October 24, 2022

Human and General Microbiome

The Association Between Microplastics and Microbiota in Placentas and Meconium: The First Evidence in Humans – Shaojie Liu – Environmental Science & Technology

The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations – Xinwei Ruan – NPJ Biofilms and Microbiomes

Role of mucus-bacteria interactions in Enterotoxigenic Escherichia coli (ETEC) H10407 virulence and interplay with human microbiome – Thomas Sauvaitre – NPJ Biofilms and Microbiomes

Commensal oral microbiota impacts ulcerative oral mucositis clinical course in allogeneic stem cell transplant recipients – Julia S Bruno – Scientific Reports

Review: Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications – Raphaela I Lau – Nature Reviews. Gastroenterology & Hepatology

Review: The microbiota and aging microenvironment in pancreatic cancer: Cell origin and fate – Zhou Chen – Biochimica et Biophysica Acta

Review: New perspectives into the vaginal microbiome with systems biology – Christina Y Lee – Trends in Microbiology

Beneficial Microbes and Compounds

Oral supplementation with selected Lactobacillus acidophilus triggers IL-17-dependent innate defense response, activation of innate lymphoid cells type 3 and improves colitis – Jiří Hrdý – Scientific Reports

Animal Model Microbiome

The Benefits of Switching to a Healthy Diet on Metabolic, Cognitive and Gut Microbiome Parameters are Preserved in Adult Rat Offspring of Mothers Fed a High-Fat, High-Sugar Diet – Michael D Kendig – Molecular Nutrition & Food Research

Jatrorrhizine alleviates ulcerative colitis via regulating gut microbiota and NOS2 expression – Jia Ling Zhang – Gut Pathogens

Non-Model Animal Microbiome

Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan – Yoshiaki Sato – Microbes and Environments

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium – Yui Sato – Microbiome

Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages – Lei Feng – Scientific data

Screening Salamanders for Symbionts – Elli Vickers – Methods in Molecular Biology

Gut microbiota differs between two cold-climate lizards distributed in thermally different regions – Jun-Qiong Chen – BMC Ecology and Evolution

Microbial community in resistant and susceptible Churra sheep infected by Teladorsagia circumcincta – Verónica Castilla Gómez de Agüero – Scientific Reports

Genome Evolution of a Symbiont Population for Pathogen Defence in Honeybees – Karl Dyrhage – Genome Biology and Evolution

Plant Microbiome

Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome – Jonathan M Conway – Nature Microbiology

Phytohormones producing rhizobacteria alleviate heavy metals stress in soybean through multilayered response –  Husna – Microbiological Research

Review: Linking plant functional genes to rhizosphere microbes: a review – Qi Liu – Plant Biotechnology Journal

Bioinformatics and Microbiome Analysis Techniques 

Resampling-based inferences for compositional regression with application to beef cattle microbiomes – Sujin Lee – Statistical Methods in Medical Research

Review: Methods used for the study of endophytic fungi: a review on methodologies and challenges, and associated tips – Jefferson Brendon Almeida Dos Reis – Archives of Microbiology

October 17, 2022

Human and General Microbiome

Comparison of microbial signatures between paired faecal and rectal biopsy samples from healthy volunteers using next-generation sequencing and culturomics – Indrani Mukhopadhya – Microbiome

Depression and fatigue in active IBD from a microbiome perspective-a Bayesian approach to faecal metagenomics – Anne Kerstin Thomann – BMC Medicine

Dynamics of human milk oligosaccharides in early lactation and relation with growth and appetitive traits of Filipino breastfed infants – Tinu M Samuel – Scientific Reports

The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis – Efrat Muller – NPJ Biofilms and Microbiomes

Review: Strains to go: interactions of the skin microbiome beyond its species – Ryan Caldwell – Current Opinion in Microbiology

Gut bacterial extracellular vesicles: important players in regulating intestinal microenvironment – Xiao Liang – Gut Microbes

Brief overview of dietary intake, some types of gut microbiota, metabolic markers and research opportunities in sample of Egyptian women – Nayera E Hassan – Scientific Reports

Profile of gut microbiota and serum metabolites associated with metabolic syndrome in a remote island most afflicted by obesity in Japan – Tsugumi Uema – Scientific Reports

The intestinal clock drives the microbiome to maintain gastrointestinal homeostasis – Marjolein Heddes – Nature Communications

Identification of bacterial lipopeptides as key players in IBS – Camille Petitfils – Gut

Gut-innervating nociceptors regulate the intestinal microbiota to promote tissue protection – Wen Zhang – Cell

BefA, a microbiota-secreted membrane disrupter, disseminates to the pancreas and increases β cell mass – Jennifer Hampton Hill – Cell Metabolism

Alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity – Nick P G Gauthier – PloS one

preprint: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes – Bryan D Merrill – bioRxiv

Beneficial Microbes and Compounds

Long-term use of Lacticaseibacillus paracasei N1115 from early life alleviates high-fat-diet-induced obesity and dysmetabolism in mice – Z H Miao – Beneficial Microbes

Animal Model Microbiome

Trimethylamine, a gut bacteria metabolite and air pollutant, increases blood pressure and markers of kidney damage including proteinuria and KIM-1 in rats – Klaudia M Maksymiuk – Journal of Translational Medicine

Animal Microbiome

Molecular detection of Coxiella-like endosymbionts and absence of Coxiella burnetii in Amblyomma mixtum from Veracruz, Mexico – Estefanía Grostieta – Experimental & Applied Acarology

Environmental Microbiome

An enriched ammonia-oxidizing microbiota enables high removal efficiency of ammonia in antibiotic production wastewater – Jiamin Chen – Chemosphere

August 22, 2022

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

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

August 16, 2022

Human and General Microbiome

Crohn’s disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome – Jonathan P Jacobs – Genome Medicine

Preservation of fecal microbiome is associated with reduced severity of Graft-versus-Host Disease – Marina Burgos da Silva – Blood

Cobamide Sharing Is Predicted in the Human Skin Microbiome – Mary Hannah Swaney – mSystems

Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age – Maximilian J Bailey – Gut Microbes

Shotgun metagenomic sequencing reveals skin microbial variability from different facial sites – Qingzhen Wei – Frontiers in Microbiology

Review: Recent insights into the role of microbiome in the pathogenesis of obesity – Eduard W J van der Vossen – Therapeutic Advances in Gastroenterology

Model Animal Microbiome

Impact of habitual chewing on gut motility via microbiota transition – Fukie Yaoita – Scientific Reports

Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function – Alexandra Proctor – mSystems

Non-model Animal Microbiome

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate – David M Needham – Nature Microbiology

Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism – Sara Ricci – Scientific Reports

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts – Min Hui – PeerJ

Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure – Angela Zou – Microbiome

Environmental Microbiome

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction – Alessandro Rossi – Microbiome

Food Microbiome

Microbiome and Metabiotic Properties of Kefir Grains and Kefirs Based on Them –  Ding Fan – Microbiology

Profiling the role of microorganisms in quality improvement of the aged flue-cured tobacco – Xinying Wu – BMC Microbiology

August 6, 2022

Human and General Microbiome

The oral microbiome and lung cancer risk: An analysis of 3 prospective cohort studies – Emily Vogtmann – Journal of the National Cancer Institute

Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries – M J Carvalho – Nature Microbiology

Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer – Namjoo Kim – Scientific Reports

Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β-Lactam Resistome – Zhiguo Zhang – Environmental Science & Technology

Review: Porphyromonas gingivalis and dental stem cells crosstalk amplify inflammation and bone loss in the periodontitis niche – Devaraj Ezhilarasan – Journal of Cellular Physiology

Beneficial Microbes and Compounds

On the effect of flavonoids and dietary fibre in lingonberries on atherosclerotic plaques, lipid profiles and gut microbiota composition in Apoe(-/-) mice – Jiyun Liu – International Journal of food Sciences and Nutrition

The Gut-Brain-Microbiome Connection: Can Probiotics Decrease Anxiety and Depression? – Jennifer Maybee – Issues in Mental Health Nursing

The effect of Lactobacillus rhamnosus B10 on alcoholic liver injury and intestinal microbiota in alcohol-induced mice model – Xia Li – Journal of Food Biochemistry

Model Animal Microbiome

The effect of young blood plasma administration on gut microbiota in middle-aged rats – Taha Ceylani – Archives of Microbiology

Non-Model Animal Microbiome

Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus – Aleksandra I Krawczyk – Microbiome

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions – Manuel Aira – FEMS Microbiology Ecology

Ruminal Microbiota Determines the High-Fiber Utilization of Ruminants: Evidence from the Ruminal Microbiota Transplant – Xiaodong Chen – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

Computational approach to modeling microbiome landscapes associated with chronic human disease progression – Lu Li – PLoS Computational Biology

Guideline for the analysis of the microbial communities of the human upper airways – Leonardo Mancabelli – Journal of Oral Microbiology

July 8, 2022

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

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 10, 2022

Several great microbiome papers out today including a review on rethinking healthy eating in Cell Host & Microbe, a large population study on the development of the infant gut microbiome (n=1900) in Science, and two studies showcasing metabolomics predictive value for recurrent CDI and NAFLD.  

Gut Microbiome

[REVIEW] Rethinking healthy eating in light of the gut microbiome – Armet et al. Cell Host & Microbe.

Gut metabolites predict Clostridioides difficile recurrence – Dawkins et al. Microbiome

Robust variation in infant gut microbiome assembly across a spectrum of lifestyles – Olm et al. Science

Risk assessment with gut microbiome and metabolite markers in NAFLD development. Leung et al. Science Translational Medicine.

Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer – Bi et al. Nature Communications

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes – Guthrie et al. Cell Host & Microbe

Animal experiments

Nisin probiotic prevents inflammatory bone loss while promoting reparative proliferation and a healthy microbiome – Gao et al. npj Biofilms & Microbiomes

Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs – Hui et al. npj Biofilms & Microbiomes

Virome

A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome – Li et al. iScience

Bioinformatics

Phylogeny-guided microbiome OTU-specific association test (POST) – Huang et al. Microbiome

May 3, 2022

General microbiome

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

Human gut microbiome

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

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

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

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

Human respiratory & oral microbiome

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

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

Animal experiments

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

Water/Extremophile microbiome

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

Bioinformatics

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

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

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

Non microbiome picks

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

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