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.



***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


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


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


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

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


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


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


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

November 20, 2021


Review: Reporting guidelines for human microbiome research: the STORMS checklist – Chloe Mirzayi – Nature Medicine → The following article “provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results”

Honey bee genetics shape the strain-level structure of gut microbiota in social transmission – Jiaqiang Wu – Microbiome → “Our results indicated that host genetics influence the bee gut composition and suggest a gut-brain connection implicated in the gut bacterial strain preference”

Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples – Seesandra V Rajagopala – Cell Reports Methods → This study reports a method to study virome and microbiome of clinically relevant respiratory samples, using a children cohort. 

Human and General Microbiome

Response of Lung Microbiota to Changes of Pulmonary Innate Immunity Under Healthy Conditions – Taro Yasuma – American Journal of Respiratory and Critical Care Medicine

Small intestinal bacterial overgrowth in Alzheimer’s disease – Karol Kowalski – Journal of Neural Transmission 

Periodontitis Salivary Microbiota Worsens Colitis – J Qian – Journal of Dental Research

The Effects of Moderate Alcohol Consumption on Circulating Metabolites and Gut Microbiota in Patients With Coronary Artery Disease – Xinyue Zhao – Frontiers in Cardiovascular Medicine

Integrative Analysis of LGR5/6 Gene Variants, Gut Microbiota Composition and Osteoporosis Risk in Elderly Population – Dong-Sheng Di – Frontiers in Microbiology

Comparison of the Gut Microbiota in Patients with Benign and Malignant Breast Tumors: A Pilot Study – Peidong Yang – Evolutionary Bioinformatics Online

Temporal variability in quantitative human gut microbiome profiles and implications for clinical research – Doris Vandeputte – Nature Communications

Association between Parkinson’s disease and the faecal eukaryotic microbiota – Severin Weis – NPJ Parkinson’s Disease

Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut – Ana Popovic – Nature Communications

An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness – Andrea Marfil-Sánchez – Gut Microbes

Efficacy and Outcomes of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection in Children with Inflammatory Bowel Disease – Maribeth R Nicholson – Journal of Crohn’s & Colitis

The anti-inflammatory effect of bacterial short chain fatty acids is partially mediated by endocannabinoids – Amrita Vijay – Gut Microbes

Human and General Microbiome – Reviews

Bile acids as regulatory molecules and potential targets in metabolic diseases – Ai-Jin Xie – Life Sciences

Renaissance for Phage-Based Bacterial Control – Cory Schwarz – Environmental Science & Technology

Sulphur metabolism in colon cancer tissues: a case report and literature review – Hironori Fukuoka – The Journal of International Medical Research

Dietary fatty acids in gut health: Absorption, metabolism and function – E Xu – Animal Nutrition

The search for aliens within us: a review of evidence and theory regarding the foetal microbiome – Richard Cariño III – Critical Reviews in Microbiology

Human immune diversity: from evolution to modernity – Adrian Liston – Nature Immunology 

Beneficial Microbes and Compounds

Review: Human Milk Oligosaccharides as a Missing Piece in Combating Nutritional Issues during Exclusive Breastfeeding – Verawati Sudarma – Pediatric Gastroenterology, Hepatology & Nutrition

Review: Advancements in the Pharmaceutical Applications of Probiotics: Dosage Forms and Formulation Technology – Kshitis Chandra Baral – International Journal of Nanomedicine

Lactobacillus rhamnosus strain LRH05 intervention ameliorated body weight gain and adipose inflammation via modulating the gut microbiota in high-fat diet-induced obese mice – Yung-Tsung Chen – Molecular Nutrition & Food Research

Bifidobacterium infantis Maintains Genome Stability in Ulcerative Colitis via Regulating Anaphase-Promoting Complex Subunit 7 – Taotao Han – Frontiers in Microbiology

Galacto-oligosaccharide Supplementation Modulates Pathogen-Commensal Competition between Streptococcus agalactiae and Streptococcus salivarius – Rebecca E Moore – Chembiochem

Animal Microbiome (Non-models)

Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes – Yuqing Feng – Communications Biology

Contrasting microbiome dynamics of putative denitrifying bacteria in two octocoral species exposed to dissolved organic carbon (DOC) and warming – Nan Xiang – Applied and Environmental Microbiology

Plant Microbiome

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis – Nan Yang – NPJ Biofilms and Microbiomes

Drops join to make a stream: high-throughput nanoscale cultivation to grasp the lettuce root microbiome – Antoine Persyn – Environmental Microbiology Reports

Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition – Alba Pacheco-Moreno – eLife

Small-scale agricultural grassland management can affect soil fungal community structure as much as continental scale geographic patterns – A Fox – FEMS Microbiology Ecology

Geographic and position-based variations in phyllospheric bacterial communities present on flue-cured tobacco – Jianbin Ye – Applied Microbiology and Biotechnology

Other Microbes

Improved quantitative microbiome profiling for environmental antibiotic resistance surveillance – Amelie Ott – Environmental Microbiome

Sediment Microbiota in Response to Circuitry of Sediment Microbial Fuel Cells, Revealed by 16S rRNA Gene Amplicon Sequencing – Yasuyuki Takemura – Microbiology Resource Announcements

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate – Hyungseok Kim – The ISME Journal

Review: Microbial ecology of tourist Paleolithic caves – Zelia Bontemps – The Science of the Total Environment

Microbiome Analysis and Bioinformatics

Multivariate statistical monitoring system for microbial population dynamics – Koji Ishiya – Physical Biology

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison – Die Dai – Nucleic Acids Research

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes – Thea Van Rossum – Bioinformatics

Assessing saliva microbiome collection and processing methods – Abigail J S Armstrong – NPJ Biofilms and Microbiomes

Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods – Maryia Khomich – PloS ONE

Technical note: overcoming host contamination in bovine vaginal metagenomic samples with Nanopore adaptive sequencing – Chian Teng Ong – Journal of Animal Science

Mian: Interactive Web-Based Microbiome Data Table Visualization and Machine Learning Platform – Boyang Tom Jin – Bioinformatics

November 17, 2021

General microbiome

Macrophages in Microbial Pathogenesis: Commonalities of Defense Evasion Mechanisms – Pandey et al. – Infection and Immunity

Human respiratory microbiome

The Influence of FUT2 and FUT3 Polymorphisms and Nasopharyngeal Microbiome on Respiratory Infections in Breastfed Bangladeshi Infants from the Microbiota and Health Study – Binia et al. – mSphere

Human gut microbiome

Fecal Microbiota Transplantation Commonly Failed in Children with Co-Morbidities – Kellermayer et al. – JPGN

Current and future applications of fecal microbiota transplantation for children – Chen & Chiu – Biomedical Journal

[REVIEW]Microbial influences on gut development and gut-brain communication – Ye & Rawls – Development

Characterization and predictive functional profiles on metagenomic 16S rRNA data of liver transplant recipients: A longitudinal study – Sivaraj et al. – Clinical Transplantation

Changes to human faecal microbiota after international travel – Kampmann et al. – Travel Medicine and Infectious Disease

Animal experiments

Cognate recognition of microbial antigens defines constricted CD4+ T cell receptor repertoires in the inflamed colon – Muschaweck et al. – Immunity

An aniline-substituted bile salt analog protects both mice and hamsters from multiple Clostridioides difficile strains – Phan et al. – Antimicrobial Agents and Chemotherapy

Analysis of Cow-Calf Microbiome Transfer Routes and Microbiome Diversity in the Newborn Holstein Dairy Calf Hindgut – Zhu et al. – Frontiers in Nutrition


Multi-omic evaluation of metabolic alterations in multiple sclerosis identifies shifts in aromatic amino acid metabolism – Fitzgerald et al. – Cell Reports Medicine


[REVIEW]It takes guts to learn: machine learning techniques for disease detection from the gut microbiome – Curry, Nute & Treangen – Emerging Topics in Life Sciences

November 15, 2021

Today’s digest contains an article about the effect of shale flowback fluid on the polluted soil microbiome. It also includes multiple preprints on topics such as long-read sequencing on the Oxford Nanopore, arctic marine protists, rapid antibiotic susceptibility testing for mixed infections, and more.

Happy reading!

General microbiome

Preprint: Rapid antibiotic susceptibility testing and species identification for mixed infections – Kandavalli et al. – bioRxiv

Preprint: Bacterial quorum sensing allows graded and bimodal cellular responses to variations in population density – Rattray et al. – bioRxiv

Preprint – Phage-encoded sigma factors alter bacterial dormancy – Schwartz et al. – bioRxiv

Human respiratory microbiome

Preprint: Aspergillus fumigatus drives tissue damage via iterative assaults upon mucosal integrity and immune homeostasis – Okaa et al. – bioRxiv

Human skin microbiome

Preprint: Cobamide sharing drives skin microbiome dynamics – Swaney et al. – bioRxiv

Plant, root, and soil microbiome

Toxic effects of shale gas fracturing flowback fluid on microbial communities in polluted soil – Zudong Mei et al. – Environmental Monitoring and Assessment

Water and extremophile microbiome

Preprint: Colonial choanoflagellate isolated from Mono Lake harbors a microbiome – Hake et al. – bioRxiv

Preprint: Linking extreme seasonality and gene expression in arctic marine protists – Wutkowska et al. – bioRxiv

Preprint: Biosorption potential and molecular characterization of metal resistant autochthonous microbes from tannery solid waste – Younas et al. – bioRxiv


Preprint: Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing – Sereika et al. – bioRxiv

Preprint: Going through phages: A Computational approach to Revealing the role of prophage in Staphylococcus aureus – Sweet et al. – bioRxiv

November 13, 2021

Human and General Microbiome

Visualized analysis of trends and hotspots in global oral microbiome research: A bibliometric study – Ga Liao – MedComm

A low abundance of genus Bacteroides in gut microbiota is negatively correlated with blood phenylalanine levels in Uygur patients with phenylketonuria – Yajie Su – Translational Pediatrics

Haematopoietic cell transplantation outcomes are linked to intestinal mycobiota dynamics and an expansion of Candida parapsilosis complex species – Thierry Rolling – Nature Microbiology

The composition of lung microbiome in lung cancer: a systematic review and meta-analysis – Sadaf Najafi – BMC Microbiology

A metaproteomic-based gut microbiota profiling in children affected by autism spectrum disorders – Stefano Levi Mortera – Journal of Proteomics

Is there an association between the vaginal microbiome and first trimester miscarriage? A prospective observational study – Monica Shahid – The Journal of Obstetrics and Gynaecology Research

Human and General Microbiome – Reviews

Review: Gut microbiota and vitamin status in persons with obesity: A key interplay – Lise Voland – Obesity Reviews

Review: Insights into the role of vaginal microbiome in women’s health – Namrata Deka – Journal of Basic Microbiology

Review: The gut virome in inflammatory bowel diseases – Guanxiang Liang – Current Opinion in Virology

Beneficial Microbiome and Compounds

Tuber flours improve intestinal health and modulate gut microbiota composition – Tao Xu – Food Chemistry: X

Effects of red ginseng on gut, microbiota, and brain in a mouse model of post-infectious irritable bowel syndrome – Seonhye Yu – Journal of Ginseng Research

Food Microbiome

The inconsistent microbiota of Budu, the Malaysian fermented anchovy sauce, revealed through 16S amplicon sequencing – Muhammad Zarul Hanifah Md Zoqratt – PeerJ

Animal Microbiome (non-models)

Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items – Zhenwei Cui – Integrative Zoology

Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers – Maria S Costantini – PeerJ

Plant Microbiome

Opinion: The end of hunger: fertilizers, microbes and plant productivity – Hang-Wei Hu – Microbial Biotechnology

Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars – Chuanfa Wu – Applied Microbiology and Biotechnology

Unexpected diversity among small-scale sample replicates of defined plant root compartments – Sally Attia – The ISME Journal

Microbiome analysis methods

Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples – Sarah Ahannach – iScience

An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome – Nicolas Nalpas – Gut Microbes

Improved Metabolite Prediction Using Microbiome Data-Based Elastic Net Models – Jialiu Xie – Frontiers in Cellular and Infection Microbiology

OtherEvaluation of Effects of Laboratory Disinfectants on Mouse Gut Microbiota – Joseph D Sciurba – Comparative Medicine

November 12, 2021

Today’s digest features the study on the Amazon River microbiome, Spanish gut microbiome, review on nanopore sequencing, 16S rRNA metabarcoding study to characterize the responses of the active gut microbiome of fathead minnows to exposure with a model contaminant (benzo[a]pyrene), and more. Happy Friday!

Lung microbiome

Review: The composition of lung microbiome in lung cancer: a systematic review and meta-analysis – Sadaf Najafi – BMC Microbiology

Skin microbiome

Charting host-microbe co-metabolism in skin aging and application to metagenomics data – Wynand Alkema – PlosOne

Gut microbiome

*The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet – Adriel Latorre-Pérez – Scientific Reports

Autism-related dietary preferences mediate autism-gut microbiome associations – Chloe X. Yap – Cell

Animal microbiome

*16S rRNA metabarcoding unearths responses of rare gut microbiome of fathead minnows exposed to benzo[a]pyrene – Abigail DeBofsky – Science of The Total Environment

Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs – Morag Clinton – BMC Microbiology

Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing – Xiaofen Hu – BMC Microbiology

Animal experiment

The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model – Eldin Jašarević – Nature Communications

Polyamine metabolism links gut microbiota and testicular dysfunction – Qi Zhao – Microbiome

A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites – Hongli Shi – Microbiome

Water microbiome

*Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters – Célio Dias Santos-Júnior – Molecular Ecology


*Review: Nanopore sequencing technology, bioinformatics and applications – Yunhao Wang – Nature Biotechnology

mBodyMap: a curated database for microbes across human body and their associations with health and diseases – Hanbo Jin – Nucleic Acids Research

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper – Alexander G McFarland – Bioinformatics

OptiFit: an improved method for fitting amplicon sequences to existing OTUs – Kelly L Sovacool – bioRxiv

November 10, 2021

Human urinary tract microbiome

[PREPRINT]Recurrent urinary tract infection and estrogen shape the taxonomic ecology and functional potential of the postmenopausal urobiome – Neugent et al. – bioRxiv

Human gut microbiome

The Impact of a Mediterranean Diet on the Gut Microbiome in Healthy Human Subjects: A Pilot Study – Rejeski et al. – Digestion

Altered diversity and composition of gut microbiota in patients with allergic rhinitis – Zhou et al. – Microbial Pathogenesis

Fecal Microbiome Transplantation for Recurrent Clostridioides difficile Infection: Treatment Efficacy, Short and Long-term Follow-up Results from Consecutive Case Series – Urbonas et al. – Journal of Gastrointestinal and Liver Diseases

Donor screening for fecal microbiota transplantation in China: Evaluation of 8,483 candidates – Zhang et al. – Gastroenterology

Faecal microbial biomarkers in early diagnosis of colorectal cancer – Olovo et al. – Journal of Cellular and Molecular Medicine

Hepatocellular Cancer and Gut Microbiome: Time to Untie Gordian’s Knot – Aygün & Tözün – Journal of Gastrointestinal Cancer

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

Cinnamic acid suppresses bone loss via induction of osteoblast differentiation with alteration of gut microbiota – Hong et al. – The Journal of Nutritional Biochemistry

Gut microbiome affects the metabolism of metronidazole in mice through regulation of hepatic cytochromes P450 expression – Zemanová et al. – PLOS One

Animal microbiome (for animals in the wild)

[PREPRINT]Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate – Baniel et al. – bioRxiv

Evidence of MHC class I and II influencing viral and helminth infection via the microbiome in a non-human primate – Montero et al. – PLOS Pathogens

Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr – Skrodenytė-Arbačiauskienė – Microbial Ecology

Plant, root, and soil microbiome

Artificial selection of stable rhizosphere microbiota leads to heritable plant phenotype changes – Jacquiod et al. – Ecology Letters

Plastic mulch debris in rhizosphere: Interactions with soil-microbe-plant systems – Liu et al. – Science of The Total Environment

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

[PREPRINT]Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens – Numberger et al. – bioRxiv


[PREPRINT]specificity : an R package for generalized specificity analysis, with example analyses of Hawaiian foliar endophytic Fungi, human gut microbiome bacteria, and Antarctic glacier bacteria – Darcy et al. – bioRxiv

[PREPRINT]Unifying the known and unknown microbial coding sequence space – Vanni et al. – bioRxiv

Identifying prognostic pairwise relationships among bacterial species in microbiome studies – Devlin, Martin & Ostrovnaya – PLOS Computational Biology

HashSeq: a Simple, Scalable, and Conservative De Novo Variant Caller for 16S rRNA Gene Data Sets – Fouladi, Young & Fodor – mSystems