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Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase
Metagenomics is revealing auxiliary metabolic genes (AMGs) in soil viral genomes. Here, authors solve the crystal structure for a soil viral AMG product, free and ligand bound, and show the protein can decompose chitin, a common carbon polymer.
- Ruonan Wu
- , Clyde A. Smith
- & Janet K. Jansson
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Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes
Here, using whole-metagenome shotgun sequencing data from patients with COVID-19 and controls, the authors reconstruct 11,584 microbial metagenome-assembled genomes (MAGs) including 5,403 non-redundant MAGs, revealing microbiota and metabolic pathways associations with SARS-CoV-2 infection at strain-level resolution.
- Shanlin Ke
- , Scott T. Weiss
- & Yang-Yu Liu
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Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort
Here, Nishijima et al. perform a large-scale analysis of the human gut virome in the Japanese 4D cohort of 4198 deeply phenotyped individuals, revealing thousands of bacteriophage genomes, virus-bacteria interactions, and describing associations with various host and environmental factors.
- Suguru Nishijima
- , Naoyoshi Nagata
- & Masahira Hattori
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Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome
This study presents a large-scale analysis of microbial diversity in deep-sea sponges. They show that sponge microbial abundance status, geographic distance, sponge phylogeny and the physical-biogeochemical environment drive microbiome composition, in descending order of relevance. The uniqueness of each deep-sea sponge ground stresses the need for their strategic preservation.
- Kathrin Busch
- , Beate M. Slaby
- & Ute Hentschel
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A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome
Here the authors present a large-scale resource of the early-life human gut microbiome from children under three years old, which comprises 32,277 metagenome-assembled gut genomes, representing 2172 species, and more than 80 million gut proteins representing >4 million protein clusters, spanning multiple clinical factors including age, delivery mode, gestational age, and feeding patterns.
- Shuqin Zeng
- , Dhrati Patangia
- & Shaopu Wang
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Integrated relationship of nasopharyngeal airway host response and microbiome associates with bronchiolitis severity
Bronchiolitis is major cause of infection, morbidity and hospitalisation. Here the authors apply transcriptomic based assessment of the host response, microbiome composition and function, and associate this to bronchiolitis severity.
- Michimasa Fujiogi
- , Yoshihiko Raita
- & Kohei Hasegawa
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Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data
Here, the authors present Sparse Estimation of Correlations among Microbiomes (SECOM), a tool devised to characterize both linear and nonlinear relationships in microbiome data. When applied to human skin and infant gut microbiome data, SECOM is able to retrieve taxa interactions undescribed by previous methods.
- Huang Lin
- , Merete Eggesbø
- & Shyamal Das Peddada
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Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments
Microbial nitrogen fixation could be important in the deep sea. Here the authors investigate metagenomes and metatranscriptomes of diazotrophs from deep sea cold seep sediments, reveal greater phylogenetic and functional diversity than hitherto known.
- Xiyang Dong
- , Chuwen Zhang
- & Chris Greening
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| Open Access
Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback
Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. Here, in a community of two competing E. coli strains, the authors show that the relative abundances of the strains can be stabilized and steered dynamically with remarkable precision by coupling the cells to an automated computer-controlled feedback-loop.
- Joaquín Gutiérrez Mena
- , Sant Kumar
- & Mustafa Khammash
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Acetate reprograms gut microbiota during alcohol consumption
Chronic alcohol use is associated with intestinal bacterial overgrowth and dysbiosis, but the contribution of ethanol is unclear. Here, using mouse models, the authors find that ethanol is not directly metabolized by the gut microbiota, and that induced changes are rather a side effect of elevated acetate levels.
- Cameron Martino
- , Livia S. Zaramela
- & Karsten Zengler
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| Open Access
Dietary protein increases T-cell-independent sIgA production through changes in gut microbiota-derived extracellular vesicles
Secretory IgA plays vital roles interfacing between the host immune system and the resident microbiota at the mucosal surface. Here the authors explore the effect of dietary protein on the production of secretory IgA, driven by the production of extracellular vesicles by the intestinal microbiota.
- Jian Tan
- , Duan Ni
- & Laurence Macia
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| Open Access
A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response
The bacterium Phocaeicola vulgatus is commonly found in the human gut. Here, the authors show that the microorganism produces an antibacterial toxin that targets the LPS core glycan of closely related species and induces a response that partially protects cells from multiple antimicrobial toxins.
- Jordan C. Evans
- , Valentina Laclare McEneany
- & Laurie E. Comstock
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| Open Access
Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment
Steatohepatitis is a chronic hepatic inflammation associated with increased risk of hepatocellular carcinoma progression. Here the authors show that intestinal dysbiosis in mice lacking the inflammasome sensor molecule NLRP6 aggravates steatohepatitis and accelerates liver cancer progression, a process that can be delayed by antibiotic treatment.
- Kai Markus Schneider
- , Antje Mohs
- & Christian Trautwein
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Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids
Efficient solubilization of plant cell wall carbohydrates is required for microbial production of biofuels from lignocellulosic biomass. Here, the authors employ metaproteomics to interrogate enzymatic strategies of a methanogenic microbiome deconstructing switchgrass at increasing solids loading.
- Payal Chirania
- , Evert K. Holwerda
- & Lee R. Lynd
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Engineering consortia by polymeric microbial swarmbots
Most attempts to co-cultivate the artificial microbial communities fail mostly due to the mismatched rates of consumption and production of nutrients among subpopulations. Here, the authors develop a microbial swarmbot mediated spatial segregation method to assemble stably coexisting consortia with both flexibility and precision.
- Lin Wang
- , Xi Zhang
- & Zhuojun Dai
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| Open Access
An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species
Here, Leviatan et al. produce 241,118 genome assemblies to produce a new human gut microbiome reference set of 3,594 species genomes, of which 310 represent previously undescribed species, making the catalog a valuable resource for further research.
- Sigal Leviatan
- , Saar Shoer
- & Eran Segal
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Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities
Fungi are expected to be more resistant and less resilient than bacteria to environmental disturbances. Here, the authors report complex responses by microbial co-occurrence networks to drought in an agricultural system, challenging simple predictions of fungal and bacterial drought responses.
- Cheng Gao
- , Ling Xu
- & John W. Taylor
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| Open Access
Engineering probiotics to inhibit Clostridioides difficile infection by dynamic regulation of intestinal metabolism
Clostridioides difficile infection (CDI) results in significant morbidity and mortality in hospitalised patients. Here the authors engineer probiotics to restore intestinal bile salt metabolism in response to antibiotic-induced microbiome dysbiosis significantly inhibit Clostridioides difficile infection in model mice, presenting a microbiome-based antimicrobial strategy
- Elvin Koh
- , In Young Hwang
- & Matthew Wook Chang
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Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis
This study shows that sea anemones acclimated to high temperatures exhibit increased resistance to thermal stress and that this improved fitness can be transferred by microbiome transplantation. These results indicate that plasticity mediated by the microbiota might be an important factor facilitating thermal adaptations in animals.
- Laura Baldassarre
- , Hua Ying
- & Sebastian Fraune
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Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome
Here, the authors characterize gut viromes in a cohort of individuals with metabolic syndrome, which they find associated with a highly widespread family of gut bacteriophages they name Candidatus Heliusviridae.
- Patrick A. de Jonge
- , Koen Wortelboer
- & Hilde Herrema
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| Open Access
Host control and the evolution of cooperation in host microbiomes
Humans, and many other species, carry a large set of beneficial microbes. Here, the authors present new theory and data to argue that these vital relationships only work when hosts can control their microbiome and suppress wayward symbionts.
- Connor Sharp
- & Kevin R. Foster
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| Open Access
Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes
Here, by characterizing gut metagenomes of at-risk children in the TEDDY project, the authors associate onset of autoimmunity leading to Type-1 diabetes with certain sets of microorganisms in the gut microbiota, and identify metabolic capabilities encoded in the genomes of these microorganisms that provide functional insights to the association.
- Li Zhang
- , Karen R. Jonscher
- & Chongle Pan
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Disentangling the genetic basis of rhizosphere microbiome assembly in tomato
Genetics factors involved in rhizosphere microbiomes assembly remain largely elusive. Here, the authors integrate microbiomics and quantitative plant genetics to reveal genetic loci associated with specific microbes and rhizobacterial traits underlying microbiome assembly in tomato.
- Ben O. Oyserman
- , Stalin Sarango Flores
- & Jos M. Raaijmakers
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Identifying plant genes shaping microbiota composition in the barley rhizosphere
A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere. Here, the authors report QTLs and the associated candidate genes underlying rhizosphere microbiome composition in barley.
- Carmen Escudero-Martinez
- , Max Coulter
- & Davide Bulgarelli
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| Open Access
Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom
Here, by analyzing 250 species of animals covering a large taxonomic spectrum, the authors show that archaea are common constituent of the animal gut throughout the animal kingdom, and identify six main genera/families of gut archaea revealing their abundance and diversity to be driven by host diet, evolutionary history and physiology.
- Courtney M. Thomas
- , Elie Desmond-Le Quéméner
- & Guillaume Borrel
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| Open Access
Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer
Bacteria from the genus Fusobacterium can promote colorectal cancer (CRC) development; however, the exact Fusobacterium species involved in this process remain underexplored. Here, the authors develop a rpoB amplicon sequencing approach to identify Fusobacterium species and subspecies in CRC patient samples.
- Dexi Bi
- , Yin Zhu
- & Huanlong Qin
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| Open Access
Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity
Commensal bacteria such as Lactobacillus rhamnosus can inhibit the pathogenicity of the fungus Candida albicans. Here, Alonso-Roman et al. investigate the interplay between C. albicans, L. rhamnosus and intestinal epithelial cells, showing that changes in the metabolic environment, induced by the bacteria, trigger adaptations in C. albicans that reduce fungal pathogenicity.
- Raquel Alonso-Roman
- , Antonia Last
- & Mark S. Gresnigt
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Machine learning aided construction of the quorum sensing communication network for human gut microbiota
Microbes communicate with each other by Quorum sensing (QS) languages. Here the authors construct a QS database and the QS communication network to decipher intricate QSbased communications and form one of the key knowledge maps for human gut microbiota.
- Shengbo Wu
- , Jie Feng
- & Jianjun Qiao
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The microbiome of cryospheric ecosystems
The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires.
- Massimo Bourquin
- , Susheel Bhanu Busi
- & Tom J. Battin
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Predicting cancer prognosis and drug response from the tumor microbiome
Computational approaches have been developed to estimate tumor microbial abundances from whole genomic and RNA-sequencing datasets. Here the authors report the predictive value of tumor microbial abundance, alone or in combination with gene expression data, for cancer prognosis and drug response.
- Leandro C. Hermida
- , E. Michael Gertz
- & Eytan Ruppin
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Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ
In this study, the concept of dynamic character displacement among interacting bacterial species from leaf-colonizing families was empirically tested using a proteomics approach. A phenotypic shift towards the utilization of alternative carbon sources was observed during coexistence, thereby minimizing niche overlap.
- Lucas Hemmerle
- , Benjamin A. Maier
- & Julia A. Vorholt
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Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter
Computational methods to analyse microbial systems rely on reference databases which do not capture their full functional diversity. Here the authors develop a deep learning model and apply it using transfer learning, creating biologically useful models for multiple different tasks.
- A. Hoarfrost
- , A. Aptekmann
- & Y. Bromberg
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| Open Access
A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease
Exercise and diet interventions are treatments for nonalcoholic fatty liver disease (NAFLD). Here the authors report that in randomized, controlled trial in patients with NAFLD exercise and diet intervention were associated with diversified gut microbiome keystone taxa. Exploratory analysis suggests gut microbial network may be used to predict the individual liver fat response to exercise intervention, if validated in future studies.
- Runtan Cheng
- , Lu Wang
- & Sulin Cheng
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| Open Access
Natural transformation allows transfer of SCCmec-mediated methicillin resistance in Staphylococcus aureus biofilms
SCCmec is a large mobile genetic element that confers resistance to β-lactam antibiotics in methicillin-resistant Staphylococcus aureus. Here, the authors show that biofilm growth conditions enhance the efficiency of natural transformation in S. aureus and allow the transfer of SCCmec to methicillin-sensitive strains.
- Mais Maree
- , Le Thuy Thi Nguyen
- & Kazuya Morikawa
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| Open Access
Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region
Coastal upwelling sustains some of the most productive ocean regions. Here, the authors find that spatial patterns and temporal changes in nutrient supply explain marine microbial community structure and diversity in the Southern California Current region.
- Chase C. James
- , Andrew D. Barton
- & Andrew E. Allen
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| Open Access
Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China
The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage sediments sampled across Southern China, showing the predominant effects of prokaryotic communities and the influence of environmental variables on viral taxonomy and function.
- Shaoming Gao
- , David Paez-Espino
- & Linan Huang
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Evolution of the murine gut resistome following broad-spectrum antibiotic treatment
Antimicrobial resistance represents an ongoing silent pandemic. Here, de Nies et al. show that a single antibiotic treatment leads to resistance in bacteria such as Akkermansia muciniphila and that integrons play a key role in mediating this resistance.
- Laura de Nies
- , Susheel Bhanu Busi
- & Paul Wilmes
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| Open Access
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
Here, the authors present SemiBin, a siamese deep neural network framework that incorporates information from reference genomes, able to extract better metagenome-assembled genomes (MAGs) in several host-associated and environmental habitats.
- Shaojun Pan
- , Chengkai Zhu
- & Luis Pedro Coelho
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| Open Access
Honeybee gut Lactobacillus modulates host learning and memory behaviors via regulating tryptophan metabolism
Eusocial honeybee is a versatile model for neurobiological research. Here, the authors established a link between honeybee gut Lactobacillus in bee learning and memory ability via indole derivatives that activate host’s aryl hydrocarbon receptor.
- Zijing Zhang
- , Xiaohuan Mu
- & Hao Zheng
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| Open Access
Gut microbiota-bile acid crosstalk contributes to the rebound weight gain after calorie restriction in mice
Caloric restriction is a common approach to weight reduction, however, weight regain is common. Here the authors report that caloric restriction reduces the abundance of Parabacteroides distasonis in the gut and alters serum bile acid (BA) profile, which contribute to weight regain in mice.
- Mengci Li
- , Shouli Wang
- & Wei Jia
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| Open Access
MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
Microbial communities are responsible for biological wastewater treatment. Here, Dueholm et al. generate more than 5 million high-quality, full-length 16S rRNA gene sequences from wastewater treatment plants across the world to construct a database with a comprehensive taxonomy, providing insights into diversity and function of these microbial communities.
- Morten Kam Dahl Dueholm
- , Marta Nierychlo
- & Per Halkjær Nielsen
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| Open Access
Gut microbiota production of trimethyl-5-aminovaleric acid reduces fatty acid oxidation and accelerates cardiac hypertrophy
Intestinal microbiota alterations may affect heart function through the production of gut-derived metabolites. Here the authors found that gut microbiota-derived TMAVA is a key determinant for the development of cardiac hypertrophy through inhibition of carnitine synthesis and subsequent fatty acid oxidation.
- Mingming Zhao
- , Haoran Wei
- & Lemin Zheng
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| Open Access
The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host
The Micrarchaeota lineage includes poorly characterized archaea with reduced genomes that likely depend on host interactions for survival. Here, the authors report a stable co-culture of a member of the Micrarchaeota and its host, and use multi-omic and physiological analyses to shed light on this symbiosis.
- Susanne Krause
- , Sabrina Gfrerer
- & Johannes Gescher
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| Open Access
Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis
Here, the authors show that treatment with a monoclonal neutralizing antibody against the lung microbiota-derived proapoptotic peptide corisin ameliorates acute exacerbation of pulmonary fibrosis and severity of endotoxin-induced acute lung injury in mice.
- Corina N. D’Alessandro-Gabazza
- , Taro Yasuma
- & Esteban C. Gabazza
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| Open Access
Assessment of global health risk of antibiotic resistance genes
Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health. Here, Zhang et al. analyze 4572 metagenomic samples to illustrate the global patterns of ARG distribution in diverse habitats. They quantitatively evaluate the health risk to humans of 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. With the machine learning, they map the antibiotic resistance threats in global marine habitats.
- Zhenyan Zhang
- , Qi Zhang
- & Haifeng Qian
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| Open Access
Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome
Here, Forster et al. compare 1354 cultured commensal strains (540 species) to 45,403 pathogen strains (12 species), identifying 64,188 MGE-mediated antibiotic resistance gene transfer events between the two groups, and show that 15 broad host range MGEs are able to transfer between phyla.
- Samuel C. Forster
- , Junyan Liu
- & Trevor D. Lawley
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| Open Access
Dynamics of plasmid-mediated niche invasion, immunity to invasion, and pheromone-inducible conjugation in the murine gastrointestinal tract
Microbial communities provide protection to their hosts by excluding colonizing pathogens. Here the authors study plasmid transfer and plasmid-mediated effects on host colonization and persistence of Enterococcus faecalis in the intestinal tract of mice.
- Helmut Hirt
- , Kerryl E. Greenwood-Quaintance
- & Gary M. Dunny
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| Open Access
Synthetic glycans control gut microbiome structure and mitigate colitis in mice
Here, the authors characterize the gut microbiome fermentation properties and therapeutic potential of chemically diverse synthetic glycans (SGs), showing they promote specific shifts in taxonomic and metabolite profiles, and exhibit therapeutic benefits in mouse models of colonic inflammation, together implying SGs as a potential avenue to treat disease by modulating the composition and metabolites produced by the gut microbiome.
- Andrew C. Tolonen
- , Nicholas Beauchemin
- & Johan E. T. van Hylckama Vlieg
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| Open Access
Changes to gut amino acid transporters and microbiome associated with increased E/I ratio in Chd8+/− mouse model of ASD-like behavior
The gut microbiota has been shown to modulate the neural function via the microbiota-gut-brain axis. Here, the authors show that Bacteroides uniformis, a gut commensal bacterium, restores the ASD-like phenotypes by reducing intestinal amino acid transport in an ASD mouse model.
- You Yu
- , Bing Zhang
- & Fangqing Zhao
Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae