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

November 9, 2021

Human and General Microbiome

Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma – Mykhaylo Usyk – Genome Medicine

A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA – Weiwei Yang – eLife

The Gut Microbiome Modifies the Association between a Mediterranean Diet and Diabetes in US Hispanic / Latino Population – Dong D Wang – The Journal of Clinical Endocrinology and Metabolism

Proteomics analysis of the gut-brain axis in a gut microbiota-dysbiosis model of depression – Yiyun Liu – Translational Psychiatry

The Capacity to Produce Hydrogen Sulfide (H(2)S) via Cysteine Degradation Is Ubiquitous in the Human Gut Microbiome – Domenick J Braccia – Frontiers in Microbiology

Identification of a novel cancer microbiome signature for predicting prognosis of human breast cancer patients – A W Mao – Clinical & Translational Oncology

Gut microbiota of adults with asthma is broadly similar to non-asthmatics in a large population with varied ethnic origins – Robert F J Kullberg – Gut Microbes

Effects of fecal microbiota transplant on DNA methylation in subjects with metabolic syndrome – Eduard W J van der Vossen – Gut Microbes

The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis – Ting-Chin David Shen – Gut Microbes

Multiple bacterial virulence factors focused on adherence and biofilm formation associate with outcomes in cirrhosis – Jasmohan S Bajaj – Gut Microbes

Long-term dynamics of the human oral microbiome during clinical disease progression – Ana Duran-Pinedo – BMC Biology

Microbiome characteristics and the key biochemical reactions identified on stone world cultural heritage under different climate conditions – Xinghua Ding – Journal of Environmental Management

Fecal biomarkers of environmental enteric dysfunction and the gut microbiota of rural Malawian children: An observational study – David Chaima – Heliyon

Review: The Evolving Role of Consensus Molecular Subtypes: a Step Beyond Inpatient Selection for Treatment of Colorectal Cancer – Javier Ros – Current Treatment Options in Oncology

Review: The role of the host microbiome in autism and neurodegenerative disorders and effect of epigenetic procedures in the brain functions – Bahman Yousefi – Neuroscience and Biobehavioral Reviews

Review: The Oral Microbiota and its Role in Carcinogenesis – Mark Stasiewicz – Seminars in Cancer Biology

Review: Gut microbiota: sculptors of the intestinal stem cell niche in health and inflammatory bowel disease – Manasvini Markandey – Gut Microbes

Review: The gastrointestinal microbiota in colorectal cancer cell migration and invasion – Charlotte Henstra – Clinical & Experimental Metastasis

Review: Akkermansia muciniphila and host interaction within the intestinal tract – Andrei M Karamzin – Anaerobe

Review: Effects of anti-aging interventions on intestinal microbiota – Yanjiao Du – Gut Microbes

Review: Impact of the environment on the microbiome – Herberto José Chong Neto – Jornal de Pediatria

Review: Progress and prospects of the healthy human gut virome – Stephen R Stockdale – Current Opinion in Virology

Forensic Microbiome

Review: Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions – Celia Díez López – Forensic Science International. Genetics

Beneficial Microbes, Compounds and Interventions

Bioactives and their metabolites from Tetrastigma hemsleyanum leaves ameliorate DSS-induced colitis via protecting the intestinal barrier, mitigating oxidative stress and regulating the gut microbiota – Tong Wu – Food & Function

Bacterial membrane vesicles and phages in blood after consumption of Lacticaseibacillus rhamnosus JB-1 – Kevin Champagne-Jorgensen – Gut Microbes

β-Glucan-triggered Akkermansia muciniphila expansion facilitates the expulsion of intestinal helminth via TLR2 in mice – Xuemin Jin – Carbohydrate Polymers

Review: The impact of a low-calorie, low-glycemic diet on systemic lupus erythematosus: a systematic review – Aline Mizusaki Imoto – Advances in Rheumatology

Review: Recent advances in the concept of paraprobiotics: Nutraceutical/functional properties for promoting children health – Harsh Kumar – Critical Reviews in Food Science and Nutrition

Review: Breastfeeding Contributes to Physiological Immune Programming in the Newborn – Alberto Camacho-Morales – Frontiers in Pediatrics

Animal Model Microbiome

Electroacupuncture could balance the gut microbiota and improve the learning and memory abilities of Alzheimer’s disease animal model – Jing Jiang – PloS ONE

Protective Effects of Bacillus amyloliquefaciens 40 Against Clostridium perfringens Infection in Mice – Zipeng Jiang – Frontiers in Nutrition

Animal Microbiome (non-models)

Evidence of MHC class I and II influencing viral and helminth infection via the microbiome in a non-human primate – B Karina Montero – PLoS Pathogens

Metagenomic and network analysis revealed wide distribution of antibiotic resistance genes in monkey gut microbiota – Yueyang Yan – Microbiological Research

Comparative Study of the Gut Microbiota Among Four Different Marine Mammals in an Aquarium – Shijie Bai – Frontiers in Microbiology

Bacterial Communities of Lab and Field Northern House Mosquitoes (Diptera: Culicidae) Throughout Diapause – Elise M Didion – Journal of Medical Entomology

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

Concerted impacts of antiherbivore defenses and opportunistic Serratia pathogens on the fall armyworm (Spodoptera frugiperda) – Charles J Mason – Oecologia

Plant Microbiome

Review: Sculpting the soil microbiota – Valéria Custódio – The Plant Journal


Review: Microbial diversity in extreme environments – Wen-Sheng Shu – Nature Reviews Microbiology

Preprint: A large-scale genome-based survey of acidophilic Bacteria suggests that genome streamlining is an adaption for life at low pH – Diego Nahuel Cortez – BioRxiv

Other Microbes

Bacterial Community Structure and Metabolic Function Succession During the Composting of Distilled Grain Waste – Shi-Peng Wang – Applied Biochemistry and Biotechnology

Bioinformatics and Microbiome Analysis

AMDB: a database of animal gut microbial communities with manually curated metadata – Junwon Yang – Nucleic Acids Research

RESCRIPt: Reproducible sequence taxonomy reference database management – Michael S 2nd Robeson – PLoS Computational Biology

Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility – Xiongbin Kang – Frontiers in Cellular and Infection Microbiology

November 6, 2021

Have a nice weekend! Today we have a good variety of papers, in several different topics. Enjoy!

Human and General Microbiome

Metataxonomic investigation of the microbial community in the trachea and oropharynx of healthy controls and diabetic patients using endotracheal tubes – Sun Young Cho – PloS ONE

Characterization of the endometrial, cervicovaginal and anorectal microbiota in post-menopausal women with endometrioid and serous endometrial cancers – Gregory M Gressel – PloS ONE

Fecal Microbiota Transplantation Relieves Gastrointestinal and Autism Symptoms by Improving the Gut Microbiota in an Open-Label Study – Ning Li – Frontiers in Cellular and Infection Microbiology

Evaluation of vaginal microbiota in women admitted to the hospital for premature labour – Bruno Arena – Acta Bio-medica

The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia – Anita Mitra – Genome Medicine

Comparative analysis of human facial skin microbiome between topical sites compared to entire face – Haeun Lee – Genes & Genomics

Lung Tissue Microbiome Is Associated With Clinical Outcomes of Idiopathic Pulmonary Fibrosis – Hee-Young Yoon – Frontiers in Medicine

Mechanisms underlying interactions between two abundant oral commensal bacteria – Dasith Perera – The ISME Journal

Epigenetic adaptations of the masticatory mucosa to periodontal inflammation – Gesa M Richter – Clinical Epigenetics

Increase of SARS-CoV-2 RNA load in faecal samples prompts for rethinking of SARS-CoV-2 biology and COVID-19 epidemiology – Mauro Petrillo – F1000Research

Microbiota-derived acetate enables the metabolic fitness of the brain innate immune system during health and disease – Daniel Erny – Cell Metabolism

Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome – Kathy N Lam – Cell Reports

Cell-surface xyloglucan recognition and hydrolysis by the human gut commensal Bacteroides uniformis – Julie M Grondin – Applied and Environmental Microbiology

Dysbiosis of Gut Microbiome Is Associated With Rupture of Cerebral Aneurysms – Shuhei Kawabata – Stroke

Effect of Long-Term and Short-Term Imbalanced Zn Manipulation on Gut Microbiota and Screening for Microbial Markers Sensitive to Zinc Status – Lingjun Chen – Microbiology Spectrum

Dietary Modulation Alters Susceptibility to Listeria monocytogenes and Salmonella Typhimurium with or without a Gut Microbiota – Mathis Wolter – mSystems

Alterations in Gut Microbiome Composition and Function in Irritable Bowel Syndrome and Increased Probiotic Abundance with Daily Supplementation – Joann Phan – mSystems

The Future Is Big-and Small: Remote Sensing Enables Cross-Scale Comparisons of Microbiome Dynamics and Ecological Consequences – Deanna S Beatty – mSystems

Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment – Marina Martínez-Álvaro – Communications Biology

Vescimonas gen. nov., Vescimonas coprocola sp. nov., Vescimonas fastidiosa sp. nov., Pusillimonas gen. nov. and Pusillimonas faecalis sp. nov. isolated from human faeces – Maki Kitahara – International Journal of Systematic and Evolutionary Microbiology

Human and General Microbiome – Reviews

Engineering temporal dynamics in microbial communities – Carlotta Ronda – Current Opinion in Microbiology

From a parts list to assembly instructions and an operating manual: how small host models can re-write microbiome theory – Nic M Vega – Current Opinion in Microbiology

Microbiota-derived extracellular vesicles in interkingdom communication in the gut – Natalia Díaz-Garrido – Journal of Extracellular Vesicles

Multiple roles of short-chain fatty acids in Alzheimer disease – Hui Chen – Nutrition 

Role of gut microbiota in functional constipation – Shengsheng Zhang – Gastroenterology Report

Gut Feelings: The Microbiota-Gut-Brain Axis on Steroids – Sik Yu So – American Journal of Physiology. Gastrointestinal and Liver Physiology

Urobiome: An outlook on the metagenome of urological diseases – Rachel Shoemaker – Investigative and Clinical Urology

Animal Models

Utilizing a reductionist model to study host-microbe interactions in intestinal inflammation – Amy M Tsou – Microbiome

Disruption of autophagy by increased 5-HT alters gut microbiota and enhances susceptibility to experimental colitis and Crohn’s disease – Sabah Haq – Science Advances

Differences in the gut microbiota composition of rats fed with soybean protein and their derived peptides – Wenhui Li – Journal of Food Science

Animal Microbiome (non-model)

Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores – Franziska Zoelzer – Animal Microbiome

The Role Transition of Dietary Species Richness in Modulating the Gut Microbial Assembly and Postweaning Performance of a Generalist Herbivore – Guoliang Li – mSystems

Age Associated Microbiome and Microbial Metabolites Modulation and Its Association With Systemic Inflammation in a Rhesus Macaque Model – Suresh Pallikkuth – Frontiers in Immunology

Strain-level analysis reveals the vertical microbial transmission during the life cycle of bumblebee – Qinzhi Su – Microbiome

Social convergence of gut microbiomes in vampire bats – Karthik Yarlagadda – Biology Letters

Shrimp AHPND Causing Vibrio anguillarum Infection: Quantitative Diagnosis and Identifying Antagonistic Bacteria – Huiyu Shen – Marine Biotechnology

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition – C E Dubé – Nature Communications

Dry and Rainy Seasons Significantly Alter the Gut Microbiome Composition and Reveal a Key Enterococcus sp. (Lactobacillales: Enterococcaceae) Core Component in Spodoptera frugiperda (Lepidoptera: Noctuidae) Corn Strain From Northwestern Colombia – Marlon Felipe Higuita Palacio – Journal of Insect Science

Invasive Amphibian Gut Microbiota and Functions Shift Differentially in an Expanding Population but Remain Conserved Across Established Populations – Carla Wagener – Microbial Ecology

Review: Microbiome Studies in Non-human Primates – Jason M Brenchley – Current HIV/AIDS Reports

Beneficial Microbes and Compounds

Regulation divergences of Lactobacillus fermentum PCC and Lactobacillus paracasei 431 on penicillin-induced upper respiratory tract microbial dysbiosis in BALB/c mice – Feng Gao – Food & Function

Dietary calcium phosphate strongly impacts gut microbiome changes elicited by inulin and galacto-oligosaccharides consumption – Jori Fuhren – Microbiome

Plant Microbiome

Effects of growth promoting microorganisms on tomato seedlings growing in different media conditions – Robert Pokluda – PloS ONE

Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production – Jean-Baptiste Floc’h – Microbial Ecology

Built Environment Microbiome

City-Scale Meta-Analysis of Indoor Airborne Microbiota Reveals that Taxonomic and Functional Compositions Vary with Building Types – You Zhou – Environmental Science & Technology

Environmental Microbiome

Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River – Qiaoling Yu – Journal of Hazardous Materials

Forensic Microbiome

Assessment of the link between evidence and crime scene through soil bacterial and fungal microbiome: A mock case in forensic study – Sukriye Karadayı – Forensic Science International

Microbiome Analysis Methods; Bioinformatics 

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification – Oliver Schwengers – Microbial Genomics

Compositional Data Analysis of Microbiome and Any-Omics Datasets: A Validation of the Additive Logratio Transformation – Michael Greenacre – Frontiers in Microbiology

Machine Learning Based Metagenomic Prediction of Inflammatory Bowel Disease – Andrea Mihajlović – Studies in Health Technology and Informatics

Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes – Solize Vosloo – Microbiology Spectrum

Evaluation of the effect of antibiotics on gut microbiota in early life based on culturomics, SMRT sequencing and metagenomics sequencing methods – Lihan Wang – Analytical Methods

October 29, 2021

Sorry for the delayed post, WordPress was playing some mean tricks on me today and there were no treats! Good morning all and happy spooky season! It’s been a moment since I’ve written a post and I write to you now as a freshly (pepper)minted PhD! I’m feeling gourd and can’t wait to pumpkin spice things up with some fangtastic papers.

Some of the highlights include a paper by McAlpine et al. examining interkingdom relationships between bacteria and fungi. Specifically, they found that the gut commensal species Lactobacillus can produce a small molecule that blocks filamentous growth of the opportunistic pathogen Candida albicans. Another interesting paper comes from Michael Adams lab at the University of Georgia, Athens which showed that members of the gut microbiota have the capacity to assimilate the metal tungsten which, in turn, allows these microbes to oxidize a broad range of aldehydes in the gut. Additionally, a paper by Plummer et al. looked at the vaginal microbiota of women who have recurrent bacterial vaginosis as well as the penile microbiota of their partners, and found that when males also underwent antibiotic treatment it led to a decrease in bacterial vaginosis in their female partners.

Hope you enjoy reading these fa-boo-lous papers and may you eat, drink, and be scary this Halloween!

General Microbiome
A small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase. – MacAlpine, J. et al., Nature Communications.

Pregnancy and Early-Life
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. – Laursen, M.F. et al., Nature Microbiology.

Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection. – Heiss, B.E. et al., Gut Microbes.

Mother’s Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis. – Gołębiewski. M. et al., Nutrients.

Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. – Pärnänen, K.M.M. et al., The American Journal of Clinical Nutrition.

Human Vaginal Microbiome
A Prospective, Open-Label Pilot Study of Concurrent Male Partner Treatment for Bacterial Vaginosis. – Plummer, E.L. et al., mBio.

Human Gut Microbiome
Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome. – Schut, G.J. et al., PNAS.

Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis. – Pernigoni, N. et al., Science.

Vertebrate host phylogeny influences gut archaeal diversity. – Youngblut, N.D. et al., Nature Microbiology.

Gut microbiota dysbiosis contributes to the development of chronic obstructive pulmonary disease. – Li, N. et al., Respiratory Research.

Oral Administration of Latilactobacillus sakei ADM14 Improves Lipid Metabolism and Fecal Microbiota Profile Associated With Metabolic Dysfunction in a High-Fat Diet Mouse Model. – Won, S.-M. et al., Frontiers in Microbiology.

Human Oral Microbiome
Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses. – Nemoto, T. et al., mSystems.

Animal Experiments
Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection. – Woo, V. et al., Cell Host & Microbe.

Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia. – Vicentini, F.A. et al., Microbiome.

Lactobacillus rhamnosus GG Derived Extracellular Vesicles Modulate Gut Microbiota and Attenuate Inflammatory in DSS-Induced Colitis Mice. – Tong, L. et al., Nutrients.

Animal Microbiome
Phage Treatment Trial to Eradicate LA-MRSA from Healthy Carrier Pigs. – Tuomala, H. et al., Viruses.

Characterization of the Eukaryotic Virome of Mice from Different Sources. – Zhang, C. et al., Microorganisms.

Supplemental L-Arginine Improves the Embryonic Intestine Development and Microbial Succession in a Chick Embryo Model. – Dai, D. et al., Frontiers in Nutrition.

Water and Extremophile Microbiome
Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. – Zrimec, J. et al., mBio.

Acrylate protects a marine bacterium from grazing by a ciliate predator. – Teng, Z.-J. et al., Nature Microbiology.

Plant, Root, and Soil Microbiome
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. – Mahdi, L.K. et al., ISME Journal.

Spatial Characterization of Microbial Communities on Multi-Species Leafy Greens Grown Simultaneously in the Vegetable Production Systems on the International Space Station. – Hummerick, M.E. et al., Life (Basel).

Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms. – Jones, M.L. et al., Elife.

High-efficiency delivery of CRISPR-Cas9 by engineered probiotics enables precise microbiome editing. – Neil, K. et al., Molecular Systems Biology.

Visualizing transfer of microbial biomolecules by outer membrane vesicles in microbe-host-communication in vivo. – Bittel, M. et al., Journal of Extracellular Vesicles.