Open AccessGut butyrate-producers confer post-infarction cardiac protection
Here, Chen et. al. characterize the relationship between the gut microbiota and plasma metabolite changes in the context of ST-elevation myocardial infarction (STEMI), unveiling a role of butyrate-producing bacteria and their ketogenesis in post-STEMI cardiac repair, a finding validated in nonhuman primate and mouse models. They show that butyrate supplementation reduces myocardial infarction severity in mice, underscoring the significance of butyrate-producing bacteria and beta-hydroxybutyrate in improving post-MI outcomes.
- Hung-Chih Chen
- , Yen-Wen Liu
- & Patrick C. H. Hsieh
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Article
| Open AccessPlanktonic microbial signatures of sinking particle export in the open ocean’s interior
Sinking of organic particles to the deep seafloor is fundamental to ocean carbon cycling. Here, the authors investigate prokaryotic communities in sinking and suspended particles, identifying depth-specific signatures of particle export and carbon cycling processes.
- Fuyan Li
- , Andrew Burger
- & Edward F. DeLong
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Article
| Open AccessEco-evolutionary feedbacks in the human gut microbiome
Little is known about how the evolution of gut microbiota is impacted by their surrounding community. Here, the authors examine the evolutionary ecology of the human gut microbiome, modelling resource competition to show that local evolutionary history can impact the structure and function of host microbiota.
- Benjamin H. Good
- & Layton B. Rosenfeld
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Article
| Open AccessRegulation of symbiotic interactions and primitive lichen differentiation by UMP1 MAP kinase in Umbilicaria muhlenbergii
The mechanisms regulating fungal-algal interactions during the formation of lichen symbioses are not clear. Here, Wang et al. establish conditions conducive to symbiotic interactions and lichen differentiation using a fungus amenable to genetic manipulation, showing the importance of a MAP kinase in lichen development.
- Yanyan Wang
- , Rong Li
- & Jin-Rong Xu
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Article
| Open AccessWastewater sequencing reveals community and variant dynamics of the collective human virome
Tisza et al. carry out a sequencing-based analysis of wastewater samples from major cities, to detect and quantify hundreds of distinct pathogenic viruses, finding striking correlations between virus abundance and local clinical cases.
- Michael Tisza
- , Sara Javornik Cregeen
- & Anthony W. Maresso
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Article
| Open AccessCoral endosymbiont growth is enhanced by metabolic interactions with bacteria
A new study reveals that bacterial partners supply essential metabolites to the vital microalgal symbionts of corals, including metabolites that boost symbiont growth. This breakthrough increases our understanding of coral microbial ecology and also opens the door to innovative ways of protecting coral reefs.
- Jennifer L. Matthews
- , Abeeha Khalil
- & Jean-Baptiste Raina
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Article
| Open AccessDisease-specific loss of microbial cross-feeding interactions in the human gut
Gut microbes rely on nutrient exchange for survival, but these cross-feeding interactions remain poorly characterized. Here, Marcelino et al. present a metabolite-exchange scoring system derived from metagenome-scale metabolic models, designed to identify the potential microbial cross-feeding interactions most affected in human diseases.
- Vanessa R. Marcelino
- , Caitlin Welsh
- & Samuel C. Forster
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Article
| Open AccessThe airway microbiota of neonates colonized with asthma-associated pathogenic bacteria
Here, Thorsen et al. bridge new and previous results from the COPSAC2000 prospective birth cohort and the later COPSAC2010 cohort, by constructing a combined bacterial pathogen score with implications for the early-life airway microbiota and the risk of asthma later in childhood
- Jonathan Thorsen
- , Xuan Ji Li
- & Jakob Stokholm
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Article
| Open AccessOxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium
Sulfate-reducing microorganisms are common in anoxic environments and represent an important link between the sulfur and carbon cycles. Here, Dyksma & Pester show that microbial sulfate reduction and aerobic respiration are not mutually exclusive in the same organism, sulfate reducers can mineralize organic polymers, and anaerobic mineralization of complex organic matter is not necessarily a multi-step process.
- Stefan Dyksma
- & Michael Pester
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Article
| Open AccessMetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
The authors develop an integrative and scalable framework to eliminate systematic biases and retrieve high-quality metagenome-assembled genomes using either long-read or short-read metagenomic Hi-C data.
- Yuxuan Du
- & Fengzhu Sun
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Article
| Open AccessGut microbiota aggravates neutrophil extracellular traps-induced pancreatic injury in hypertriglyceridemic pancreatitis
Given the association of gut microbiota dysbiosis with hypertriglyceridemic pancreatitis (HTGP), authors assess the gut microbial diversity of patients with HTGP, and provide immunological insight utilising a murine model.
- Guanqun Li
- , Liwei Liu
- & Bei Sun
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Article
| Open AccessRepressed Blautia-acetate immunological axis underlies breast cancer progression promoted by chronic stress
Chronic stress can promote breast cancer progression. Here the authors show that a reduction in the levels of Blautia and its metabolite acetate contributes to chronic stress-promoted breast cancer progression, associated with decreased CD8 + T cell anti-tumor immunity.
- Ling Ye
- , Yuanlong Hou
- & Haiping Hao
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Article
| Open AccessEcological mechanisms and current systems shape the modular structure of the global oceans’ prokaryotic seascape
This study investigated how ecological mechanisms and large-scale oceanic current systems shape prokaryotic microbial community patterns. They show that prokaryotic communities in the upper 200 m of the Pacific and Atlantic Ocean, the southern Indian Ocean, and the Mediterranean Sea have a modular structure of co-occurring taxa with similar environmental preferences.
- Felix Milke
- , Jens Meyerjürgens
- & Meinhard Simon
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Article
| Open AccessThe leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes
The human pathogen Streptococcus pyogenes secretes a short peptide (LCP) that mediates intercellular communication and controls bacterial virulence. Here, the authors show that LCP homologues act as bacterial intercellular signals and regulate gene expression also in other bacteria.
- Shifu Aggarwal
- , Elaine Huang
- & Muthiah Kumaraswami
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Article
| Open AccessA subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil
Rewetting of seasonally dry soils induces dramatic shifts in viral biomass and diversity. Combining stable isotope probing, metagenomics, and viromics Nicolas et al. provide evidence that viral lysis contributes to microbial turnover and the associated CO2 efflux.
- Alexa M. Nicolas
- , Ella T. Sieradzki
- & Steven J. Blazewicz
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Article
| Open AccessSocial and psychological adversity are associated with distinct mother and infant gut microbiome variations
Here, in a cohort of mother-child dyads, the authors show that maternal prenatal social disadvantage and psychosocial stressors associate with distinct gut microbiome taxonomic and functional diversity in both the mothers and their four-month children.
- Barbara B. Warner
- , Bruce A. Rosa
- & Makedonka Mitreva
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Article
| Open AccessEcophysiology and interactions of a taurine-respiring bacterium in the mouse gut
Authors utilise a multi-omics approach for the ecophysiological characterization of a taurine-respiring mouse gut bacterium.
- Huimin Ye
- , Sabrina Borusak
- & Alexander Loy
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Article
| Open AccessBridging of host-microbiota tryptophan partitioning by the serotonin pathway in fungal pneumonia
Serotonin regulates mood as well as intestinal homeostasis, but its role in lung immune homeostasis is less clear. Here, Renga et al. show that serotonin regulates immune and microbial metabolic functions in respiratory pneumonia, beyond its mood regulatory function, by modulating tryptophan metabolism in the cystic fibrosis lung.
- Giorgia Renga
- , Fiorella D’Onofrio
- & Luigina Romani
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Article
| Open AccessGrowth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes
Here, the authors present a novel approach for inferring in vivo growth phases of human gut bacteria from metagenomic time series data. These inferences can be used to better-constrain community scale metabolic modeling in the gut.
- Joe J. Lim
- , Christian Diener
- & Sean M. Gibbons
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Article
| Open AccessSingle-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum
Bacterial remineralization of algal organic matter promotes algal growth but is rarely quantified. Here, Mayali et al. quantify bacterial incorporation of algal-derived organic carbon and nitrogen, and algal incorporation of remineralized carbon and nitrogen, for 15 bacterial co-cultures growing with the diatom Phaeodactylum tricornutum to identify functional guilds of metabolic interactions.
- Xavier Mayali
- , Ty J. Samo
- & Peter K. Weber
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Article
| Open AccessInter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation
Abiotic stress is thought to promote microbial mutualism, although there is a paucity of research in this area. Here, Zhao et al. study microbial communities in a quasi-natural composting system, where temperature variation (20°C−70°C) is the main abiotic stress, showing how high temperature favours mutualism and reduces competition at both the community and species levels.
- Yuxiang Zhao
- , Zishu Liu
- & Baolan Hu
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Article
| Open AccessGenome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater
Anaerobic digestion of municipal mixed sludge is a microbial-mediated process that produces renewable natural gases such as methane. Here, Kieft et al. present the results of a two-year study of microbial community structure and function at a wastewater treatment plant, shedding light on metabolic interactions between microorganisms in relation with methane production.
- Brandon Kieft
- , Niko Finke
- & Steven J. Hallam
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Article
| Open AccessRemoval of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites
Here, leveraging species-specific Type IIB restriction endonuclease digestion sites as reference instead of universal markers or whole microbial genomes, the authors introduce MAP2B, a metagenomic profiler, showing it can significantly remove false-positive identification and generate highly accurate taxonomic profiling results.
- Zheng Sun
- , Jiang Liu
- & Yang-Yu Liu
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Article
| Open AccessThe interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis
Here, Schoeler et al. investigate how interaction between dietary lipids and the gut microbiota affect hepatic steatosis and host metabolism, showing that dietary lipids impact the gut microbiota composition independent on fiber intake in humans and mice.
- Marc Schoeler
- , Sandrine Ellero-Simatos
- & Robert Caesar
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Article
| Open AccessDelayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease
Here, using participants in the CHILD birth cohort, the authors reveal that impaired 1-year microbiota maturation may be universal to 5-year pediatric allergies, mediated by functional and metabolic imbalances of compromised mucous integrity, elevated oxidative activity, decreased fermentation, and elevated trace amines.
- Courtney Hoskinson
- , Darlene L. Y. Dai
- & Stuart E. Turvey
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Article
| Open AccessFiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential
Here, the authors show that fiber supplementation protects from antibiotic-induced gut microbiome damage by reducing the abundance of aerobic bacteria as well as metabolic pathways associated with oxidative metabolism.
- Swathi Penumutchu
- , Benjamin J. Korry
- & Peter Belenky
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Article
| Open AccessAntibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites
Broad-spectrum antibiotics can kill harmless bacteria in our intestine, thus facilitating invasion by antibiotic-resistant bacteria such as carbapenem-resistant Enterobacteriaceae (CRE). Here, Yip et al. show that killing gut bacteria with antibiotics leads to enrichment of nutrients and depletion of inhibitory microbial metabolites, which overall potentiates CRE growth.
- Alexander Y. G. Yip
- , Olivia G. King
- & Julie A. K. McDonald
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Article
| Open AccessMicrodiversity of the vaginal microbiome is associated with preterm birth
Here, Liao et al. analyze the vaginal microbiome during pregnancy, and find a unique population genetic structure associated with preterm birth, suggesting that evolutionary processes acting on vaginal bacteria may play a role in prematurity.
- Jingqiu Liao
- , Liat Shenhav
- & Tal Korem
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Perspective
| Open AccessExtreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology
The ecology and evolution of eukaryotic microbes in extreme environments are poorly understood. In this Perspective, Rappaport and Oliverio summarize data from over 80 studies of protists in extreme environments and identify lineages of particular interest as targets for future research.
- Hannah B. Rappaport
- & Angela M. Oliverio
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Article
| Open AccessSystematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations
This study unified cnidarian microbiome data from 186 studies (~ 6.5 billion sequence reads), providing novel insights into cnidarian microbial communities and highlighting key bacteria across sub-phylum, geography, depth and microhabitat. Understanding factors governing microbiome health will support ongoing and future coral preservation efforts.
- M. McCauley
- , T. L. Goulet
- & S. Loesgen