Category Archives: Animal experiments

January 12, 2022

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General microbiome

[PERSPECTIVE]It’s the Economy, Stupid: Applying (Micro)economic Principles to Microbiome Science – Kashtan, Bushong and Leveau – mSystems

[PERSPECTIVE]Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes – Pfister et al. – mSystems

Human endometrial microbiome

Endometrial microbiota composition is associated with reproductive outcome in infertile patients – Moreno et al. – Microbiome

Human oral microbiome

[REVIEW]Temporal development of the infant oral microbiome – Blum et al. – Critical Reviews in Microbiology

Human gut microbiome

Effect of antibiotic pretreatment on bacterial engraftment after Fecal Microbiota Transplant (FMT) in IBS-D – Singh et al. – Gut Microbes

[REVIEW]The gut microbiota can orchestrate the signaling pathways in colorectal cancer – Bennedsen et al. – Journal of Pathology, Microbiology and Immunology

Age-Associated Gut Dysbiosis, Marked by Loss of Butyrogenic Potential, Correlates With Altered Plasma Tryptophan Metabolites in Older People Living With HIV – Ghare et al. – Journal of Acquired Immune Deficiency Syndrome

Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome – Zhou et al. – mSystems

The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection – Chanderraj et al. – Microbiome

Animal microbiome

Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets – Li et al. – Animal Microbiome

Maternal regulation of biliary disease in neonates via gut microbial metabolites – Jee et al. – Nature Communications

Reduced calorie diet combined with NNMT inhibition establishes a distinct microbiome in DIO mice – Dimet-Wiley et al. – Scientific Reports

Comparison of Gut Microbiota and Metabolic Status of Sows With Different Litter Sizes During Pregnancy – Chen et al. – Front. Vet. Sci.

Modulation of gut microbiota impacts diet-induced and drug-induced alopecia in mice – Lam et al. – Gut

Sex-specific differences in the gut microbiota and fecal metabolites in an adolescent valproic acid-induced rat autism model – Gu et al. – Frontiers in Bioscience Landmark

Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism – Lee et al. – Microbiome

Plant, root, and soil microbiome

Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities – Ponsford et al. – mSystems

Bioinformatics

A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer – Armour et al. – mBio

Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer – Casimiro-Soriguer et al. – Scientifi Reports

Techniques

[PREPRINT]Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes – Poulsen et al. – bioRxiv

January 4, 2022

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Happy new year! Today’s digest is jam packed with articles published over the Christmas period. This includes the Skin Microbial Genome Collection (SMGC), a fascinating study linking the gut virome to rotavirus vaccine response, multiple cancer-microbiome papers and a catalogue of the human gut archaeome

General microbiome

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes – Bossche et al. Microbiome

Directional Gaussian Mixture Models of the Gut Microbiome Elucidate Microbial Spatial Structure – Pasarkar et al. mSystems

Human gut microbiome

Human gut-microbiome-derived propionate coordinates proteasomal degradation via HECTD2 upregulation to target EHMT2 in colorectal cancer – Ryu et al. ISME

Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network – Goffau et al. Nature Microbiology.

Reuterin in the healthy gut microbiome suppresses colorectal cancer growth through altering redox balance – Bell et al. Cancer Cell. 

Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease – Walker et al. Genome Medicine

Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants – Kim et al. Cell Host & Microbe

Maternal gut bacteria drive intestinal inflammation in offspring with neurodevelopmental disorders by altering the chromatin landscape of CD4+ T cells – Kim et al. Immunity

Lactobacillus gallinarum modulates the gut microbiota and produces anti-cancer metabolites to protect against colorectal tumourigenesis – Sugimura et al. Gut

A catalogue of 1,167 genomes from the human gut archaeome – Chibani et al. Nature Microbiology

Variation and transmission of the human gut microbiota across multiple familial generations – Valles-Colomer et al. Nature Microbiology. 

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping – Beresford-Jones et al. Cell Host & Microbe

Human skin & oral microbiome

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions – Kashaf et al. Nature Microbiology.

Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics – Jo et al. Science Translational Medicine

Microbiome-mediated incapacitation of interferon lambda production in the oral mucosa – Rodriguez-Hernandez et al. PNAS

Plant microbiome

Glutamic acid reshapes the plant microbiota to protect plants against pathogens – Kim et al. Microbiome. 

Water microbiome

Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy – Garber et al. mSphere

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution – Bowers et all. ISME

Bioinformatics

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro – Shi et al. Nature Biotechnology

Rapid screening and identification of viral pathogens in metagenomic data – Song et al. BMC Medical Genomics. 

December 22, 2021

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General microbiome

[PREPRINT]Unconstrained coevolution of bacterial size and the latent period of plastic phage – Bonachela, Choua & Heath – bioRxiv

Not a ‘they’ but a ‘we’: the microbiome helps promote our well-being – Ragsdale – Journal of Biological Chemistry

Microbial metabolite delta-valerobetaine is a diet-dependent obesogen – Liu et al. – Nature Metabolism

[EDITORIAL]15 years of microbial biotechnology: the time has come to think big—and act soon – de Lorenzo – Microbial Biotechnology

Pregnancy and early life

Microbial community networks across body sites are associated with susceptibility to respiratory infections in infants – Reyman et al. – Communications Biology

Human oral microbiome

Profiling the oral microbiomes in patients with Alzheimer’s disease – Guo et al. – Oral Diseases

Human skin microbiome

[REVIEW]Human Skin Microbiota in Health and Disease – Bay & Ring – Journal of Pathology, Microbiology and Immunology

Human vaginal microbiome

Human implantation: The complex interplay between endometrial receptivity, inflammation, and the microbiome – Sehring & Jeelani – Placenta

Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population – Ng et al. – NPJ Biofilms and Microbiomes

Human gut microbiome

The potential of gut microbiome as a non-invasive predictive biomarker for early detection of pancreatic cancer and hepatocellular carcinoma – Kaźmierczak-Siedlecka – European Review for Medical and Pharmacological Sciences

The effect of antibiotics on the human microbiome: a systematic review – van Zyl et al. – International Journal of Antimicrobial Agents

[REVIEW]Non-alcoholic fatty liver disease: the interplay between metabolism, microbes and immunity – Tilg et al. – Nature Metabolism

Clinical efficacy of fecal microbial transplantation treatment in adults with moderate-to-severe atopic dermatitis – Mashiah et al. – Immunity, Inflammation and Disease

Deviated and early unsustainable stunted development of gut microbiota in children with autism spectrum disorder – Lou et al. – Gut

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Oat Fiber Modulates Hepatic Circadian Clock via Promoting Gut Microbiota-Derived Short Chain Fatty Acids – Han et al. – J. Agric. Food Chem.

Animal microbiome (for animals in the wild)

Effects of sublethal azadirachtin on the immune response and midgut microbiome of Apis cerana cerana (Hymenoptera: Apidae) – Zhao et al. – Ecotoxicology and Environmental Safety

Analysis of the microbial diversity in the fecal material of the critically endangered African wild dog, Lycaon pictus – Sanches et al. – Archives of Microbiology

Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species – Maltseva et al. – PLOS One

Gut microbiome composition, not alpha diversity, is associated with survival in a natural vertebrate population – Worsley et al. – Animal Microbiome

Clinical health issues, reproductive hormones, and metabolic hormones associated with gut microbiome structure in African and Asian elephants – Keady et al. – Animal Microbiome

Early life skin microbial trajectory as a function of vertical and environmental transmission in Bornean foam-nesting frogs – McGrath-Blaser et al. – Animal Microbiome

Plant, root, and soil microbiome

[PRERPINT]Disentangling the genetic basis of rhizosphere microbiome assembly in tomato – Oyserman et al. – bioRxiv

[PREPRINT]Amino acid availability determines plant immune homeostasis in the rhizosphere microbiome – Liu et al. – bioRxiv

Techniques

Ancient Metagenomic Studies: Considerations for the Wider Scientific Community – der Sarkissian et al. – mSystems

Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition – Holzhausen et al. – Gut Pathogens

December 20, 2021

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Today’s digest is a grab bag that includes research articles on the vaginal microbiota, the gut microbiota of dairy calves, microbial loads in medical waste, and more! I’ve also highlighted a non-microbiology article that found that pet dog owners were significantly less depressed than non-pet owners during the pandemic. So if you’re looking for more reasons to adopt a new furry friend, you can add this one to the list!

General microbiome

Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei – Zulkefli et al. – PLOS One

Human vaginal microbiome

Vaginal microbiota of American Indian women and associations with measures of psychosocial stress – Borgogna et al. – PLOS One

Human gut microbiome

Gut microbiota features associated with Clostridioides difficile colonization in dairy calves – Redding et al. – PLOS One

Animal microbiome

Culicoides Latreille (Diptera: Ceratopogonidae) as potential vectors for Leishmania martiniquensis and Trypanosoma sp. in northern Thailand – Sunantaraporn et al. – PLOS Neglected Tropical Diseases

Migratory wild birds carrying multidrug-resistant Escherichia coli as potential transmitters of antimicrobial resistance in China – Yuan et al. – PLOS One

Plant, root, and soil microbiome

Characterization of soils conducive and non-conducive to Prunus replant disease – Khan et al. – Plos One

Built environment

Disposal habits and microbial load of solid medical waste in sub-district healthcare facilities and households in Yilo-Krobo municipality, Ghana – Egbenyah et al. – PLOS One

Phages and viruses

A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus – Celone et al. – PLOS Neglected Tropical Diseases

Bioinformatics

Genomic prediction using low-coverage portable Nanopore sequencing – Lamb et al. – PLOS One

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations – Lim et al. – PLOS One

Kara’s non-microbiology pick

***Depression, anxiety, and happiness in dog owners and potential dog owners during the COVID-19 pandemic in the United States – Martin et al. – PLOS One

December 16, 2021

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Today’s digest features the Global Microbial Gene Catalog, studies on group B Streptococcus vaginal colonization in a murine model and Patescibacteria in oxic and anoxic groundwater, and more. Happy holidays!

Important NEWS from the Microbiome Virtual International Forum:
The recordings of the MVIF #4 with Jonathan Eisen and other speakers are available here.
The registration for the MVIF #5 with Eran Elinav is open.
The abstract submission for the MVIF #6 with Susan Holmes is open.

Global microbiome

*Towards the biogeography of prokaryotic genes – Luis Pedro Coelho – Nature

Review: Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research – Imane Allali – Microbiome

Human milk microbiome

Factors influencing the microbial composition of human milk – Anastasia Mantziaria and Samuli Rautavab – Seminars in Perinatology

Animal experiments

*Group B Streptococcus CAMP Factor Does Not Contribute to Interactions with the Vaginal Epithelium and Is Dispensable for Vaginal Colonization in Mice – Mallory B. Ballard – Microbiology Spectrum

Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing – Jongoh Shin – Microbiome

Water microbiome

*The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers – Narendrakumar M. Chaudhari – Environmental Microbiome

Bioinformatics

EXPERT: Transfer Learning-enabled context-aware microbial source tracking – Hui Chong – bioRxiv
https://www.biorxiv.org/content/10.1101/2021.01.29.428751v2

NEWS from NCBI taxonomy

December 15, 2021

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Nasal microbiome

Deep nasal sinus cavity microbiota dysbiosis in Parkinson’s disease – Pal et al – NPJ Parkinson’s disease

Pregnancy and early life

Influence of Family Integrated Care on the Intestinal Microbiome of Preterm Infants With Necrotizing Enterocolitis and Enterostomy: A Preliminary Study – Yang et al. – Front. Pediatr.

Multi-site human microbiome

[PREPRINT]Alternations of fecal microbes and lung tissue microbes in Lung Cancer patients is more consistent than that of sputum – Yanze et al. – bioRxiv

Human oral microbiome

[PREPRINT]A core salivary microbiome shows the high prevalence of bacterial members yet variability across human populations – Ruan et al. – bioRxiv

Human eye microbiome

Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease – Liang et al. – Front. Cell Dev. Biol.

Human vaginal microbiome

[REVIEW]Beyond bacterial vaginosis: vaginal lactobacilli and HIV risk – Armstrong & Kaul – Microbiome

Human gut mycobiome/microbiome

The fecal mycobiome in non-alcoholic fatty liver disease – Demir et al. – Journal of Hepatology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Intermittent Fasting Reshapes the Gut Microbiota and Metabolome and Reduces Weight Gain More Effectively Than Melatonin in Mice – Liu et al. – Front. Nutr.

Analyzing gut microbiota composition in individual Anopheles mosquitoes after experimental treatment – Fofana et al. – iScience

Microbial interaction-driven community differences as revealed by network analysis – Pan et al. – Computational and Structural Biotechnology Journal

[PREPRINT]Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycle – Hoces et al. – bioRxiv

[PREPRINT]Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community – Lyalina et al – bioRxiv

Gut microbiota modulates weight gain in mice after discontinued smoke exposure – Fluhr et al. – Nature

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

[PREPRINT]Stratified microbial communities are highly sensitive towards multiple combined global change factors, revealing antagonistic and synergistic effects – Suleiman et al. – bioRxiv

Bioinformatics / Databases

Cow Rumen v1.0 – Database

[REVIEW]A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data – Yang et al. – Computational and Structural Biotechnology Journal

Microbiome podcast

The Microbiome Facts, Not the Hype – Kristina Campbell

December 14, 2021

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Today’s digest contains several great recent papers, but in particular I’d like to highlight a Nature Methods paper on applying network biology approaches to the microbiome, and a Nature paper which disentangles the effects of drugs and disease on host and microbiome.

General microbiome

Fast and flexible analysis of linked microbiome data with mako – Röttjers & Faust – Nature Methods. 

Combinatorial, additive and dose-dependent drug–microbiome associations – Forslund et al. Nature 

Mammalian gut metabolomes mirror microbiome composition and host phylogeny – Gregor et al. – ISME 

Human gut microbiome

Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity – Wang et al. – Genome Biology

Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM – Chen et al.  – Microbiome

Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement – Jacobs et al. – Microbiome. 

Human oral microbiome

Impact of sleep on the microbiome of oral biofilms – Sotozono et al. – PLOS One

Functional screening of a human saliva metagenomic DNA reveal novel resistance genes against sodium hypochlorite and chlorhexidine – Wigand et al. BMC Oral Health

Animal Experiments

The immunotoxicity, but not anti-tumor efficacy, of anti-CD40 and anti-CD137 immunotherapies is dependent on the gut microbiota – Blake et al. – Cell Reports Medicine

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Zhang et al. – ISME

Sexual dimorphism in glucose metabolism is shaped by androgen-driven gut microbiome – Gao et al. – Nature Communications

December 08, 2021

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General microbiome

Clinical medicine journals lag behind science journals with regards to “microbiota sequence” data availability – Pryor et al. – Clinical and Translational Medicine

Role of the Microbiome in Regulating Bone Metabolism and Susceptibility to Osteoporosis – Cronin et al. – Calcified Tissue International

Defining and quantifying the core microbiome: Challenges and prospects – Neu, Allen & Roy – PNAS

Clean room microbiome complexity impacts planetary protection bioburden – Hendrickson et al. – Microbiome

[PREPRINT]Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment – Bischofberger & Hall – bioRxiv

Microbiota and stress: a loop that impacts memory – Kraimi et al. – Psychoneuroendocrinology

Species- and site-specific genome editing in complex bacterial communities – Rubin et al. – Nature Microbiology

Human respiratory microbiome

Integrated metabolic and microbial analysis reveals host–microbial interactions in IgE-mediated childhood asthma – Chiu et al. – Scientific Reports

Human oral microbiome

Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome – Liu et al. – Cell Discovery

Human gut microbiome

Interaction Between Intestinal Microbiota, Immunology Molecular Mimicry, and AID – Pan et al. – Journal of Immunology Research

[REVIEW]The Gut Microbiome and Hepatocellular Carcinoma – Akkiz – Journal of Gastrointestinal Cancel

Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn’s disease – Lee et al. – International Journal of Systematic and Evolutionary Microbiology

Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers – Mao et al. – Journal for ImmunoTherapy of Cancer

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota – Palomba et al. – NPJ Biofilms and Microbiomes

Animal microbiome (for animals in the wild)

Diet-driven mercury contamination is associated with polar bear gut microbiota – Watson et al. – Scientific Reports

Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development – Blyton et al. – Environmental Microbiology

[PREPRINT]Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi – McMurtie et al. – bioRxiv

Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey (Rhinopithecus roxellana hubeiensis) – Yao et al. – BioMed Research International

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Looking through the FOG: microbiome characterization and lipolytic bacteria isolation from a fatberg site – Court et al. – Microbiology

The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation – Iasakov et al. – Marine Environmental Research

Bioinformatics

3MCor: an integrative web server for metabolome-microbiome-metadata correlation analysis – Sun et al. – Bioinformatics

Techniques

Microbiome Methods in Experimental Autoimmune Encephalomyelitis – Daberkow et al. – Current Protocols

[PREPRINT]A wipe-based stool collection and preservation kit for microbiome community profiling – Hua et al. – bioRxiv

December 2, 2021

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Happy December from Pittsburgh!

Today’s digest includes original research on the impacts of fungal entomopathogens on Wolbacia infections and the influence of nutrient status on the response of a diatom to oil and dispersant. I have also included a study protocol for oral microbiome transplant for the treatment of dental caries and periodontal disease as well as preprints on a variety of topics. Finally, I want to highlight two articles I included that are little different from my usual content: the first is on predictors of willingness to receive the COVID-19 vaccination and the second is focused on transparency in peer review.

Enjoy!

COVID-19

***To vaccinate or not to vaccinate!? Predictors of willingness to receive Covid-19 vaccination in Europe, the U.S., and China – Brailovskaia et al. – PLOS One

General microbiome

Preprint: Copper nanoparticles as modulator of active bacterial population and their physiology in ecosphere – Alboloushi et al. – bioRxiv

Preprint: Metabolite Damage and Damage-Control in a Minimal Genome – Haas et al. – bioRxiv

Development and characterization of an oral microbiome transplant among Australians for the treatment of dental caries and periodontal disease: A study protocol – Nath et al. – PLOS One

Preprint: Heat activation and inactivation of bacterial spores. Is there an overlap? – Wen et al. – bioRxiv

Animal experiments

Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial – van Tonder et al. – PLOS Pathogens

Animal microbiome

Impacts of fungal entomopathogens on survival and immune responses of Aedes albopictus and Culex pipiens mosquitoes in the context of native Wolbachia infections – Ramirez et al. – PLOS Neglected Tropical Diseases

Water and extremophile microbiome

Influence of nutrient status on the response of the diatom Phaeodactylum tricornutum to oil and dispersant – Kamalanathan et al. – PLOS One

Preprint: Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiome – Seong et al. – bioRxiv

Preprint: Microbial cysteine degradation is a source of hydrogen sulfide in oxic freshwater lakes – Tran et al. – bioRxiv

Bioinformatics

When and why direct transmission models can be used for environmentally persistent pathogens – Benson – PLOS Computational Biology

Techniques

Preprint: The processing of staphylococcal biofilm images from Fluorescence and Confocal Microscopy to assess in vitro efficacy of antiseptic molecules – Krasowski et al. – bioRxiv

Science, publishing, and career

***Transparency in peer review: Exploring the content and tone of reviewers’ confidential comments to editors – O’Brien et al. – PLOS One

December 01, 2021

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General microbiome

Searching for New Microbiome-Targeted Therapeutics through a Drug Repurposing Approach – Barone et al. – Journal of Medicinal Chemistry

Current status of intratumour microbiome in cancer and engineered exogenous microbiota as a promising therapeutic strategy – Chen et al. – Biomedicine & Pharmacotherapy

Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide – Hoyles et al. – Microbiome

Modeling host-associating microbes under selection – Bansept et al. – The ISME Journal

Human oral microbiome

Bacterial variation in the oral microbiota in multiple sclerosis patients – Zangeneh – PLOS One

Human gut microbiome

[REVIEW]Gut microbiota as a transducer of dietary cues to regulate host circadian rhythms and metabolism – Choi, Rao & Chang – Nature Reviews Gastroenterology & Hepatology

[REVIEW]Gut microbiota-derived short-chain fatty acids and colorectal cancer: Ready for clinical translation? – Hou et al. – Cancer Letters

Analysis of changes in microbiome compositions related to the prognosis of colorectal cancer patients based on tissue-derived 16S rRNA sequences – Coi et al. – Journal of Translational Medicine

The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum Disorder – Dilmore et al. – mSystems

Characterization of gut microbial structural variations as determinants of human bile acid metabolism – Wang et al. – Cell Host & Microbe

Animal microbiome

Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis – Hinrichsen et al. – Cell Metabolism

Bacterial communities from vagina of dairy healthy heifers and cows with impaired reproductive performance – Moreno et al. – Research in Veterinary Science

Plant, root, and soil microbiome

Artificial Selection on Microbiomes To Breed Microbiomes That Confer Salt Tolerance to Plants – Mueller et al. – mSystems

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations – ter Horst et al. – Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments – Castro et al. – The ISME Journal

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients – Schauberger et al. – The ISME Journal

Bioinformatics

Disentangling environmental effects in microbial association networks – Deutschmann et al. – Microbiome

Negative Binomial factor regression with application to microbiome data analysis – Muller, Mishra

Techniques

Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses – Chen et al. – The ISME Journal