May 21, 2022

Human and General Microbiome

Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors – Jesse R Willis – NPJ Biofilms and Microbiomes

Gut Microbiome Was Highly Related to the Regulation of Metabolism in Lung Adenocarcinoma Patients – Sheng Wang – Frontiers in Oncology

Host-Population Microbial Diversity Scaling of Chinese Gut Microbiomes in Gout Patients – Jieshang Zhou – Evolutionary Bioinformatics Online

Combined Microbiome and Metabolome Analysis Reveals a Novel Interplay Between Intestinal Flora and Serum Metabolites in Lung Cancer – Sai Chen – Frontiers in Cellular and Infection Microbiology

Decreased Diversity of Gut Microbiota Is Associated with Decreased Muscle Mass and Function in Older Adults Residing in a Nursing Home – Y Ishida – The Journal of Nutrition, Health & Aging

The role of the mucin-glycan foraging Ruminococcus gnavus in the communication between the gut and the brain – Erika Coletto – Gut Microbes

A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients – Jinyuan Yan – Scientific Data

The gut microbiota: stable bioreactor of variable composition? – Gilles Mithieux – Trends in Endocrinology and Metabolism

Characterizing the mucin-degrading capacity of the human gut microbiota – Janiece S Glover – Scientific Reports

Mapping microbiome-redox spectrum and evaluating Microbial-Redox Index in chronic gastritis – Manas Kumar Panigrahi – Scientific Reports

Endometrial microbiome: sampling, assessment, and possible impact on embryo implantation – Marco Reschini – Scientific Reports

Temporal relationship among adiposity, gut microbiota, and insulin resistance in a longitudinal human cohort – Kui Deng – BMC Medicine

The respiratory microbiome associated with chronic obstructive pulmonary disease comorbidity in non-small cell lung cancer – Masamitsu Shimizu – Thoracic Cancer

Cervicovaginal loads of Gardnerella spp. are increased in immunocompetent women with persistent high-risk human papillomavirus infection – Rafael Belleti – Journal of Medical Microbiology

Review: Dysbiotic relationship between arthritis and the oral-gut microbiome. A critical review – Rubelisa Candido Gomes de Oliveira – Journal of Periodontal Research

Microbiome and COVID19

Intestinal microbiota composition of children with infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and multisystem inflammatory syndrome (MIS-C) – Cansu Suskun – European Journal of Pediatrics

Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients – Tian Qin – Microbiology Spectrum

Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome – Priti Devi – Microbiology Spectrum

Beneficial Microbes and Compounds

In vitro anti-tuberculosis effect of probiotic Lacticaseibacillus rhamnosus PMC203 isolated from vaginal microbiota – Md Abdur Rahim – Scientific Reports

Commensal bacteria-derived extracellular vesicles suppress ulcerative colitis through regulating the macrophages polarization and remodeling the gut microbiota – Liping Liang – Microbial Cell Factories

More Microbes

Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids – F Repoila – Scientific Reports

The OmpA of commensal Escherichia coli of CRC patients affects apoptosis of the HCT116 colon cancer cell line – Mahsa Mirzarazi – BMC Microbiology

Non-Model Animal Microbiome

Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey – Anastasios Galanis – Molecular Ecology Resources

Time for a change! A spotlight on the many neglected facets of sponge microbial biotechnology – Bruno Francesco Rodrigues de Oliveira – Current Pharmaceutical Biotechnology

Dietary wheat and reduced methane yield are linked to rumen microbiome changes in dairy cows – Keith W Savin – PloS ONE

Review: Role of Insect Gut Microbiota in Pesticide Degradation: A Review – Junaid Ali Siddiqui – Frontiers in Microbiology

Plant Microbiome

The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines – Birgit Wassermann – Microbial Biotechnology

Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides – Chunbo Dong – Frontiers in Microbiology

Acquisition of a complex root microbiome reshapes the transcriptomes of rice plants – Christian Santos-Medellín – The New Phytologist

Water deficit affects inter-kingdom microbial connections in plant rhizosphere – Kathryn E Bazany – Environmental Microbiology

Review: Facilitating Reforestation Through the Plant Microbiome: Perspectives from the Phyllosphere – Posy E Busby – Annual Review of Phytopathology

Bioinformatics and Microbiome Analysis

The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling – Natalia Szóstak – Scientific Reports

Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype – Wontack Han – Journal of Computational Biology

May 14, 2022

Human and General Microbiome

Gut Microbiome

Noninvasive assessment of gut function using transcriptional recording sentinel cells – Florian Schmidt – Science

Perspective about this paper: Recording bacterial responses to changes in the gut environment – Liron Zahavi – Science

Contribution of the Microbiome to Western Diet-Induced Gene Expression Changes in the Intestine and Vasculature – Alyssa N Cavalier – FASEB Journal

The Gut Microbiota Metabolite Succinate promotes Adipose Tissue Browning in Crohn’s Disease – D Monfort-Ferré – Journal of Crohn’s & Colitis

Changes in Gut Microbiome Composition with Healthy Aging in Humans: Links to Vascular Endothelial Function – Nathan Greenberg – FASEB Journal

The Gut Microbiota Modulates Gene Expression in the Kidney – Brittni Moore – FASEB Journal

Rapid evolution and strain turnover in the infant gut microbiome – Daisy W Chen – Genome Research

Review: The role of short-chain fatty acids in Clostridioides difficile infection: A review – Zi-Rou Ouyang – Anaerobe

Respiratory Microbiome

Lung microbiome composition and bronchial epithelial gene expression in patients with COPD versus healthy individuals: a bacterial 16S rRNA gene sequencing and host transcriptomic analysis – Mohammadali Yavari Ramsheh – The Lancet. Microbe

Therapeutic Targeting of the Respiratory Microbiome – Sanjay H Chotirmall – American Journal of Respiratory and Critical Care Medicine

Temporal Dynamics of the Nasopharyngeal Microbiome and its Relationship with Childhood Asthma Exacerbation – Jinpao Hou – Microbiology Spectrum

Oral Microbiome

Role of Oral Microbiota Biofilms in Recurrent Tonsillitis and Sleep-Disordered Breathing in Children – Thibault Allain – FASEB Journal

Oral Microbiota of Amazonian Kichwa Infants From Equador During the First Six Months of Life – Diana Maldonado Lino – FASEB Journal

Child saliva microbiota and caries: a randomized controlled maternal education trial in rural Uganda – Grace K M Muhoozi – Scientific Reports

Microbiome and Cancer

Review: Gut microbiota: Role and Association with Tumorigenesis in Different Malignancies – Altamas Ali – Molecular Biology Reports

Fusobacterium nucleatum as a Marker for Epithelial to Mesenchymal Transition in Colorectal Cancer – Angela Huang – FASEB Journal

L-norvaline affects the proliferation of breast cancer cells based on the microbiome and metabolome analysis – Qin Zhu – Journal of Applied Microbiology

Microbiome across Age

Integrative multiomics analysis reveals host-microbe-metabolite interplays associated with the aging process in Singaporeans – Liwei Chen – Gut Microbes

Association of antibiotics exposure within the first 2 years after birth with subsequent childhood type 1 diabetes – Dahye Lee – Endocrine

Review: The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy – Robert Thänert – Cell Host & Microbe

Review: The developing infant gut microbiome: A strain-level view – Hagay Enav – Cell Host & Microbe

Multi-site Microbiome

The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle – Maria Christine Krog – Human Reproduction

Multi-scale study of the oral and gut environments in children with high and low threshold peanut allergy – Lingdi Zhang – The Journal of Allergy and Clinical Immunology

Beneficial Microbes and Compounds

Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants – Jumana Samara – Cell host & Microbe

Review: Effective Regulation of Gut Microbiota With Probiotics and Prebiotics May Prevent or Alleviate COVID-19 Through the Gut-Lung Axis – Lei Xu – Frontiers in Pharmacology

Review: A Reciprocal Link Between Gut Microbiota, Inflammation and Depression: A Place for Probiotics? – Ahmed Eltokhi – Frontiers in Neuroscience

Animal Model Microbiome

Reduced housing density improves statistical power of murine gut microbiota studies – Amber Russell – Cell Reports

Investigation of Effects of Hyperglycaemia on the Lung Microbiome in Diabetic Mice – Stanislavs Vasiljevs – FASEB Journal

Dietary Impacts on Changes in Diversity and Abundance of the Murine Microbiome During Progression and Treatment of Cancer – Holly Paden – FASEB Journal

Impact of Gut R. torques on Type 2 Diabetes in Selenium-deficient Mice – Ying-Chen Huang – FASEB Journal

Interaction between gut microbiota dysbiosis and lung infection as gut-lung axis caused by Streptococcus suis in mouse model – Wenjie Yang – Microbiological Research

The influence of maternal unhealthy diet on maturation of offspring gut microbiota in rat – Kyoko Hasebe – Animal Microbiome

Lactoferrin modulates gut microbiota and Toll-like receptors (TLRs) in mice with dysbiosis induced by antibiotics – Andrea Bellés – Food & Function

Non-Model Animal Microbiome

Serotonin modulates insect gut bacterial community homeostasis – Tian Zeng – BMC Biology

Plant and Soil Microbiome

Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes – Peng Wang – Journal of Experimental Botany

Beyond the snapshot: identification of the timeless, enduring indicator microbiome informing soil fertility and crop production in alkaline soils – Jianwei Zhang – Environmental Microbiome

Environmental Microbiome

The role of microbiome in carbon sequestration and environment security during wastewater treatment – Xuefeng Zhu – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

Variational Approximation-Based Model Selection for Microbial Network Inference – Shibu Yooseph – Journal of Computational Biology

Review: Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation – Sijia Liu – Microbiome

May 7, 2022

Human and General Microbiome

Signature of Alzheimer’s Disease in Intestinal Microbiome: Results From the AlzBiom Study – Christoph Laske – Frontiers in Neuroscience

The Fungal Gut Microbiome Exhibits Reduced Diversity and Increased Relative Abundance of Ascomycota in Severe COVID-19 Illness and Distinct Interconnected Communities in SARS-CoV-2 Positive Patients – Johanna Reinold – Frontiers in Cellular and Infection Microbiology

The associations between low abundance of Mycoplasma hominis and female fecundability: a pregnancy-planning cohort study – Xiang Hong – BMC Microbiology

Insights into the Profile of the Human Expiratory Microbiota and Its Associations with Indoor Microbiotas – Yin Zhang – Environmental Science & Technology

Oral microbiome of Crohn’s Disease patients with and without oral manifestations – Shijia Hu – Journal of Crohn’s & Colitis

Systematic Review: SARS-CoV-2 and Prevotella spp.: friend or foe? A systematic literature review – Zohreh Tamanai-Shacoori – Journal of Medical Microbiology

Review: The Game for Three: Salmonella-Host-Microbiota Interaction Models – Krzysztof Grzymajlo – Frontiers in Microbiology

Review: Host gene effects on gut microbiota in type 1 diabetes – Keyu Guo – Biochemical Society Transactions

Minireview: Host-microbial interactions in metabolic diseases: from diet to immunity – Ju-Hyung Lee – Journal of Microbiology

Preprint: Bacterial association with metals enables in vivo tracking of microbiota using magnetic resonance imaging – Sarah C Donnelly – bioRxiv

Beneficial Microbes and Compounds

Natural Garlic Organosulfur Compounds Prevent Metabolic Disorder of Lipid and Glucose by Increasing Gut Commensal Bacteroides acidifaciens – Keyu Chen – Journal of Agricultural and food Chemistry

Animal Model Microbiome

Circulating gut microbiota-related metabolites influence endothelium plaque lesion formation in ApoE knockout rats – Hsiao-Li Chuang – PloS ONE

Depletion of the gut microbiota enhances the blood pressure-lowering effect of captopril: implication of the gut microbiota in resistant hypertension – Jun Kyoung – Hypertension Research

Non-Model Animal Microbiome

Fecal microbiota and diets of muskox female adults and calves – Ji-Yeon Cheon – Ecology and Evolution

Temporal Changes in Gut Microbiota Composition and Pollen Diet Associated with Colony Weakness of a Stingless Bee – Karen Luisa Haag – Microbial Ecology

Interaction between MHC diversity and constitution, gut microbiota and Astrovirus infections in a neotropical bat – Ramona Fleischer – Molecular Ecology

Review: Symbiont transmission in marine sponges: reproduction, development, and metamorphosis – Tyler J Carrier – BMC Biology

Preprint: A new microbiological weapon against lepidopteran pests – Vyacheslav Martemyanov – bioRxiv

Environmental Microbiome

Associations between bacterial communities and microplastics from surface seawater of the Northern Patagonian area of Chile – Patricia Aguila-Torres – Environmental Pollution

Plant and Soil Microbiome

Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons – Mingsheng Qi – The ISME Journal

A metagenomic study of the bacteria in snow algae microbiomes – Kurt Michael Yakimovich – Canadian Journal of Microbiology

Soil microbial diversity and functional profiling of a tropical rainforest of a highly dissected low hill from the upper Itaya river basin revealed by analysis of shotgun metagenomics sequencing data – Marianela Cobos – Data in Brief

Bioinformatics and Data Analysis

Accessible analysis of longitudinal data with linear mixed effects models – Jessica I Murphy – Disease Models & Mechanisms

Scalable in-memory processing of omics workflows – Vadim Elisseev – Computational and Structural Biotechnology Journal

DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation – Rui Gan – Frontiers in Genetics

A New Approach to Testing Mediation of the Microbiome at Both the Community and Individual Taxon Levels – Ye Yue – Bioinformatics

May 3, 2022

General microbiome

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women – Worby et al. Nature Microbiology. 2022

Human gut microbiome

Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins – Yang et al. Gut

Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics – Button et al. Cell Host & Microbe

Gut microbial similarity in twins is driven by shared environment and aging – Vilchez-Vargas et al. eBioMedicine

Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas. Kwan et al. mSystems

Human respiratory & oral microbiome

Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation – Widder et al. Microbiome

Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective – Zhang et al. mBio

Animal experiments

Effects of ‘Healthy’ Fecal Microbiota Transplantation against the Deterioration of Depression in Fawn-Hooded Rats – Hu et al. mSystems

Water/Extremophile microbiome

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans – Duncan et al. Microbiome

Bioinformatics

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype – Martino et al. mSystems

BiomeHorizon: Visualizing Microbiome Time Series Data in R – Fink et al. mSystems

Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies. Yarmosh et al. mSphere

Non microbiome picks

Ancestry-inclusive dog genomics challenges popular breed stereotypes – Morrill et al. Science. 

Dietary fibre in hypertension and cardiovascular disease management: systematic review and meta-analyses – Reynolds et al. BMC Medicine

March 25, 2022

Human gut microbiome

In Vitro and In Silico Based Approaches to Identify Potential Novel Bacteriocins from the Athlete Gut Microbiome of an Elite Athlete Cohort – Wosinska et al. Microorganisms

Cancer pharmacomicrobiomics: targeting microbiota to optimise cancer therapy outcomes – Ting et al. Gut

Human respiratory microbiome

Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis – D’Alessandro-Gabazza et al. Nature Communications

Probiotics

Gut microbiota and fermentation-derived branched chain hydroxy acids mediate health benefits of yogurt consumption in obese mice – Daniel et al. Nature Communications

Animal experiments

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue – Agranyoni et al. npj biofilms and microbiomes

The microbiota restrains neurodegenerative microglia in a model of amyotrophic lateral sclerosis – Cox et al. Microbiome

Water & Extremophile microbiome

Spatial organization of the kelp microbiome at micron scales – Ramirez-Puebla et al. Microbiome

Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite – Murakami et al. Microbiome.

Virome

Phages and their satellites encode hotspots of antiviral systems – Rousset et al. Cell Host & Microbe

Fungi

Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity – Li et al. Cell Host & Microbe

The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors – Sharma et al. npj Biofilms and microbiomes

Bioinformatics

Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases – Armstrong et al. mSystems

March 1, 2022

General microbiome

Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analyses – Ramaloko et al. – Environmental Microbiology

Global diversity and distribution of mushroom-inhabiting bacteria – Gohar et al. – Environmental Microbiology Reports

Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on blaNDM Transmission – Dong et al. – Microbiology Spectrum

Multi-site human microbiome

Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis – Cai et al. – Microbiology Spectrum

Human respiratory microbiome

Early life inter-kingdom interactions shape the immunological environment of the airways – C Pattaroni et al. – Microbiome

Human gut microbiome

Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers – Coker et al. – Microbiome

Animal experiments

Development of a rational framework for the therapeutic efficacy of fecal microbiota transplantation for calf diarrhea treatment – Islam et al. – Microbiome

Animal microbiome

Comparative microbiome analysis of Diaphorina citri and its associated parasitoids Tamarixia radiata and Diaphorencyrtus aligarhensis reveals Wolbachia as a dominant endosymbiont – Ashraf et al. – Environmental Microbiology

Plant, root, and soil microbiome

Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured – Kajihara et al. – New Phytologist

Embracing mountain microbiome and ecosystem functions under global change –  Wang et al. – New Phytologist

Nitrogen fertilization disrupts the temporal dynamics of arbuscular mycorrhizal fungal hyphae but not spore density and community composition in a wheat field – Babalola et al. – New Phytologist

Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain – Pang et al. – Microbiology Spectrum

Seed microbiota revealed by a large-scale meta-analysis including 50 plant species – Simonin et al. – New Phytologist

Viewpoint: Plant–microbe eco-evolutionary dynamics in a changing world – Angulo et al. – New Phytologist

Stem traits, compartments, and tree species affect fungal communities on decaying wood – Yang et al. – Environmental Microbiology

Microplastics reduce soil microbial network complexity and ecological deterministic selection – Shi et al. – Environmental Microbiology

The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA – Rolando et al. – Microbiome

Water and extremophile

“Boom-and-busted-dynamics” of phytoplankton-virus interactions explain the paradox of the plankton – Flynn et al. – New Phytologist

Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts – Taylor et al. – Environmental Microbiology

Global 16S rRNA diversity of provannid snail endosymbionts from Indo-Pacific deep-sea hydrothermal vents – Breusing et al. – Environmental Microbiology Reports

Sources of protein diet differentially stimulate the gut and water microbiota under freshwater crayfish, marron (Cherax cainii, Austin 2002) culture – Foysal et al. – Environmental Microbiology Reports

February 28, 2022

Human and General Microbiome

Fusobacterium nucleatum promotes colorectal cancer cells adhesion to endothelial cells and facilitates extravasation and metastasis by inducing ALPK1/NF-κB/ICAM1 axis – Ying Zhang – Gut Microbes

Oral and Intestinal Bacterial Substances Associated with Disease Activities in Patients with Rheumatoid Arthritis: A Cross-Sectional Clinical Study – Kaori Kitamura – Journal of Immunology Research

Cervicovaginal Microbiota Predicts Neisseria gonorrhoeae Clinical Presentation – Angela Lovett – Frontiers in Microbiology

Gut microbiota from Mexican patients with metabolic syndrome and HIV infection: an inflammatory profile – Fernando Amador-Lara – Journal of Applied Microbiology

Dysbiosis of skin microbiome and gut microbiome in melanoma progression – Chahrazed Mekadim – BMC Microbiology

Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants – Sami Khabthani – International Journal of Molecular Sciences

Dynamics of the Gut Bacteria and Fungi Accompanying Low-Carbohydrate Diet-Induced Weight Loss in Overweight and Obese Adults – Dan Yu – Frontiers in Nutrition

The Gut Microbiome as a Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma – Takehiro Otoshi – Anticancer Research

Impact Of The Ileal Microbiota On Surgical Site Infections In Crohn’s Disease: A Nationwide Prospective Cohort – Clément Julien – Journal of Crohn’s & Colitis

A multiple-dimension model for microbiota of patients with colorectal cancer from normal participants and other intestinal disorders – Jian Shen – Applied Microbiology and Biotechnology

Gut Microbiota Regulate Pancreatic Growth, Exocrine Function and Gut Hormones – Khyati Girdhar – Diabetes

Respiratory dysfunction three months after severe COVID-19 is associated with gut microbiota alterations – Beate Vestad – Journal of Internal Medicine

Gut microbiota and BMI throughout childhood: the role of firmicutes, bacteroidetes, and short-chain fatty acid producers – Timothy A Houtman – Scientific Reports

Review: Cross-reactivity between microbial and tumor antigens – Laurence Zitvogel – Current Opinion in Immunology

Review: The role of nutrition in inflammaging – Paolo Di Giosia – Ageing Research Reviews

Review: Impact of antibiotics on the human microbiome and consequences for host health – Dhrati V Patangia – MicrobiologyOpen

Beneficial Microbes and Compounds

Randomized, Double-blind, Placebo-controlled Study to Assess the Effect of Two Probiotics on the Preterms’ Gut Microbiota – Bárbara Moreno-Sanz – Journal of Pediatric Gastroenterology and Nutrition

Streptococcus strain C17(T) as a potential probiotic candidate to modulate oral health – Wen Xiao Zhang – Letters in Applied Microbiology

Animal Microbiome

Antimicrobial resistance profile of gram-positive isolates belonging to the microbiota of non-human primates – Melissa M Zaniolo – Journal of Medical Primatology

Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish – Lasse Nyholm – PeerJ

An experimental test of disease resistance function in the skin-associated bacterial communities of three tropical amphibian species – Myra C Hughey – FEMS Microbiology Ecology

Gut Microbiome Characteristics in feral and domesticated horses from different geographic locations – Li Ang – Communications Biology

Plant Microbiome

Long-term effect of epigenetic modification in plant-microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process – Chen Chen – Microbiome

Changes in root microbiome during wheat evolution – Somayeh Gholizadeh – BMC Microbiology

Plant organ and sampling time point determine the taxonomic structure of microbial communities associated to apple plants in the orchard environment – Claudia Maria Oliveira Longa – Microbiological Research

Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant – Or Shalev – Nature Ecology & Evolution

Review: Major Biological Control Strategies for Plant Pathogens – Manisha Arora Pandit – Pathogens

Bioinformatics

ADDAGMA: A database for domestic animal gut microbiome atlas – Yueren Xu – Computational and Structural Biotechnology Journal

To rarefy or not to rarefy: robustness and efficiency trade-offs of rarefying microbiome data – Johnny Hong – Bioinformatics

Techniques

Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies – Anne Plauzolles – Frontiers in Cellular and Infection Microbiology

February 21, 2022

Today’s digest features two excellent metagenome – metabolome association studies in Nature Medicine and a great article in Genome Biology showing that the sustained software development is what you should look for in a bioinformatic software, not what journal it was published in.

Human gut microbiome

Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease – Talmor-Barkan et al. Nature Medicine. 

Microbiome and metabolome features of the cardiometabolic disease spectrum – Fromentin et al. Nature Medicine

Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort – Aasmets et al. Nature Communications

Animal Microbiome

Drivers of gut microbiome variation within and between groups of a wild Malagasy primate – Rudolph et al. Microbiome

Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle – Xue et al. Microbiome

The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome – Yang et al Microbiome

Virome

Independent host- and bacterium-based determinants protect a model symbiosis from phage predation – Lynch et al. Cell Reports

Virome characterization of game animals in China reveals a spectrum of emerging pathogens – He et al. Cell

Water and extremophile microbiome

Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal – Freudenthal et al. Microbiome

Bioinformatics

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks – Zhou et al. Microbiome

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software – Gardner et al. Genome Biology

Non-Microbiome picks

If you’ve listened to The Dropout podcast you might like this editorial.  

The post-Theranos world – Nature Biotechnology. 

February 2, 2022

General microbiome

Genomic structure predicts metabolite dynamics in microbial communities – Gowda et al. – Cell 

Inhalable antibiotic resistomes emitted from hospitals: metagenomic insights into bacterial hosts, clinical relevance, and environmental risks – Wu et al. – Microbiome

Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge – Dai et al. – Microbiome

Understanding microbiome alterations in autism – Nature Medicine

Human gut microbiome

3β-Hydroxysteroid dehydrogenase expressed by gut microbes degrades testosterone and is linked to depression in males – Li et al. – Cell Host & Microbe

Pregnancy and early life

Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections – Piters et al. – Nature Microbiology

Meconium Microbiome of Very Preterm Infants across Germany – Klopp et al. – mSphere

Water and extremophile microbiome

Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts – Zhang et al. – Microbiome

A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss) – Rasmussen et al. – Microbiome

Bioinformatics

MUON: multimodal omics analysis framework – Bredikhin et al. – Genome Biology

Non Microbiome Picks

A Toast to All the Rejects – The Atlantic. An insightful article on celebrating your rejections in academia. 

January 21, 2022

Human and General Microbiome

Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation – Kirstine J Bell – Microbiome

GWAS-associated bacteria and their metabolites appear to be causally related to the development of inflammatory bowel disease – Zhenhuang Zhuang – European Journal of Clinical Nutrition

The vaginal Torquetenovirus titer varies with vaginal microbiota composition in pregnant women – Tania Regina Tozetto-Mendoza – PloS ONE

Can the Acid-formation Potential of Saliva Detect a Caries-related Shift in the Oral Microbiome? – Cornelia Frese – Oral Health & Preventive Dentistry

Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients – Zhonghan Sun – BMC Medicine

Predicting Treatment Nonresponse in Hispanic/Latino Children Receiving Silver Diamine Fluoride for Caries Arrest: A Pilot Study Using Machine Learning – Ryan Richard Ruff – Frontiers in Oral Health

The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control – Smadar Shilo – Diabetes Care

Evaluation of Bacterial Diversity and Evolutionary Dynamics of Gut Bifidobacterium longum Isolates Obtained from Older Individuals in Hubei Province, China – Zhendong Zhang – Microbiology Spectrum

Review: Frontiers in Oral Mucosal Immunity and the Microbiome – Georgios N Belibasakis – Frontiers in Oral Health

Review: The microbiota-gut-brain axis: pathways to better brain health. Perspectives on what we know, what we need to investigate and how to put knowledge into practice – Anirikh Chakrabarti – Cellular and Molecular Life Sciences

Meta-Analysis: Predictors of Fecal Microbiota Transplant Failure in Clostridioides difficile Infection: An Updated Meta-analysis – Azizullah Beran – Journal of Clinical Gastroenterology

Systematic Review: The Role of Gut Microbiota-Brain Axis in Pathophysiology of ADHD: A Systematic Review – Salman Shirvani-Rad – Journal of Attention Disorders

Systematic Review: Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries – Naile Dame-Teixeira – Frontiers in Oral Health

Beneficial Microbes and Compounds

Peppermint oil effects on the gut microbiome in children with functional abdominal pain – Santosh Thapa – Clinical and Translational Science

SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection – Paul Feuerstadt – The New England Journal of Medicine

Lactiplantibacillus plantarum CCFM1019 attenuate polycystic ovary syndrome through butyrate dependent gut-brain mechanism – Yufeng He – Food & Function

Causal relationship between gut microbiota and serum vitamin D: evidence from genetic correlation and Mendelian randomization study – Xiaolin Yang – European Journal of Clinical Nutrition

Review: Modulation of Gut Microbiota and Immune System by Probiotics, Pre-biotics, and Post-biotics – Yue Liu – Frontiers in Nutrition

Review: Outlook on next-generation probiotics from the human gut – Francesca De Filippis – Cellular and Molecular Life Sciences

Animal Microbiome

Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda – Guangping Huang – Cell Reports

Seasonal variations in the composition and functional profiles of gut microbiota reflect dietary changes in plateau pikas – Chao Fan – Integrative Zoology

N-acyl-homoserine lactone produced by Rahnella inusitata isolated from the gut of Galleria mellonella influences Salmonella phenotypes – Leonardo Luiz de Freitas – Brazilian Journal of Microbiology

Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt – Ahmed M Serag – Applied Biochemistry and Biotechnology

Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula – Dhivya P Kanisan – Microbial Ecology

The Harris’ hawk (Parabuteo unicinctus) as a source of pathogenic human yeasts: a potential risk to human health – Gustavo Dornelles – Future Microbiology

Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys – Julia Craft – Applied and Environmental Microbiology

Comparative Evaluation of the Effect of Metformin and Insulin on Gut Microbiota and Metabolome Profiles of Type 2 Diabetic Rats Induced by the Combination of Streptozotocin and High-Fat Diet – Nan Hu – Frontiers in Pharmacology

Plant Microbiome

Modulating the rhizosphere microbiome by altering the cocktail of root secretions – Wei Zhang – Plant Physiology

Book Chapter: Characterization of Tobacco Microbiome by Metagenomics Approach – R Suresh Kumar – Methods in Molecular Biology 

Bioinformatics and Genomics

Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes – Nicholas D Youngblut – Environmental Microbiology

Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment – Vittorio Boscaro – Microbial Ecology

Adaptive and powerful microbiome multivariate association analysis via feature selection – Kalins Banerjee – NAR Genomics and Bioinformatics

Metabolic modeling of host-microbe interactions for therapeutics in colorectal cancer – Prerna Bhalla – NPJ Systems Biology and Applications