December 22, 2021

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

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 17, 2021

Human and General Microbiome

Association of microbial dynamics with urinary estrogens and estrogen metabolites in patients with endometriosis – Nhung Le – PloS ONE

Gut Microbiome in Probable Intestinal Tuberculosis and Changes following Anti-Tuberculosis Treatment – Hyuk Yoon – Yonsei Medical Journal

Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis – Tomohiro Hayashi – Frontiers in Cardiovascular Medicine

Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community – Yongyong Kang – Microbiology Spectrum

Stability of healthy subgingival microbiome across space and time – Ryan Tamashiro – Scientific Reports

Successional Stages in Infant Gut Microbiota Maturation – Leen Beller – mBio

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Peng Zhang – The ISME Journal

Bacterial vaginosis and health-associated bacteria modulate the immunometabolic landscape in 3D model of human cervix – Paweł Łaniewski – NPJ Biofilms and Microbiomes

Acute malnutrition and its determinants of preschool children in Bangladesh: gender differentiation – Md Reazul Karim – BMC Pediatrics

SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts – M Nazmul Hoque – Scientific Reports

Gut Mycobiota Dysbiosis in Pulmonary Tuberculosis Patients Undergoing Anti-Tuberculosis Treatment – Demin Cao – Microbiology Spectrum

Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid – Michael E J Buhl – International Journal of Systematic and Evolutionary Microbiology

Human and General Microbiome – Reviews

Review: The Role of Gut Microbiota and Genetic Susceptibility in the Pathogenesis of Pancreatitis – Fumin Xu – Gut and Liver

Review: Transcript host-RNA signatures to discriminate bacterial and viral infections in febrile children – Danilo Buonsenso – Pediatric Research

Review: The role of anaerobic bacteria in the development and prevention of colorectal cancer: A review study – Mehrdad Mohammadi – Anaerobe

Review: Lung microbiome, gut-lung axis and chronic obstructive pulmonary disease – Kuppan Gokulan – Current Opinion in Pulmonary Medicine

Systematic review: Gut microbiota modulation as a possible mediating mechanism for fasting-induced alleviation of metabolic complications: a systematic review – Pooneh Angoorani – Nutrition & Metabolism

Systematic review: The relation between the gut microbiome and osteoarthritis: A systematic review of literature – Emanuele Chisari – PloS ONE

Outlook: Ovarian cancer and the microbiome: a complex relationship – Julianna Photopoulos – Nature

Beneficial Microbes and Compounds

Oligofructose-enriched inulin intake, gut microbiome characteristics and the V̇O2peak response to high-intensity interval training in healthy inactive adults – Camilla J Williams – The Journal of Nutrition

Lactiplantibacillus plantarum DMDL 9010 alleviates dextran sodium sulfate (DSS)-induced colitis and behavioral disorders by facilitating microbiota-gut-brain axis balance – Yan-Yan Huang – Food & Function

Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial – Dorit Vedel Ankersen – Journal of Medical Internet Research

Effect of dietary selenium intake on gut microbiota in older population in Enshi region – Zi-Xiong Zhang – Genes and Environment

Animal Microbiome

The bacterial biome of ticks and their wildlife hosts at the urban-wildland interface – Siobhon L Egan – Microbial Genomics

The gut microbiota of wild wintering great bustard (Otis tarda dybowskii): survey data from two consecutive years – Zhiyuan Lu – PeerJ

You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches – Melissa R Ingala – Animal Microbiome

Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level – Rupert Mazzucco – Proceedings of the Royal Society B. Biological Sciences

Plant and Fungi Microbiome

The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host – Maria J Soto-Giron – Scientific Reports

Autotoxin Rg(1) Induces Degradation of Root Cell Walls and Aggravates Root Rot by Modifying the Rhizospheric Microbiome – Yanguo Xu – Microbiology Spectrum

Multitrophic Interactions Between Arbuscular Mycorrhizal Fungi, Foliar Endophytic Fungi and Aphids – Nadia Ab Razak – Microbial Ecology

Other Microbes

Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia – Anna G Burrichter – BMC Microbiology

Methods

Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes – Angie Mordant – Microbiology Spectrum

Sample Processing for Metaproteomic Analysis of Human Gut Microbiota – Carmen García-Durán – Methods in Molecular Biology Enhancing Microbiome Research through Genome-Scale Metabolic Modeling – Nana Y D Ankrah – mSystems

December 16, 2021

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 14, 2021

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

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 4, 2021

Human and General Microbiome

Multivariate associative patterns between the gut microbiota and large-scale brain network connectivity – N Kohn – Gut Microbes

Cervicovaginal levels of human beta defensins during bacterial vaginosis – Nathalia Mayumi Noda-Nicolau – PloS ONE

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health – Francesco Marabita – Cell Systems

A specific structure and high richness characterize intestinal microbiota of HIV-exposed seronegative individuals – Tulio J Lopera – PloS ONE

Central role of intestinal epithelial glucocorticoid receptor in alcohol- and corticosterone-induced gut permeability and systemic response – Pradeep K Shukla – The FASEB Journal

Proof-of-principle demonstration of endogenous circadian system and circadian misalignment effects on human oral microbiota – Sarah L Chellappa – The FASEB Journal

Gender Variations in the Oral Microbiomes of Elderly Patients with Initial Periodontitis – Jie Zhao – Journal of Immunology Research

Characterization of Esophageal Microbiota in Patients With Esophagitis and Esophageal Squamous Cell Carcinoma – Zongdan Jiang – Frontiers in Cellular and Infection Microbiology

Gender-Specific Differences in Gut Microbiota Composition Associated with Microbial Metabolites for Patients with Acne Vulgaris – Yukun Huang – Annals of Dermatology

Gut microbiota develop towards an adult profile in a sex-specific manner during puberty – Katri Korpela – Scientific Reports

Gut microbiota-driven brain Aβ amyloidosis in mice requires microglia – Hemraj B Dodiya – The Journal of Experimental Medicine

Associations of the oral microbiota and Candida with taste, smell, appetite and undernutrition in older adults – Kristina S Fluitman – Scientific Reports

Altered cervicovaginal microbiota in premenopausal ovarian cancer patients – Asuka Morikawa – Gene

Social overcrowding impacts gut microbiota, promoting stress, inflammation, and dysglycemia – Clara Delaroque – Gut Microbes

Research Highlight: Gut microbiome and autism spectrum disorder – Eleni Kotsiliti – Nature Reviews Gastroenterology & Hepatology

Human and General Microbiome (Reviews)

Metagenomics studies for the diagnosis and treatment of prostate cancer – Ali Zarei – The Prostate

Regulation of common neurological disorders by gut microbial metabolites – Jeongho Park – Experimental & Molecular Medicine

The gut microbiota in retinal diseases – Marie-Agnès Bringer – Experimental Eye Research

Microbe-based management for colorectal cancer – Zi-Yun Gao – Chinese Medical Journal

Novel Strategies for Inhibition of Bacterial Biofilm in Chronic Rhinosinusitis – Aref Shariati – Journal of Applied Microbiology

Regulation of para-cresol production in Clostridioides difficile – Mark A Harrison – Current Opinion in Microbiology

Animal Microbiome (Non-Models)

Gut microbiome and metabolome in a non-human primate model of chronic excessive alcohol drinking – Daria Piacentino – Translational Psychiatry

A holobiont view of island biogeography: unraveling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates – Ellie E Armstrong – Molecular Ecology

Interactions of Muscovy duck reovirus, gut microbiota, and host innate immunity: Transcriptome and gut microbiota analysis – Zheng Zhu – Veterinary Microbiology

Antibiotics, antibiotic resistance genes and microbial community in grouper mariculture – Lu-Xi He – The Science of the Total Environment

Beneficial Microbes and Compounds

Lactobacillus alleviated obesity induced by high-fat diet in mice – Wei Song – Journal of Food Science

Effect of prophylactic dextrose gel on the neonatal gut microbiome – Sophie L St Clair – Archives of Disease in Childhood

Polydextrose with and without Bifidobacterium animalis ssp. lactis 420 drives the prevalence of Akkermansia and improves liver health in a multi-compartmental obesogenic mice study – Christian Clement Yde – PloS ONE

Review: Studies and Application of Sialylated Milk Components on Regulating Neonatal Gut Microbiota and Health – Yushuang Wang – Frontiers in Nutrition

Environmental Microbiome

The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes – Andrés E Marcoleta – The Science of the Total Environment

Other Microbiomes

In vitro interaction network of a synthetic gut bacterial community – Anna S Weiss – The ISME Journal

Plant and Fungi Microbiome

Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots – Katarzyna W Wolinska – PNAS

An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation – Nick C Snelders – PNAS

Seed inhabiting bacterial endophytes of maize promote seedling establishment and provide protection against fungal disease – Gaurav Pal – Microbiological Research

December 2, 2021

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

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

November 26, 2021

General microbiome

Metabolomics-Microbiome Crosstalk in the Breast Cancer Microenvironment – Al-Ansari – Metabolites

Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection – Barber et al. – Nature Microbiology

Human gut microbiome

Human gut bacterial metabolism drives Th17 activation and colitis – Alexander et al. – Cell Host & Microbiome

Integrative Analysis of Metabolome and Microbiome in Patients with Progressive Alcohol-Associated Liver Disease – Gao et al. – Metabolites

Human Fecal Metabolome Reflects Differences in Body Mass Index, Physical Fitness, and Blood Lipoproteins in Healthy Older Adults – Cui et al. – Metabolites

[REVIEW]Gut Microbiota, Microbial Metabolites and Human Physical Performance – Lensu & Pekkala – Metabolites

[Editorial]Next steps after 15 stimulating years of human gut microbiome research – Clavel et al. – Microbial Biotechnology

[REVIEW]The microbiome, Gastrointestinal cancer and immunotherapy – Newsome, Yang & Jobin – Journal of Gastroenterology and Hepatology

Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease – Doron et al. – Nature Microbiology

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

Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-brain axis – Zhao et al. – Microbiome

Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs – Wang et al. Microbiome

Animal microbiome (for animals in the wild)

Circadian dynamics of the teleost skin immune-microbiome interface – Ellison, Wilcockson & Cable – Microbiome

Honey bee genetics shape the strain-level structure of gut microbiota in social transmission – Wu et al. – Microbiome

Plant, root, and soil microbiome

Evidence for host–microbiome co-evolution in apple – Abdelfattah et al. – New Phytologist

Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen – Vogel et al. – Nature Microbiology

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis – Yang et al. – npj Biofilms and Microbiomes

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

Cross-regional scale pollution of freshwater biofilms unveiled by antibiotic resistance genes – Yao et al. – Science of The Total Environment

Functional metagenomic analysis of quorum sensing signaling in a nitrifying community – Tan et al. – npj Biofilms and Microbiomes

Bioinformatics

Multivariable association discovery in population-scale meta-omics studies – Mallick et al. – PLOS Computational Biology

Techniques

Assessing saliva microbiome collection and processing methods – Armstrong, Parmar & Blaser – npj Biofilms and Microbiomes