Category Archives: General Microbiome

September 10, 2021

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In today’s digest read about a discovery of new Bordetella bronchiseptica-specific temperate and highly abundant siphoviruses that lead to the creation of a new genus Vojvodinavirus, biases in public human microbiome data, infant gut strain persistence, and more. Also, check out a list of upcoming microbiome events. Happy Friday!

Global microbiome

*Public human microbiome data dominated by highly developed countries – Richard J. Abdill – bioRxiv

Gut microbiome

Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization – Jing Lu – npj Biofilms and Microbiomes

Gut microbiota alterations in response to sleep length among African-origin adults – Na Fei – PlosOne

Bioaccumulation of therapeutic drugs by human gut bacteria – Martina Klünemann – Nature

*Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition – Yue Clare Lou – Cell Reports Medicine

Skin microbiome

Cotton and Surgical Face Masks in Community Settings: Bacterial Contamination and Face Mask Hygiene – Lize Delanghe – Frontiers in Medicine

Animal microbiome

The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? – Chiara Crestani – Microbial Genomics

Viruses and phages

*Are Bordetella bronchiseptica Siphoviruses (Genus Vojvodinavirus) Appropriate for Phage Therapy—Bacterial Allies or Foes? – Aleksandra Petrovic Fabijan – Viruses

Water microbiome

Functional Redundancy in Ocean Microbiomes Controls Trait Stability – Taylor M. Royalty and Andrew D. Steen – bioRxiv

Bioinformatics

SHOOT: phylogenetic gene search and ortholog inference – David Emms and Steven Kelly – bioRxiv

Ultra-resolution Metagenomics: When Enough Is Not Enough – Falk Hildebrand – mSystems

Computational challenges and opportunities in spatially resolved transcriptomic data analysis – Lyla Atta & Jean Fan – Nature Communications

*BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data – Chenhao Li – Plos Computational Biology

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – September 14/16 (Atlantic/Pacific)

Course + Symposium: 2021 ISB Virtual Microbiome Series – October 13-15

Webinar: EMBARK Fall Webinars – a webinar series where invited speakers will be presenting their AMR research and be contrasted to EMBARK members presenting the work performed in the project.

For more, check out a collection of microbiome events HERE!

September 7, 2021

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Today’s digest features some excellent human and mouse microbiome research, a highly detailed study of human associated Bifidobacterium longum, as well as a non microbiome picks on the history of rhinoceros in Cell and how to write a lab protocol in Nature.

General microbiome

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory – Bittleston et al. mSystems

Human gut microbiome

Effects of antibiotic duration on the intestinal microbiota and resistome: The PIRATE RESISTANCE project, a cohort study nested within a randomized trial – Leo et al. EBioMedicine

Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals  – Tarallo et al. Gut

Associations between the gut microbiome and metabolome in early life – Nguyen et al. BMC Microbiology

Animal Experiments

The composition of the gut microbiota following early-life antibiotic exposure affects host health and longevity in later life – Lynn et al. Cell Reports

Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model – Xiao et al. Microbiome

Water Microbiome

Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage–bacteria interplay in deep-sea snail holobionts – Zhou et al. Microbiome

Soil microbiome

Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil – Starr et al. mSphere

Bioinformatics

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ) – Ling et al. Microbiome

Non-microbiome picks

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family – Lie et al. Cell

Five keys to writing a reproducible lab protocol – Nature

September 06, 2021

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General microbiome

[PREPRINT]Host-microbiome protein-protein interactions capture mechanisms in human disease – Zhou, Beltran & Brito – bioRxiv

Prognostic correlations with the microbiome of breast cancer subtypes – Banerjee et al. – Cell Death & Disease

Pregnancy and early life

[REVIEW]Composition of the vaginal microbiota during pregnancy in women living in sub-Saharan Africa: a PRISMA-compliant review – Juliana et al. – BMC Pregnancy and Childbirth

Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage – Seki et al. – Cell Host & Microbe

Multi-site human microbiome

[PREPRINT]Comparing Fecal, Saliva, and Chicha Microbiomes Between Mothers and Children in an Indigenous Ecuadorian Cohort – Adams et al. – bioRxiv

Human respiratory microbiome

Alterations of gut microbiota in patients with active pulmonary tuberculosis in China: A pilot study – Shi et al. – International Journal of Infectious Diseases

Human oral microbiome

The effects of periodontitis associated microbiota on the development of oral squamous cell carcinoma – Hu, Shen & Tian – Biochemical and Biophysical Research Communications

Human gut microbiome

Parasites and diet as main drivers of the Malagasy gut microbiome richness and function – Mondot et al. – Scientific Reports

[REVIEW]The second brain: The connection between gut microbiota composition and multiple sclerosis = Farshbafnadi, Agah & Rezaei – Journal of Neuroimmunology

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

Thymic development of gut-microbiota-specific T cells – Zegarra-Ruiz et al – Nature

High-fat diet alters stress behavior, inflammatory parameters and gut microbiota in Tg APP mice in a sex-specific manner – Yanguas-Casas – Neurobiology of Diesease

Sex-dependent effects on the gut microbiota and host metabolome in type 1 diabetic mice – Zhang et al. – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

Bioinformatics

Efficient computation of Faith’s phylogenetic diversity with applications in characterizing microbiomes – Armstrong et al. – Genome Research

September 4, 2021

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Have a nice weekend! Today we have a good set of papers. Highlights: articles about microbiome crosstalk in acute leukemia, the relationship between trimethylamine N-oxide and hypertension, and the quantification of rapid bacterial evolution in a murine model. 

Highlights

Altered microbiota-host metabolic crosstalk preceding neutropenic fever in patients with acute leukemia – Armin Rashidi – Blood Advances

Gut microbiota dependent trimethylamine N-oxide aggravates angiotensin II-induced hypertension – Shan Jiang – Redox Biology

Quantifying rapid bacterial evolution and transmission within the mouse intestine – Kimberly S Vasquez – Cell Host & Microbe

Human and General Microbiome

Letter: Human oral microbiome cannot predict Pleistocene starch dietary level, and dietary glucose consumption is not essential for brain growth – Miki Ben-Dor – PNAS

Free threonine in human breast milk is related to infant intestinal microbiota composition – Monika Riederer – Amino Acids

Sickle cell disease children’s gut colonization by extended-spectrum β-lactamase (ESBL)-producing Enterobacterales: an antibiotic prophylaxis effect? – Adriano de Souza Santos Monteiro – Journal of Medical Microbiology

Disruption of the oral microbiota is associated with a higher risk of relapse after allogeneic hematopoietic stem cell transplantation – Vinícius Campos de Molla – Scientific Reports

The bladder microbiome and interstitial cystitis: is there a connection? – Melinda G Abernethy – Current opinion in Obstetrics & Gynecology

Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome – Petri Vänni – Scientific Reports

Changes in Conjunctival Microbiota Associated With HIV Infection and Antiretroviral Therapy – Qun Liu – Investigative Ophthalmology & Visual Science

Activation of the gut microbiota-kynurenine-liver axis contributes to the development of nonalcoholic hepatic steatosis in nondiabetic adult. – Guoyuan Sui – Aging

Review: Recent progress in research on the gut microbiota and highland adaptation on the Qinghai-Tibet Plateau. – Kui Liu – Journal of Evolutionary Biology

Review: Investigating dairy microbiome: an opportunity to ensure quality, safety and typicity. – Ilario Ferrocino – Current Opinion in Biotechnology

Review: Novel approaches to intervene gut microbiota in the treatment of chronic liver diseases. – Chang Liu – The FASEB journal

Review: Tryptophan-derived serotonin-kynurenine balance in immune activation and intestinal inflammation – Sabah Haq – The FASEB journal

Human gut microbiome impacts skeletal muscle mass via gut microbial synthesis of the short-chain fatty acid butyrate among healthy menopausal women – Wan-Qiang Lv – Journal of Cachexia, Sarcopenia and Muscle

Effects of gut microbiota-derived extracellular vesicles on obesity and diabetes and their potential modulation through diet – Ester Díez-Sainz – Journal of Physiology and Biochemistry

Animal Microbiome

Integrated Bacterial and Fungal Diversity Analysis Reveals the Gut Microbial Alterations in Diarrheic Giraffes – Aoyun Li – Frontiers in microbiology

Comparative study of gut microbiota from captive and confiscated-rescued wild pangolins – Chunbing Liu – Journal of Genetics and Genomics

Sugar feeding protects against arboviral infection by enhancing gut immunity in the mosquito vector Aedes aegypti – Floriane Almire – PLoS pathogens

Bacterial community dynamics on bats and the implications for pathogen resistance – Aoqiang Li – Environmental Microbiology

Draft Genome Sequence of Enterobacter oligotrophicus, Isolated from the Microbiome of a Lizard in the Caribbean. – Matthieu Pot – Microbiology Resource Announcements

Animal Model Microbiome

Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson’s disease – Yaping Yan – NPJ biofilms and microbiomes

Eugenol Alleviates Dextran Sulfate Sodium-Induced Colitis Independent of Intestinal Microbiota in Mice – Shuai Chen – Journal of Agricultural and Food Chemistry

Integrative analysis of the gut microbiome and metabolome in a rat model with stress induced irritable bowel syndrome – Yue Hu – Scientific Reports

Lycium barbarum polysaccharide attenuates emotional injury of offspring elicited by prenatal chronic stress in rats via regulation of gut microbiota – Feng Zhao – Biomedicine & Pharmacotherapy

Sex-specific effects of the microbiota on adult carbohydrate intake and body composition in a polyphagous fly – Binh Nguyen – Journal of Insect Physiology

Beneficial Microbes and Compounds

Commentary: Targeted diets for the gut microbiota and the potential cardiovascular effects – Gemma Chiva-Blanch – Cardiovascular Research

Review: Galacto-oligosaccharides as infant prebiotics: production, application, bioactive activities and future perspectives – Valentina Ambrogi – Critical Reviews in Food Science and Nutrition

Synbiotics Containing Nanoprebiotics: A Novel Therapeutic Strategy to Restore Gut Dysbiosis. – Liang Hong – Frontiers in Microbiology

Environmental Microbiome

Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic – Xiaofen Wu – Environmental Science & Technology

Microbiome analysis and techniques

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ) – Wodan Ling – Microbiome

High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts. – Žana Kapustina – Microbial Genomics

September 01, 2021

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General microbiome

Circulating microbiome DNA: An emerging paradigm for cancer liquid biopsy – Chen et al. – Cancer letters

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics – Letten et al. – The ISME Journal

[PERSPECTIVE]Crosstalk between γδ T cells and the microbiota – Papotto, Yilmaz & Silva-Santos – Nature Microbiology

Pregnancy and early life

Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life – Tsukuda et al. – The ISME Journal

Deterministic transition of enterotypes shapes the infant gut microbiome at an early age – Xiao et al. – Genome Biology

Human oral microbiome

[REVIEW]Association between metabolic syndrome and periodontitis: The role of lipids, inflammatory cytokines, altered host response, and the microbiome – Pirih et al. – Periodontology 2000

[REVIEW]Fungal diseases: Oral dysbiosis in susceptible hosts – Villar & Dongari-Bagtzoglou – Periodontology 2000

[REVIEW]The oral microbiome: Role of key organisms and complex networks in oral health and disease – Sedghi et al. – Periodontology 2000

Human gut microbiome

Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes – Kim et al. – Genome Medicine

[REVIEW]The promise of the gut microbiome as part of individualized treatment strategies – Schupack et al. – Nature Reviews Gastroenterology & Hepatology

[REVIEW]The gut microbiome and efficacy of cancer immunotherapy – Robiello et al. – Pharmacology & Therapeutics

Integrated analysis of the faecal metagenome and serum metabolome reveals the role of gut microbiome-associated metabolites in the detection of colorectal cancer and adenoma – Chen et al. – Gut

Animal/Insect microbiome

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes – Gupta et al. – Microbiome

Social networks strongly predict the gut microbiota of wild mice – Raulo et al. – The ISME Journal

Genetic identity and genotype × genotype interactions between symbionts outweigh species level effects in an insect microbiome – Smee, Raines & Ferrari – The ISME Journal

[REVIEW]The effects of raw-meat diets on the gastrointestinal microbiota of the cat and dog: a review – Butowski et al. – New Zealand Veterinary Journal

Plant, root, and soil microbiome

Predicting spatial patterns of soil bacteria under current and future environmental conditions – Mod et al. – The ISME Journal

Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype – Stopnisek & Shade – The ISME Journal

Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota – Wippel et al. – Nature Microbiology

Bioinformatics/Techniques

Functional meta-omics provide critical insights into long- and short-read assemblies – Galata et al. – Briefings in Bioinformatics

[PREPRINT]BiomeHorizon: visualizing microbiome time series data in R – Fink et al. – bioRxiv

Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Shibata et al. – PLOS ONE

MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data – Mongad et al. – Genomics

August 28, 2021

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Events

Free Webinar: Convergence Of Circadian Rhythms And Gut Microbes: Maintaining The Metronome Of Life – September 7, 2021 (10:00 am – 11:00 am) – Organized by The Institute for the Advancement of Food and Nutrition Sciences

Highlights!

Review: The importance of Faecalibacterium prausnitzii in human health and diseases – M Parsaei – New Microbes and New Infections

Review: The gut microbiome in feast and famine – Hannah D Holscher – Nature Reviews Gastroenterology & Hepatology

Prophylactic Administration of a Bacteriophage Cocktail Is Safe and Effective in Reducing Salmonella enterica Serovar Typhimurium Burden in Vivo – Quentin Lamy-Besnier – Microbiology Spectrum

Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users – Divya Gopinath – Clinical Oral Investigations

Cross-sectional comparisons of subgingival microbiome and gingival fluid inflammatory cytokines in periodontally healthy vegetarians versus non-vegetarians – Ahmed Khocht – Journal of Periodontal Research

Human and General Microbiome

Review: Gut microbiota as the critical correlation of polycystic ovary syndrome and type 2 diabetes mellitus. – Liyun Duan – Biomedicine & Pharmacotherapy

Review: The Gut Microbiome, Metformin, and Aging – Sri Nitya Reddy Induri – Annual Review of Pharmacology and Toxicology

Review: Microbe defines the efficacy of chemotherapeutic drug: A complete paradigm – P Dalal – FEMS Microbiology Letters

Review: Gut Microbiota Profiles in Early- and Late-Onset Colorectal Cancer: A Potential Diagnostic Biomarker in the Future – Murdani Abdullah – Digestion

Review: Manipulating the neonatal gut microbiome: current understanding and future perspectives. – Emma Wong – Archives of Disease in Childhood

Review: Dietary advanced glycation end-products elicit toxicological effects by disrupting gut microbiome and immune homeostasis – Yingjia Chen – Journal of Immunotoxicology

Perspective: The microbiome extends host evolutionary potential – Lucas P Henry – Nature Communications

Perspective: How microbiota improve immunotherapy – Eduard Ansaldo – Science

Alterations in microbiota and their metabolites are associated with beneficial effects of bile acid sequestrant on icteric primary biliary Cholangitis – Bo Li – Gut Microbes

The gut microbiome in sickle cell disease: Characterization and potential implications – Hassan Brim – PloS ONE

Bacterial resistance to CRISPR-Cas antimicrobials – Ruben V Uribe – Scientific Reports

Depression: A Gut Microbiome Feeling! – Ahmed Naguy – The Journal of Nervous and Mental Disease

The potential prebiotic effect of 2-Butyloctanol on the human axillary microbiome – Min Li – International Journal of Cosmetic Science

Fecal Bacteria as Non-Invasive Biomarkers for Colorectal Adenocarcinoma – Biao Yuan – Frontiers in Oncology

Beneficial Compounds and Microbes

Review: Molecular genetics for probiotic engineering: dissecting lactic acid bacteria – Ronit Suissa – Trends in Microbiology

The effect of probiotic supplementation on the gut microbiota of preterm infants – Erica L Plummer – Journal of Medical Microbiology

Noni (Morinda citrifolia L.) Fruit Polysaccharides Regulated IBD Mice Via Targeting Gut Microbiota: Association of JNK/ERK/NF-κB Signaling Pathways – Ming-Yu Jin – Journal of Agricultural and Food Chemistry

Long-term personalized low FODMAP diet improves symptoms and maintains luminal Bifidobacteria abundance in irritable bowel syndrome – Heidi M Staudacher – Neurogastroenterology and Motility

New Lactiplantibacillus plantarum and Lacticaseibacillus rhamnosus strains: well tolerated and improve infant microbiota – Gunilla Önning – Pediatric Research

Multi-targeted properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 against enterotoxigenic Escherichia coli (ETEC) H10407 pathogenesis across human gut models – Charlène Roussel – Gut Microbes

Animal Microbiome 

Review: A role for bacterial experimental evolution in coral bleaching mitigation? – Justin Maire – Trends in Microbiology

Microbial bioindicators of Stony Coral Tissue Loss Disease identified in corals and overlying waters using a rapid field-based sequencing approach – Cynthia C Becker – Environmental Microbiology

Assessing age, breeding stage, and mating activity as drivers of variation in the reproductive microbiome of female tree swallows – Jessica Hernandez – Ecology and Evolution

Study in Drosophila: Activation of innate immunity during development induces unresolved dysbiotic inflammatory gut and shortens lifespan – Kyoko Yamashita – Disease Models & Mechanisms

Study in Mice: The composition of the gut microbiota following early-life antibiotic exposure affects host health and longevity in later life – Miriam A Lynn – Cell Reports

Study in Mice: Redundant cytokine requirement for intestinal microbiota-induced Th17 cell differentiation in draining lymph nodes – Teruyuki Sano – Cell reports

Honeybee intestines retain low yeast titers, but no bacterial mutualists, at emergence. – James P Tauber – Yeast (Wiley)

The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans – Jaelle C Brealey – Current Biology

Breed differences in the expression levels of gga-miR-222a in laying hens influenced H(2)S production by regulating methionine synthase genes in gut bacteria – Si-Cheng Xing – Microbiome

Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the  Southeastern United States – Jesse C Thomas IV – Microbiology spectrum

Ingestion of Lactobacillus rhamnosus modulates chronic stress-induced feather pecking in chickens – Claire Mindus – Scientific Reports

Wolves, dogs and humans in regular contact can mutually impact each other’s skin microbiota. – Stefanie Urimare Wetzels – Scientific Reports

Label-free proteomic analysis reveals differentially expressed Wolbachia proteins in Tyrophagus putrescentiae: Mite allergens and markers reflecting population-related  proteome differences – Tomas Erban – Journal of Proteomics

Teaching old mice new tricks: the utility of aged mouse models of C. difficile infection to study pathogenesis and rejuvenate immune response – Jae Hyun Shin – Gut Microbes

Soil and Plant Microbiome

Review: A review of root exudates and rhizosphere microbiome for crop production – Haishu Sun – Environmental Science and Pollution Research International

The biodiversity effect of reduced tillage on soil microbiota – Tobias Guldberg Frøslev – Ambio

Microbiome-mediated response to pulse fire disturbance outweighs the effects of fire legacy on plant performance – Daniel Revillini – The New Phytologist

Interactions between soil compositions and the wheat root microbiome under drought stress: From an in silico to in planta perspective – Jiyeon Si – Computational and Structural Biotechnology Journal

Environmental Science

Review: Temporal and Spatial Signaling Mediating the Balance of the Plankton Microbiome – Yun Deng – Annual Review of Marine Science

Protocols, Methods and Techniques

Archive for Research in Child Health (ARCH) and Baby Gut: Study Protocol for a Remote, Prospective, Longitudinal Pregnancy and Birth Cohort to Address Microbiota  Development and Child Health – Eliot N Haddad – Methods and Protocols

Benchmarking laboratory processes to characterise low-biomass respiratory microbiota – Raiza Hasrat – Scientific Reports

Simultaneous feature selection and outlier detection with optimality guarantees – Luca Insolia – Biometrics

SMDI: An Index for Measuring Subgingival Microbial Dysbiosis – T Chen – Journal of dental researchTrends in inflammatory bowel disease treatment in the past two decades-a high-level text mining analysis of PubMed publications – Eyal Klang – United European Gastroenterology Journal

August 25, 2021

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General microbiome

[REVIEW]The longitudinal and cross-sectional heterogeneity of the intestinal microbiota – Miller et al. – Current Opinion in Microbiology

Pregnancy and early life

Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California – Alderete et al. – Gut Microbes

Human respiratory microbiome

Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients – Gao et al. – Advanced Science

Human gut microbiome

Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese – Tomofuji et al. – Annals of the Rheumatic Diseases

Gut microbes participate in food preference alterations during obesity – d’Oplinter et al. – Gut Microbes

Altered gut microbiome compositions are associated with the severity of asthma – Wang et al. – Journal of Thoracic Disease

Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales – Scanlan – mSystems

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

Propamocarb exposure has the potential to accelerate the formation of atherosclerosis in both WT and ApoE−/− mice accompanied by gut microbiota dysbiosis – Jin et al. – Science of The Total Environment

Inflammation-relevant microbiome signature of the stroke brain, gut, spleen, and thymus and the impact of exercise – Kingsbury et al. – Journal of Cerebral Blood Flow & Metabolism

Animal microbiome (for animals in the wild)

Comparative Analysis of Skin Bacterial Diversity and Its Potential Antifungal Function Between Desert and Pine Forest Populations of Boreal Toads Anaxyrus boreas – Basanta et al. – Host Microbe Interactions

Plant, root, and soil microbiome

Herbivory shapes the rhizosphere bacterial microbiota in potato plants – Malacrino et al. – Environmental Microbiology Reports

[PREPRINT]Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea – Szitenberg et al. – bioRxiv

Techniques/Bioinformatics

The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota – McAdams et al. – Cells

Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies – Ammer-Herrmenau et al. – mSystems

August 22nd, 2021

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Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of really interesting preprints and published studies. If you are interested in soil microbiology, take a look at the preprint by Nelson and collaborators, who characterized the soil microbiome across a wildfire burn severity gradients in coniferous forests and made their dataset available in the Fire Responding Ecogenomic database (FiRE-db).

Looking at a large variety of ecosystems, Rodriguez-Gijon and collaborators used a vast collection of Metagenomes Assembled Genomes (MAGs), to investigate the genomes size of prokaryotes in these ecosystems. They show that, while the environment of origin can be linked to genome size, it seems like evolutionary phylogenetic history is in many cases a stronger predictor.

Finally, today’s non-microbiology pick is a great “10 simples rules” paper reviewing best practices on organizing bioinformatics workshops in low and middle-income countries.

Have a great Weekend!

General microbiome

Preprint: A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy – Rodriguez-Gijon et al. – BioRXiV

Multi-site human microbiome

Review : Host-Microbe Metagenomics: a Lens To Refocus Our Perspective
on Infectious and Inflammatory Diseases – Kalantar and Langelier – mSystems

Human gut microbiome

Rectal bacteriome and virome signatures and clinical outcomes in community-acquired pneumonia: An exploratory study – Kullberg et al. – EClinicalMedicine

Review: The important role of fungi in inflammatory bowel diseases – Wang et al. – Scandinavian Journal of Gastroenterology

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

Preprint: A bacterial genome and culture collection of gut microbial in weanling piglet – Dong et al. – BioRXiV

Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms – Lührmann et al. – Plos One

Plant, root, and soil microbiome

Preprint: Does plant diversity determine the diversity of the rhizosphere microbial community? – Zverev et al. – BioRXiV

Preprint: Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire – Nelson et al. – BioRXiV

Peatland microbial community responses to plant functional group and drought are depth-dependent – Lamit et al. – Molecular ecology

Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China – Ni et al. – Global ecology and Biogeography

Water and extremophile microbiome

Preprint: The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments – Nishimura et al. – BioRXiV

Food microbiology

Preprint: Mixed culture metagenomics of the microbes making sour beer – Piraine et al. – BioRXiV

Preprint: Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh – Tanzina et al. – BioRXiV

Preprint: Microbial communities in retail draft beers and the biofilms they produce – Bose et al. – BioRXiV

Bioinformatics

Book chapter: Bioinformatics Tools and Software – Gupta et al. – Advances in Bioinformatics, Springer, Singapore

MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes – Lee et al. – New biotechnology

My non-microbiology picks

Ten simple rules for organizing a bioinformatics training course in low– and middle-income countries – Moore et al. – PLOS computational biology

August 18, 2021

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Call for Papers

Cells is calling for papers for a special issue on “Interplay of Gene Expression Regulation and Microbiome”. Deadline for paper submission: 30th of November 2021

General microbiome

[REVIEW]The Cancer Microbiome: Recent Highlights and Knowledge Gaps – Knippel, Drewes & Sears – Cancer Discoveries

[REVIEW]Healthy Patients Are Not the Best Controls for Microbiome-Based Clinical Studies: Example of Sjögren’s Syndrome in a Systematic Review – Doare et al. – Frontiers in Immunology

[REVIEW]The varying effects of antibiotics on gut microbiota – Yang et al. – AMB Express

[REVIEW]Prevotella diversity, niches and interactions with the human host – Tett et al. – Nature Reviews Microbiology

Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study – Klassert et al. – Microbiome

Long-term biodiversity intervention shapes health-associated commensal microbiota among urban day-care children – Roslund et al. – Environment International

Multi-site human microbiome

Different responses of the oral, nasal and lung microbiomes to cigarette smoke – Pfeiffer et al. – Thorax

Human skin microbiome

[REVIEW]The power and potential of BIOMAP to elucidate host-microbiome interplay in skin inflammatory diseases – Alenius et al. – Experimental Dermatology

[PREPRINT]Bacterial DNA on the skin surface overrepresents the viable skin microbiome – Acosta et al. – bioRxiv

Human oral microbiome

[REVIEW]The role of oral bacteria in inflammatory bowel disease – Read, Curtis & Neves

Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long-COVID – Haran et al. – JCI insight

Human gut microbiome

[REVIEW]Phage Diversity in the Human Gut Microbiome: a Taxonomist’s Perspective – Adriaenssens – mSystems

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

IL-10 Deficiency Accelerates Type 1 Diabetes Development via Modulation of Innate and Adaptive Immune Cells and Gut Microbiota in BDC2.5 NOD Mice – Huang et al. – Frontiers in Immunology

Genetically determined hypertensive phenotype affects gut microbiota composition, but not vice versa – Konopelski et al. – Journal of Hypertension

Plant, root, and soil microbiome

Plant developmental stage drives the differentiation in ecological role of the maize microbiome – Xiong et al. – Microbiome

Bioinformatics

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach – Dovrolis et al. – PLOS Computational Biology

[PREPRINT]SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs) – Pan et al. – bioRxiv

[PREPRINT]Network analysis of ten thousand genomes shed light on Pseudomonas diversity and classification – Passarelli-Araujo, Franco & Venancio – bioRxiv

Techniques

[PREPRINT]The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS – Lao et al. – bioRxiv

August 17, 2021

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Today’s digest covers a variety of topics including an interesting preprint on how the maternal immune system shapes offspring immunity in a microbiota dependent fashion and a large human study of the Rotavirus vaccine and gut microbiota. Non microbiology picks cover some recent COVID-19 advances and a very interesting article in Science investigating energy expenditure through the human life course.

COVID-19 

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing – Smits et al. Cell Reports

Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants. Wang et al. Science 

Long-term perturbation of the peripheral immune system months after SARS-CoV-2 infection -Ryan et al. MedRxiv

General microbiome

Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study – Klassert et al. Microbiome

Acute SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa in the nose – Rhoades et al. Cell Reports 

Meta-analysis of Clinical Microbiome Studies in Urolithiasis Reveal Age, Stone Composition, and Study Location as the Predominant Factors in Urolithiasis-Associated Microbiome Composition – mBio. Kachroo et al. 

Human gut microbiome

The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants – Robertson et al. Vaccine

Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors – Brown et al. Cell Host & Microbe

Pregnancy and Early-Life

Maternal γδ T Cells Shape Offspring Pulmonary Type-2 Immunity In A Microbiota-Dependent Manner – Papotto et al. BioRxiv

Food Microbiology

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures – Somerville et al. ISME

Water Microbiome

Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities – Alarcón-Schumacher et al. mSystems

Soil microbiome

Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria – Wicaksono et al. Microbiome

Bioinformatics

HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes. Tan et al. Bioinformatics

Sparse least trimmed squares regression with compositional covariates for high dimensional data. Monti and Filzmoser. Bioinformatics. 

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation. Schaffer et al. BMC Bioinformatics.

Non-microbiome picks

Daily energy expenditure through the human life course – Pontzer et al. Science

Analysis of scientific society honors reveals disparities – Le et al. Cell Systems