July 1, 2022

We made it to the end of the week, we made it through the end of June. To celebrate, check out the two (!) articles about the pig gut microbiome, try out a new tool for network analysis (MicNet Toolbox), or enjoy an NPR Short Waves podcast episode about Agar Art. Or maybe you’re spending the afternoon preparing a research talk or fieldwork event? If that’s the case, check out the article presenting 10 rules for improving communication among scientists or the one on the hidden labor of managing threats to safety by women in fieldwork.

General microbiome

Assessment of disinfectant efficacy in reducing microbial growth – Alajlan et al. – PLOS One

Animal experiments

Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses – Apiwatsiri et al. – PLOS One

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig – Gaio et al. – PLOS One

Preprint: Using axenic and gnotobiotic insects to examine the role of different microbes on the development and reproduction of the kissing bug Rhodnius prolixus (Hemiptera: Reduviidae) – Gilliland et al. – bioRxiv

Bioinformatics

MicNet toolbox: Visualizing and unraveling a microbial network – Favila et al. – PLOS One
Techniques

Evaluating the impact of sample storage, handling, and technical ability on the decay and recovery of SARS-CoV-2 in wastewater – Beattie et al. – PLOS One

Microbes in the news

NPR’s Short Wave Podcast: Let’s Get Crafty With Agar Art (11 minute episode)!

Science, publishing, and career

Ten simple rules for improving communication among scientists – Bautista et al. – PLOS Computational Biology

You can’t report your feelings: The hidden labor of managing threats to safety by women in global public health fieldwork – McAuliffe et al. – PLOS Global Public Health

June 22, 2022

General microbiome

A 16th century Escherichia coli draft genome associated with an opportunistic bile infection – Long et al. – Communications Biology

Pregnancy and early life

[PREPRINT]Strong pathogen competition in neonatal gut colonisation – Mäklin et al. – bioRxiv

Human skin microbiome

Dysbiosis of Skin Microbiota with Increased Fungal Diversity is Associated with Severity of Disease in Atopic Dermatitis – Schmid et al. – JEADV

Human gut microbiome

Loss of Novel Diversity in Human Gut Microbiota Associated with Ongoing Urbanization in China – Sun et al. – mSystems

A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer – Yuan et al. – Investigational New Drugs

[REVIEW]Vegetarianism, Microbiota and Cardiovascular health: Looking back, and forward – Kumar et al. – European Journal of Preventive Cardiology

[REVIEW]Effects of a low FODMAP diet on the colonic microbiome in irritable bowel syndrome: a systematic review with meta-analysis – So, Loughman & Staudacher – The American Journal of Clinical Nutrition

Profiling gut microbiota and bile acid metabolism in critically ill children – Kean et al. – Scientific Reports

Super-taxon in human microbiome are identified to be associated with colorectal cancer – Dai et al. – BMC Bioinformatics

The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease – Xu et al. – Gut Pathogenes

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

Immune checkpoint inhibitors unleash pathogenic immune responses against the microbiota – Hu et al. – PNAS

Deletion of both Dectin-1 and Dectin-2 affects the bacterial but not fungal gut microbiota and susceptibility to colitis in mice – Wang et al. – Microbiome

Animal microbiome (for animals in the wild)

Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems – Weinert-Nelson, Biddle & Williams – Animal Microbiome

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

Full-Length 16S rRNA Gene Sequences from Raw Sewage Samples Spanning Geographic and Seasonal Gradients in Conveyance Systems across the United States – LaMartina, Schmoldt & Newton – Microbiology Resource Announcements

Techniques

SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level – Ge et al. – PNAS

June 8, 2022

Happy Friday! Today’s digest includes articles about Gardnerella vaginalis clades in pregnancy, how a Japanese herbal medicine may alleviate a leaky gut, and a feasibility study of the impact of oral activated charcoal on healthy volunteers.

General microbiome

Clinical Burkholderia pseudomallei isolates from north Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains – Burnard et al. – PLOS Neglected Tropical Diseases

Preprint: The energy requirements of ion homeostasis determine the lifespan of starving bacteria – Schink et al. – bioRxiv

Preprint: A novel bacterial speciation process observed in a symbiotic marine population – Wang et al. – bioRxiv

Human vaginal microbiome

Gardnerella vaginalis clades in pregnancy: New insights into the interactions with the vaginal microbiome – Severgnini et al. – PLOS One

Human gut microbiome

Saireito, a Japanese herbal medicine, alleviates leaky gut associated with antibiotic-induced dysbiosis in mice – Ozaka et al. – PLOS One

A dose-finding safety and feasibility study of oral activated charcoal and its effects on the gut microbiota in healthy volunteers not receiving antibiotics – Rashidi et al. – PLOS One

Water and extremophile microbiome

The microbial community and functional potential in the Midland Basin reveal a community dominated by both thiosulfate and sulfate-reducing microorganisms – Tinker et al. – Microbiology Spectrum

Techniques

Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations – Ganz et al.- PLOS One

June 6, 2022

Have a nice Monday! Today, in this Digest we have some pendant papers from last week.

Human and General Microbiome

The role of immune cells in the liver tumor microenvironment: an involvement of gut microbiota-derived factors – Tomonori Kamiya – International Immunology

Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention – Stephanie B Orchanian – Advanced Biology

Short chain fatty acids-producing and mucin-degrading intestinal bacteria predict the progression of early Parkinson’s disease – Hiroshi Nishiwaki – NPJ Parkinson’s Disease

Intestinal inflammation alters the antigen-specific immune response to a skin commensal – Geil R Merana – Cell Reports

Characterization of resistome in Lactobacillus genomic sequences from the human gut – Jale Moradi – Journal of Global Antimicrobial Resistance

Clustering Analysis of the Multi-Microbial Consortium by Lactobacillus Species Against Vaginal Dysbiosis Among Ecuadorian Women – David Pacha-Herrera – Frontiers in Cellular and Infection Microbiology

Nutritional Intake and Gut Microbiome Composition Predict Parkinson’s Disease – Michal Lubomski – Frontiers in Aging Neuroscience

Beneficial Microbes and Compounds

Review: Bacteriocin-Producing Probiotic Lactic Acid Bacteria in Controlling Dysbiosis of the Gut Microbiota –  Anjana – Frontiers in Cellular and Infection Microbiology

Review: Relationship between gut microbiota and colorectal cancer: Probiotics as a potential strategy for prevention – Seung Yun Lee – Food Research International 

Review: Health benefits of microalgae and their microbiomes – Ines Krohn – Microbial Biotechnology

Lactobacillus reuteri J1 prevents obesity by altering the gut microbiota and regulating bile acid metabolism in obese mice – Chenxi Zhang – Food & Function

Non-Model Animal Microbiome 

16S rRNA Gene Sequencing Reveals Specific Gut Microbes Common to Medicinal Insects – Jin Geng – Frontiers in Microbiology

Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets – Leli Wang – Microbiome

Composition and Diversity of Gut Bacterial Community in Different Life Stages of a Leaf Beetle Gastrolina depressa – Meiqi Ma – Microbial Ecology

Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia coli infection – Zhiyuan He – Microbiome

Plant Microbiome

Recovery of metagenome-assembled genomes from the phyllosphere of 110 rice genotypes – Pin Su – Scientific Data

Environmental Microbiome

Mercury drives microbial community assembly and ecosystem multifunctionality across a Hg contamination gradient in rice paddies – Qiang Pu – Journal of Hazardous Materials

The sanitary indoor environment-a potential source for intact human-associated anaerobes – Manuela-Raluca Pausan – NPJ Biofilms and Microbiomes

More Microbes

Review: Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications – Pranami Goswami – NPJ Biofilms and Microbiomes

Bioinformatic and Experimental Microbiome Analysis

Review: Emerging technologies in the study of the virome – Sophie E Smith – Current Opinion in Virology

EasyMap – An Interactive Web Tool for Evaluating and Comparing Associations of Clinical Variables and Microbiome Composition – Ehud Dahan – Frontiers in Cellular and Infection Microbiology

Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples – Anaïs Biclot – Microbiome

BiGAMi: Bi-Objective Genetic Algorithm Fitness Function for Feature Selection on Microbiome Datasets – Mike Leske – Methods and Protocols

June 4, 2022

Highlights!

Review: Translating Microbiome Research From and To the Clinic – Zhenrun J Zhang – Annual Review of Microbiology → An exploration of different experimental studies associating the gut microbiota with certain human diseases, highlighting translational advances 

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome – Wenshan Zheng – Science → A powerful technique to obtain single amplified genomes (SAG) from human microbiome samples 

Human and General Microbiome

Review: Gut microbiota and atopic dermatitis in children: a scoping review – Yue Liu – BMC Pediatrics

Review: Gut microbiome and autoimmune disorders – Walaa Abdelaty Shaheen – Clinical and Experimental Immunology

Altered Vaginal Microbiota Composition Correlates With Human Papillomavirus and Mucosal Immune Responses in Women With Symptomatic Cervical Ectopy – Mariana López-Filloy – Frontiers in Cellular and Infection Microbiology

Profile of the Nasopharyngeal Microbiota Affecting the Clinical Course in COVID-19 Patients – Ornella la Fortune Tchoupou Saha – Frontiers in Microbiology

Machine learning aided construction of the quorum sensing communication network for human gut microbiota – Shengbo Wu – Nature Communications

Metagenomic assembled plasmids of the human microbiome vary across disease cohorts – S R Stockdale – Scientific Reports

Gut microbial metabolites in Parkinson’s disease: Association with lifestyle, disease characteristics, and treatment status – Robin M Voigt – Neurobiology of Disease

Mechanistic insights into accelerated α-synuclein aggregation mediated by human microbiome-associated functional amyloids – Sujeet S Bhoite – The Journal of Biological Chemistry

Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death – Yun Teng – Cell Host & Microbe

Beneficial Microbes and Compounds

Review: A Review: Cereals on Modulating the Microbiota/Metabolome for Metabolic Health – Jayani Kulathunga – Current Nutrition Reports

Anti-Diabetic Potential of Chlorella pyrenoidosa-Based Mixture and its Regulation of Gut Microbiota – Wenyu Xiong – Plant Foods for Human Nutrition

Exploring the Ecological Effects of Naturally Antibiotic-Insensitive Bifidobacteria in the Recovery of the Resilience of the Gut Microbiota during and after Antibiotic Treatment – Chiara Argentini – Applied and Environmental Microbiology

Animal Microbiome

Synchrony and idiosyncrasy in the gut microbiome of wild baboons – Johannes R Björk – Nature Ecology & Evolution

Environmental Microbiome

A synergistic bacterial pool decomposes tebuthiuron in soil – Edivaldo Wilson de Lima – Scientific Reports

The microbiome of cryospheric ecosystems – Massimo Bourquin – Nature Communications

Extremophiles

Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil – Sabrina Behairi – Extremophiles

Bioinformatics and Microbiome Analysis

Multiscale analysis of count data through topic alignment – Julia Fukuyama – Biostatistics

SAMBA: A Multicolor Digital Melting PCR Platform for Rapid Microbiome Profiling – Yongqiang Luo – Small Methods

June 3, 2022

Happy Friday!

Today’s digest has articles on COVID-19 vaccine hesitancy, a new R package to extract network backbones, and a class of novel antibiotics that targets a Mycobacterium tuberculosis PE-PGRS protein. There also preprints on biofilm winkling in Bacillus subtilis, the dental calculus microbiome, and the relationship between eukaryotic genomes and ocean plankton in a global metagenomic dataset.

Events

Next week is ASM Microbe! I’ll be there, wearing a KN-95 and clutching a box of rapid tests. Feel free to comment or reach out if you’re also attending.

COVID-19

Oro-facial mucocutaneous manifestations of Coronavirus Disease-2019 (COVID-19): A systematic review – Fakhruddin et al. – PLOS ONE

Preprint: The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity – Kim et al. – bioRxiv

Determinants of the COVID-19 vaccine hesitancy spectrum – Piltch-Loeb et al. – PLOS ONE

General microbiome

Preprint: Fatty acid synthesis knockdown promotes biofilm wrinkling and inhibits sporulation in Bacillus subtilis – Arjes et al. – bioRxiv

Association of Strongyloides stercoralis infection and type 2 diabetes mellitus in northeastern Thailand: Impact on diabetic complication-related renal biochemical parameters – Yingklang et al. – PLOS ONE

Analysis of secondary metabolite gene clusters and chitin biosynthesis pathways of Monascus purpureus with high production of pigment and citrinin based on whole-genome sequencing – Zhang et al. – PLOS ONE

Human respiratory microbiome

A novel class of antimicrobial drugs selectively targets a Mycobacterium tuberculosis PE-PGRS protein – Seo et al. – PLOS Biology

Human oral microbiome

Preprint: Assessing the influence of the Mediterranean diet on dental calculus microbiome composition: a pilot study – Innocenti et al. – bioRxiv

Human gut microbiome

Lactobacillus plantarum improves LPS-induced Caco2 cell line intestinal barrier damage via cyclic AMP-PKA signaling – Wei et al. – PLOS ONE

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

Preprint: Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton – Alexander et al. – bioRxiv

Bioinformatics

backbone: An R package to extract network backbones – Neal – PLOS ONE


May 28, 2022

Highlights!

Recently, Science released a special issue about microbiomes, with the following articles:

Human and General Microbiome  

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes – Adair L Borges – Nature Microbiology

Characteristics of the gut microbiota in women with premenstrual symptoms: A cross-sectional study – Takashi Takeda – PloS ONE

Dynamic colonization of gut microbiota and its influencing factors among the breast-feeding infants during the first two years of life – Ping Li – Journal of Microbiology

Metabolomics analysis reveals molecular linkages for the impact of vitamin D on childhood allergic airway diseases – Yu-Ho Chang – Pediatric Allergy and Immunology

Lysophosphatidylserines derived from microbiota in Crohn’s disease elicit pathological Th1 response – Yuriko Otake-Kasamoto – Journal of Experimental Medicine 

Tumor tissue-specific bacterial biomarker panel for colorectal cancer: Bacteroides massiliensis, Alistipes species, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis – Rizwana Hasan – Archives of Microbiology

Lung Microbiota of Critically Ill COVID-19 Patients are Associated with Non-Resolving Acute Respiratory Distress Syndrome – Robert F J Kullberg – American Journal of Respiratory and Critical care Medicine

Altered Gut Microbiome in Patients With Dermatomyositis – Sangmee Sharon Bae – ACR Open Rheumatology

Review: Importance of crosstalk between the microbiota and the neuroimmune system for tissue homeostasis – Kunyu Li – Clinical & Translational Immunology

Review: Dietary influences on symptomatic and non-symptomatic toxicities during cancer treatment: A narrative review – Alan J Kim – Cancer Treatment Reviews

Review: How can patients with Clostridioides difficile infection on concomitant antibiotic treatment be best managed? – Fidelma Fitzpatrick – The Lancet. Infectious Diseases

Model Animal Microbiome

Protocol: Mouse Model to Study Salmonella-Induced Colitis – Katrin Ehrhardt – Methods in Molecular Biology

Amino acid-balanced diets improved DSS-induced colitis by alleviating inflammation and regulating gut microbiota – Sen Li – European Journal of Nutrition

Excess growth hormone alters the male mouse gut microbiome in an age-dependent manner – Elizabeth A Jensen – Endocrinology

Non-Model Animal Microbiome

Metagenomic Analysis of the Gastrointestinal Microbiota of Gadus morhua callarias L. Originating from a Chemical Munition Dump Site – Wojciech Wilczynski – Toxics

Bacterial Symbionts in Ceratitis capitata – Alessia Cappelli – Insects

Egg microbiota is the starting point of hatchling gut microbiota in the endangered yellow-spotted Amazon river turtle – Ana Sofia Carranco – Molecular Ecology

Unveiling the egg microbiota of the loggerhead sea turtle Caretta caretta in nesting beaches of the Mediterranean Sea – Luca Vecchioni – PloS ONE

Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis – Nyok-Sean Lau – Microbial Ecology

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates – Guangping Huang – The Science of the Total Environment

Beneficial Microbes and Compounds

Review: Functional fermented probiotics, prebiotics and synbiotics from non-dairy products: A perspective from nutraceutical – Dharmendra Kumar – Molecular Nutrition & Food Research

Bifidobacterium longum CCFM752 prevented hypertension and aortic lesion, improved antioxidative ability, and regulated the gut microbiome in spontaneously hypertensive rats – Wenwei Lu – Food & Function

Intestinal Flora Mediates Antiobesity Effect of Rutin in High-Fat-Diet Mice – Xu Yan – Molecular Nutrition & Food Research

Multi-Probiotics ameliorate Major depressive disorder and accompanying gastrointestinal syndromes via serotonergic system regulation – Peijun Tian – Journal of Advanced Research

Butyrate, a postbiotic of intestinal bacteria, affects pancreatic cancer and gemcitabine response in in vitro and in vivo models – Concetta Panebianco – Biomedicine & Pharmacotherapy

Plant and Fungi Microbiome

Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease – Kuleshwar Prasad Sahu – Environmental Microbiome

Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts – Sunde Xu – Nature Microbiology

Other studies

Indoor microbiome, microbial and plant metabolites, chemical compounds and asthma symptoms in junior high school students: a multicentre association study in Malaysia – Yu Sun – The European Respiratory Journal

Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes – Marcos Pérez-Losada – Frontiers in Microbiology

May 20, 2022

General microbiome

[Review]Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation – Liu et al. Microbiome

Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter – Hoarfost et al. – Nature Communications

Covid19 and Metabolome

Sex differences in global metabolomic profiles of COVID-19 patients – Escarcega et al. – Cell Death & Disease

Pregnancy and early life

Does the uterine microbiota affect the reproductive outcomes in women with recurrent implantation failures? – Keburiya et al. – BMC Women’s Health

Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies – Lebeaux et al. – Pediatric Research

Should we modulate the neonatal microbiome and what should be the goal? – van Best – Microbiome

Human respiratory microbiome

The respiratory microbiome associated with chronic obstructive pulmonary disease comorbidity in non-small cell lung cancer – Shimizu et al. – Thoacic Cancer

Human skin microbiome

SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata – Agostinetto et al. – Databases

Human gut microbiome

Dynamic microbiome and metabolome analyses reveal the interaction between gut microbiota and anti-PD-1 based immunotherapy in hepatocellular carcinoma – Wu et al. – International Journal of Cancer

[Review]Exploring the multifactorial aspects of Gut Microbiome in Parkinson’s Disease – Pavan et al. – Folia Microbiologica

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

[Preprint]Gut microbiota of homing pigeons shows summer-winter variation under constant diet indicating a substantial effect of temperature – Dietz et al. – bioRxiv

Animal microbiome (for animals in the wild)

[Review]Bumblebees with the socially transmitted microbiome: A novel model organism for gut microbiota research – Zhang & Zheng – Insect Science

Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats – Xiao et al. – The ISME Journal

Comparative Analysis of Gut Microbiota Between Healthy and Diarrheic Horses – Li et al. – Front. Vet. Sci.

Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates – Microbiology Spectrum

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

Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats – Liu et al. – Microbiome

Bioinformatics

CBEA: Competitive balances for taxonomic enrichment analysis – Nguyen, Hoen & Frost – PLOS Computational Biology

Clustering compositional data using Dirichlet mixture model – Pal & Heumann – PLOS One

Techniques

Generation and application of pseudo–long reads for metagenome assembly – Sim et al. – Giga Science

[Preprint]A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities – Shaffer et al. – bioRxiv

[Preprint]Estimating Microbial Population Data from Optical Density – Mira, Yeh & Hall – bioRxiv

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