Category Archives: Human reproductive or urinary

August 10, 2022

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General microbiome

Microbiome-associated human genetic variants impact phenome-wide disease risk – Markowitz et al. – PNAS

Microbial risk score for capturing microbial characteristics, integrating multi-omics data, and predicting disease risk – Wang et al. – Microbiome

[REVIEW]A framework for testing the impact of co-infections on host gut microbiomes – Schmid et al. – Animal Microbiome

Human vaginal microbiome

Vaginal microbiota and personal risk factors associated with HPV status conversion—A new approach to reduce the risk of cervical cancer? – Yang et al. – PLOS One

Human gut microbiome

[REVIEW]The role of the gut microbiota in multiple sclerosis – Correale, Hohlfeld & Baranzini

Specific gut microbiota alterations in essential tremor and its difference from Parkinson’s disease – Zhang et al. – NPJ Parkinson’s Disease

Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics – Podlesny et al. – Cell Reports Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Cheung et al. – Journal of Gastroenterology and Hepatology

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation – Federici et al. – Cell

Animal microbiome

Camel milk microbiota: A culture-independent assessment – Rahmeh et al. – Food Research International

Effect of processing on the anti-inflammatory efficacy of cocoa in a high fat diet-induced mouse model of obesity – Weikart et al. – The Journal of Nutritional Biochemistry

The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs – Gaire et al. – Microbiome

Plant, root, and soil microbiome

Soil microbial community structures are shaped by agricultural systems revealing little temporal variation – Fox, Widmer & Lüscher – Environmental Research

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

The streamwater microbiome encodes hydrologic data across scales – URycki et al. – Science of The Total Environment

Bioinformatics / Data

[PREPRINT]Lake iTag measurements over nineteen years, introducing the limony dataset – Rohwer & McMahon – bioRxiv

July 13, 2022

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Today’s digest features studies on the leaf-microbiome of 🍅 and 🍓 plants (+ bumblebees and mites), human gut and wastewater resistome, and more. Happy reading!

Reproductive tract

Female reproductive tract microbiota and recurrent pregnancy loss: a nested case-control study – Pirkko Peuranpää – Reproductive BioMedicine Online

Gut microbiome

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties – Sudarshan A. Shetty – Journal of the International Society for Microbial Ecology

*Within-patient evolution of plasmid-mediated antimicrobial resistance – Javier DelaFuente – bioRxiv

An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species – Sigal Leviatan – Nature Communications

Animal microbiome

Carpenter Bees (Xylocopa) Harbor a Distinctive Gut Microbiome Related to That of Honey Bees and Bumble Bees – Jo-anne C. Holley – Applied and Environmental Microbiology

Animal experiments

Gardnerella Exposures Alter Bladder Gene Expression and Augment Uropathogenic Escherichia coli Urinary Tract Infection in Mice – Nicole M. Gilbert – Frontiers in Cellular and Infection Microbiology

Plant microbiome

*The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites – Marie Legein – Microbiology Spectrum

Food microbiome

Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities – Christina C. Saak – bioRxiv

New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria – Muhammad Yasir – Food Research International

Water microbiome

*High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent – Kevin Kaibond Chau – bioRxiv

Pilot investigation on biostability of drinking water distribution systems under water source switching – Kejia Zhang – Applied Microbiology and Biotechnology

Bioinformatics

*BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J. Pavia – bioRxiv

getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories – Vincent Moco – BMC Bioinformatics

baseLess: Lightweight detection of sequences in raw MinION data – Ben Noordijk – bioRxiv

June 29, 2022

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General microbiome

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station – Urbaniak et al. – Microbiome

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology – Lai, Hayashi & Lu – Current Opinion in Chemical Biology

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom – Thomas et al. – Nature Communications

Human oral microbiome

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women – Kato et al. – BMC Oral Health

Human urinary microbiome

Concordance of Urinary Microbiota Detected by 16S rRNA Amplicon Sequencing Versus Expanded Quantitative Urine Culture – Vaughan et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Dietary variety relates to gut microbiota diversity and abundance in humans – Huang et al. – European Journal of Nutrition

The gut microbiota composition in patients with right- and left-sided colorectal cancer and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing – Suga et al. – BMC Gastroenterology

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis – Troci et al. – Molecular Nutrition & Food Research

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – Münzker et al. – Microbiome

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

Perinatal transmission of a probiotic Bifidobacterium strain protects against early life stress-induced mood and gastrointestinal motility disorders – Zhu et al. – Food & Function

Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder – Xu et al. – Microbiology Spectrum

Animal microbiome (for animals in the wild)

Gut microbiome of century-old snail specimens stable across time in preservation – Chalifour, Elder & Li – Microbiome

Plant, root, and soil microbiome

Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense – Zhang et al. – Microbiome

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

A genome and gene catalog of glacier microbiomes – Liu et al. – Nature Biotechnology

Bioinformatics / Data

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans – Lemos et al. – Scientific Data

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota – Campos et al. – Poultry Science

[PREPRINT]Predicting metabolomic profiles from microbial composition through neural ordinary differential equations – Wang et al. – bioRxiv

June 18, 2022

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Have a nice weekend! Today, in this Digest: The effect of the gut dysbiosis on prostate cancer, microbial inheritance, bee microbiome, rhizosphere microbiota, a comparison of DNA isolation techniques for deep amplicon sequencing, and more…

Human and General Microbiome

Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-κB-IL6-STAT3 axis – Weibo Zhong – Microbiome

On the effect of inheritance of microbes in commensal microbiomes – Román Zapién-Campos – BMC Ecology and Evolution

Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth – Sunwha Park – Scientific Reports

Deep Grouping Analysis of the Altered Cervical Canal Microbiota in Intrauterine Adhesion Patients – Xiangdong Hua – Reproductive Sciences

Intestinal microbiota transplantation: do not forget the metabolites – Benjamin H Mullish – The Lancet. Gastroenterology & Hepatology

Characterization of oral and gut microbiome and plasma metabolomics in COVID-19 patients after 1-year follow-up – Guang-Ying Cui – Military Medical Research

Congenitally underdeveloped intestine drives autism-related gut microbiota and behavior – Jie Li – Brain, Behavior, and Immunity

Beneficial Microbes and Compounds

Lacticaseibacillus rhamnosus HA-114 improves eating behaviors and mood-related factors in adults with overweight during weight loss: a randomized controlled trial – Béatrice S-Y Choi – Nutritional Neuroscience

Model Animal Microbiome

New Strains of Akkermansia muciniphila and Faecalibacterium prausnitzii are Effective for Improving the Muscle Strength of Mice with Immobilization-Induced Muscular Atrophy – Hye Rim Byeon – Journal of Medicinal food

Non-Model Animal Microbiome

Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes – Wyatt A Shell – Communications Biology

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review – Sonam Dixit – Animal Biotechnology

Plant Microbiome

Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees – Maximilian Fernando Becker – Environmental Microbiome

Identifying plant genes shaping microbiota composition in the barley rhizosphere – Carmen Escudero-Martinez – Nature Communications

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato – Ben O Oyserman – Nature Communications

Environmental Microbiome

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables – Jessica L Gronniger – Environmental Microbiology

Microplastics alter nitrous oxide production and pathways through affecting microbiome in estuarine sediments – Cheng Chen – Water Research

500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China – Lei Zhou – Scientific Data

Food Microbiome

Microbiome and -omics application in food industry – Ilario Ferrocino – International Journal of Food Microbiology

Bioinformatic and Experimental Microbiome Analysis

A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities – Justin P Shaffer – BioTechniques

Review: Machine Learning Advances in Microbiology: A Review of Methods and Applications – Yiru Jiang – Frontiers in Microbiology

June 8, 2022

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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 13, 2022

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Today’s digest features metagenomics for clinical UTI diagnostics, microbial diversity in kombucha tea, microbial source tracking using single nucleotide variants, and more. Happy reading!

Neonatal microbiome

Editorial: More data needed on neonatal microbiome seeding – W. Florian Fricke & Jacques Ravel – Microbiome

Urinary microbiome

The Urobiomes of Adult Women With Various Lower Urinary Tract Symptoms Status Differ: A Re-Analysis – Cara Joyce – Frontiers in Cellular and Infection Microbiology

*Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study – Victoria A Janes – The Lancet Microbe

Gut microbiome

Perspective: Tiny Gatekeepers: Microbial Control of Host Drug Transporters – Than S. Kyaw and Peter J. Turnbaugh – Clinical Pharmacology & Therapeutics

Host hepatic metabolism is modulated by gut microbiota-derived sphingolipids – Henry H. Le – Cell Host & Microbe

Linking gastrointestinal microbiota and metabolome dynamics to clinical outcomes in paediatric haematopoietic stem cell transplantation – Gintare Vaitkute – Microbiome

Animal microbiome

Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis – Vittorio Boscaro – Nature Microbiology

Water microbiome

Cyanopeptides restriction and degradation co-mediate microbiota assembly during a freshwater cyanobacterial harmful algal bloom (CyanoHAB) – Han Gao – Water Research

Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster – Irmarie Cotto – bioRxiv

Soil microbiome

Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies – Ying Wang – Frontiers in Microbiology

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra – Igor S. Pessi – bioRxiv

Food

*Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations – Elizabeth A. Landis – mSystems

Spontaneous Riboflavin-Overproducing Limosilactobacillus reuteri for Biofortification of Fermented Foods – Irina Spacova, Sarah Ahannach – Frontiers in Nutrition

Bioinformatics

coda4microbiome: compositional data analysis for microbiome studies – M.Luz Calle & Antoni Susin – bioRxiv

GeneToList: A web application to assist with gene identifiers for the non-bioinformatics-savvy scientist – Joshua D. Breidenbach – bioRxiv

*Microbiome source tracking using single nucleotide variants – Leah Briscoe – bioRxiv

June 4, 2022

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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

May 20, 2022

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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

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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 11, 2022

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General microbiome

[REVIEW]Cross-talk between the microbiome and chronic inflammation in esophageal cancer: potential driver of oncogenesis – Sharma et al. – Cancer and Metastasis Reviews

Systematic and quantitative view of the antiviral arsenal of prokaryotes – Tesson et al. – Nature Communications

Pregnancy and early life

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy – Sun et al. – Scientific Reports

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

[Commentary]Space travel and early childhood gut microbiome: is space dirty enough to raise a child? – Loh, Henriques & Tang – Future Microbiology

Human skin microbiome

[PREPRINT]On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis – Key et al. – bioRxiv

Human oral microbiome

Oral microbiome of Crohn’s Disease patients with and without oral manifestations – Hu et al. – Journal of Crohn’s and Colitis

Integrating the salivary microbiome in the forensic toolkit by 16S rRNA gene: potential application in body fluid identification and biogeographic inference – Liang et al. – International Journal of Legal Medicine

Human gut microbiome

An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome – Delannoy-Bruno et al. – PNAS

A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota – Sommer et al. – PLOS Computational Biology

Microbiota and gastric cancer – Bessede & Megraud – Seminars in Cancer Biology

[REVIEW]Host—microbial interactions in metabolic diseases: from diet to immunity – Lee & Park – Journal of Microbiology

A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease – Cheng et al. – Nature Communications

Animal experiments

Sex-dependent host-microbiome dynamics in zebrafish: Implications for toxicology and gastrointestinal physiology – Martyniuk et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models – Shin et al. – Scientific data

A total infectome approach to understand the etiology of infectious disease in pigs – Huang et al. – Microbiome

Synergistic interaction of gut microbiota enhances the growth of nematode through neuroendocrine signaling – Lo et al. – Current Biology

Plant, root, and soil microbiome

Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America – Renaudin, Laforest-Lapointe & Bellenger – Science of The Total Environment

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

Antimicrobial resistance in Antarctica: is it still a pristine environment? – Hwengwere et al. – Microbiome

[PREPRINT]Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps – Dong et al. – bioRxiv

Bioinformatics

Evaluating metagenomic assembly approaches for biome-specific gene catalogues – Delgado & Andersson – Microbiome

Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets – Xu et al. – Science of The Total Environment