Category Archives: Human respiratory

August 22, 2022

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Highlights!!

Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance – Jotham Suez – Cell → a randomized-controlled trial (120 healthy adults) observed the effects of saccharin, sucralose, aspartame, and stevia on the human microbiome showed person-specific, microbiome-dependent glycemic alterations. Saccharin and sucralose significantly impaired glycemic responses.

A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions – Lu Yang – Microbiome → assessment of several differential abundance analysis (DAA) tools, using real data-based simulations, suggests that “none of the evaluated methods is simultaneously robust, powerful, and flexible, which makes the selection of the best DAA tool difficult”. These findings suggest that the application of a DAA method depends of data context.  

Systematic Review: Probiotics and Synbiotics Supplementation Improve Glycemic Control Parameters in Subjects with Prediabetes and Type 2 Diabetes Mellitus: A GRADE-assessed systematic review, meta-analysis, and meta-regression of randomized clinical trials – Kaveh Naseri – Pharmacological Research → “Our findings suggest that probiotic and synbiotic intake has favorable effects on glycemic profile in patients with prediabetes and T2DM.”

Human and General Microbiome

The diversity and abundance of gut microbiota are associated with the pain sensation threshold in the Japanese population – Yuki Takeuchi – Neurobiology of Disease

Oral microbiota associated with gingiva of healthy, gingivitis and periodontitis cases – Nemmat A Hussein – Microbial Pathogenesis

Effects of extracellular vesicles derived from oral bacteria on osteoclast differentiation and activation – Hyun Young Kim – Scientific Reports

Porphyromonas gingivalis is a risk factor for the development of nonalcoholic fatty liver disease via ferroptosis – Chao Yao – Microbes and Infection

Review: The Role of a Gut Microbial-Derived Metabolite, Trimethylamine N-Oxide (TMAO), in Neurological Disorders – Sankar Simla Praveenraj – Molecular Neurobiology

Review: The association between early-life gut microbiota and childhood respiratory diseases: a systematic review – Cristina Garcia-Maurino Alcazar – The Lancet. Microbe

Beneficial Microbes and Compounds

Effect of Bifidobacterium animalis subsp. lactis SF on enhancing the tumor suppression of irinotecan by regulating the intestinal flora – Zhongyue Ren – Pharmacological Research

Effect of probiotic supplementation on plasma metabolite profile after Roux-Y gastric bypass: a prospective, randomized, double-blind, placebo-controlled clinical trial – Marília Rizzon Zaparolli Ramos – International Journal of Obesity 

Faecalibaculum rodentium remodels retinoic acid signaling to govern eosinophil-dependent intestinal epithelial homeostasis – Y Grace Cao – Cell Host & Microbe

Human milk nutrient fortifiers alter the developing gastrointestinal microbiota of very-low-birth-weight infants – Michelle R Asbury – Cell Host & Microbe

More Microbes

Diversity of ethanolamine utilization by human commensal Escherichia coli – Maria Ines Moreira de Gouveia – Research in Microbiology

Review: Archaea from the gut microbiota of humans: Could be linked to chronic diseases? – Denise Mafra – Anaerobe

Animal Microbiome

Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates – Zongjun Li – The ISME Journal

Environmental Microbiome

Microbiota and mobile genetic elements influence antibiotic resistance genes in dust from dense urban public places – Tianshu Feng – Environmental Pollution 

Review: Synergy between microalgae and microbiome in polluted waters – Noreen Ashraf – Trends in Microbiology

Bioinformatic Tools and Microbiome Analysis Techniques

Review: Molecular tools for probing the microbiome – Marcelo Der Torossian Torres – Current Opinion in Structural Biology

August 20, 2022

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Have a nice weekend! Today, in this brief Digest: Lung microbiota and PM exposure, Akkermansia genomic variability, sulfonation, microbiome and cholesterol, and a new role for Blautia wexlerae.

Human and General Microbiome

The Lung Microbiota Affects Pulmonary Inflammation and Oxidative Stress Induced by PM(2.5) Exposure – Simin Wang – Environmental Science & Technology

A thousand metagenome-assembled genomes of Akkermansia reveal phylogroups and geographical and functional variations in the human gut – Qing-Bo Lv – Frontiers in Cellular and Infection Microbiology

Intestinal TLR4 deletion exacerbates acute pancreatitis through gut microbiota dysbiosis and Paneth cells deficiency – Mei Qi-Xiang – Gut Microbes

A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria – Lina Yao – Nature Microbiology

Review: Altered gut microbiota patterns in COVID-19: Markers for inflammation and disease severity – Chiranjib Chakraborty – World Journal of Gastroenterology

Animal Model Microbiome and Experiments

Characterization of interactions of dietary cholesterol with the murine and human gut microbiome – Henry H Le – Nature Microbiology

Gut-derived bacterial flagellin induces beta-cell inflammation and dysfunction – Torsten P M Scheithauer – Gut Microbes

Rapid evolution of a novel protective symbiont into keystone taxon in Caenorhabditis elegans microbiota – Alejandra Wu-Chuang – Scientific Reports

Beneficial Microbes and Compounds

Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota – Koji Hosomi – Nature Communications

Fecal microbiota transplantation can improve cognition in patients with cognitive decline and Clostridioides difficile infection – Soo-Hyun Park – Aging

July 18th, 2020

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God morgon! Good morning from Sweden. Today’s digest features only three articles but I am sure everyone will enjoy reading it, especially a super interesting article highlighting the importance of older siblings on development of an individual’s airway and gut microbiota. The study asserts that having a closely aged older sibling has more impact on one’s microbiota as compared to having more than one older sibling. Another featured article demonstrates how gut microbiota can improve the quality of chicken by preventing intestinal inflammation. From animal farming we go over to plant farming. Another article in today’s digest shows how monocropping (growing the same crop over and over) negatively impacts the diversity of soil bacteria which eventually shows up as poor yield. This makes it imperative to consider the soil microbiota while taking decisions on crop cycle. I hope you will enjoy reading today’s digest and have a great week!

Human microbiome

The developing airway and gut microbiota in early life is influenced by age of older siblings – Emil Dalgaard Christensen, et al., Microbiome

Animal microbiome

Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation – Xiaolong Zhang, et al., Microbiome

Plant root and soil microbiome

Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems – Pengfa Li, et al., Microbiome

July 8, 2022

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A selection of some great microbiome research and I’ve highlighted some resources for spatial transcriptomics for my non-microbiome picks.

General microbiome

Host control and the evolution of cooperation in host microbiomes – Sharp & Foster. Nature Communications

Effect of Helicobacter pylori Eradication on Gastric Cancer Prevention: Updated Report From a Randomized Controlled Trial With 26.5 Years of Follow-up – Yan et al. Gastroenterology

Gut microbiome

Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome – Xu et al. Microbiome

Long-Term Effects of Developmental Exposure to Oxycodone on Gut Microbiota and Relationship to Adult Behaviors and Metabolism – Lyu et al. mSystems

Biogeographic variation and functional pathways of the gut microbiota in celiac disease – Constante et al. Gastroenterology.

Animal experiments

Akkermansia muciniphila prevents cold-related atrial fibrillation in rats by modulation of TMAO induced cardiac pyroptosis – Luo et al. eBioMedicine

Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome – Machado et al. Cell Reports.

Virome

Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome – Jonge et al. Nature Communications

Respiratory microbiome

Host lung microbiota promotes malaria-associated acute respiratory distress syndrome – Mukherjee et al. Nature Communications

Bioinformatics

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

Non-microbiome picks

As spatial transcriptomics grows in popularity you might be interested in some recent reviews & examples of the technology in use

An introduction to spatial transcriptomics for biomedical research – Williams et al. Genome Medicine

Deciphering tissue structure and function using spatial transcriptomics – Walker et al. Communications biology

Method of the Year: spatially resolved transcriptomics – Marx. Nature Methods

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays – Chen et al. Cell (The recent famous Cell cover using Stereo-Seq)

Museum of spatial transcriptomics – Moses & Pachter. Nature Methods

July 5, 2022

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Highlights!

A volatile from the skin microbiota of flavivirus-infected hosts promotes mosquito attractiveness – Hong Zhang – Cell → The production of acetophenone, a potent attractant for mosquitoes, is induced by Flavivirus by a microbiota-based mechanism. This finding shows an interesting example of the interplay between certain viral agents and the microbiota to influence host susceptibility to interact with other species. 

Human and General Microbiome

Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID-19 and its Association with Microbiota in the Gut – Yifei Shen – Advanced Science

Interaction of n-3 polyunsaturated fatty acids with host CD36 genetic variant for gut microbiome and blood lipids in human cohorts – Zelei Miao – Clinical Nutrition 

A weight-loss model based on baseline microbiota and genetic scores for selection of dietary treatments in overweight and obese population – Amanda Cuevas-Sierra – Clinical Nutrition

Beneficial Microbes and Compounds

Restoration of cefixime-induced gut microbiota changes by a prebiotic blend in a mouse model – Jingyi Yuan – Applied Microbiology and Biotechnology

A synbiotics, long chain polyunsaturated fatty acids, and milk fat globule membranes supplemented formula modulates microbiota maturation and neurodevelopment – Tomás Cerdó – Clinical Nutrition

Animal Model Microbiome

Multi-omics data reveals the disturbance of glycerophospholipid metabolism caused by disordered gut microbiota in depressed mice – Tian Tian – Journal of Advanced Research

C-section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [clostridium] scindens in mice – Sean H Adams – Physiological Reports

A single respiratory tract infection early in life reroutes healthy microbiome development and affects adult metabolism in a preclinical animal model – Soner Yildiz – NPJ Biofilms and Microbiomes

Non-Model Animal Microbiome

Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis – Laura Baldassarre – Nature Communications

Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis – Ana Carolina Borsanelli – Microbial Ecology

Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria – Anna Voulgari-Kokota – Scientific Reports

Plant and Soil Microbiome

Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area – Gargi Das – Current Microbiology

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning – Kendra E Walters – The ISME Journal

Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.) – Davide Francioli – Scientific Reports

Bioinformatics and Microbiome Analysis

MB-SupCon: Microbiome-based predictive models via Supervised Contrastive Learning – Sen Yang – Journal of Molecular Biology

June 3, 2022

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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 21, 2022

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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 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 3, 2022

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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