February 16, 2019

Today’s digest is full of interesting articles about virome and phages, sinonasal microbiome and human milk microbiota. Enjoy weekend reading!

General microbiome

Bacteria and archaea on Earth and their abundance in biofilms – Hans-Curt Flemming – Nature Reviews Microbiology

The Impact of Low-FODMAPs, Gluten-Free, and Ketogenic Diets on Gut Microbiota Modulation in Pathological Conditions – Sofia Reddel – Nutrients

Impact of Gut Microbiota on Host Glycemic Control – Celine Gérard – Frontiers in Endocrinology

Intestinal Microbiota as a Host Defense Mechanism to Infectious Threats – Simona Iacob – Frontiers in Microbiology

Pregnancy and early life

Composition and Variation of the Human Milk Microbiota Are Influenced by Maternal and Early-Life Factors – Shirin Mossavi – Cell Host and Microbe

Human microbiome

Gut microbiota diversity associates with cardiorespiratory fitness in post-primary treatment breast cancer survivors – Stephen J. Carter – Experimental Physiology

Alterations in fecal short-chain fatty acids in patients with irritable bowel syndrome: A systematic review and meta-analysis – Qinghua Sun – Medicine

Mucosa-associated microbiota drives pathogenic functions in IBD-derived intestinal iNKT cells – Claudia Burrello – Life Science Alliance

The international sinonasal microbiome study (ISMS): a multi-centre, international characterization of sinonasal bacterial ecology – Sathish Paramasivan – BioRxiv

Microbiotyping the sinonasal microbiome – Ahmed Bassiouni – BioRxiv

Prevotella copri in individuals at risk for rheumatoid arthritis – Deshire Alpizar-Rodriguez – Annals of Rheumatic Diseases

Gut Microbiota Dysbiosis Is Not Independently Associated With Neurocognitive Impairment in People Living With HIV – Fengdi Zhang – Frontiers in Microbiology

Animal experiments

Gut microbiota signatures and lipids metabolism profiles by exposure to polyene phosphatidylcholine – Haining Yu – Biofactors

Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs – Jianping Quan – Frontiers in Microbiology

Plant root soil microbiome

Successive phytoextraction alters ammonia oxidation and associated microbial communities in heavy metal contaminated agricultural soils – Jipeng Luo – Science of The Total Environment

Water microbiome and extremophiles

Low concentrations of copper oxide nanoparticles alter microbial community structure and function of sediment biofilms – Lingzhan Miao – Science of the Total Environment

Characterizing the microbiome in petroleum reservoir flooded by different water sources – Xiaotong Wang – Science of the Total Environment

Baseline characterisation of aerobic hydrocarbon degrading microbial communities in deep‐sea sediments of the Great Australian Bight, Australia – Jodie van de Kamp – Environmental Microbiology

Viruses and phages

Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis – Lasha Gogokhia – Cell Host and Microbe

Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins – J. Leonardo Moreno-Gallego – Cell Host and Microbe

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome – Andrey N. Shkoporov – Cell Host and Microbe

Non-microbiology picks

Function and mechanisms of enteroendocrine cells and gut hormones in metabolism – Fiona M. Gribble – Nature Reviews Endocrinology

 

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February 14, 2019

If you are feeling butterflies in your stomach today, it might not be a gut microbiome imbalance – you might’ve caught the love bug! Happy Valentines Day!  Today’s digest features some human gut/FMT studies, a few animal gut biome studies and a couple probiotic publications.  Enjoy!

General microbiome

The next step towards anticancer microbiota therapeutics – Ursula Hofer – Nature Reviews [letter]

Expanding diversity of the human microbiome – Andrea Du Toit – Nature Reviews [in brief]

FMT in the clinic – Ashley York – Nature Reviews [research highlight]

Human respiratory microbiome

Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects – Anny Camelo-Castillo – Frontiers in Microbiology

Human gut microbiome

Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome – Daniel E. Almonacid – PLoS One

[pre -print] The Human Nickel Microbiome and its relationship to Allergy and Overweight in Women – Elena Angela Lusi – bioRxiv

The Relationship between Platelet Count and Host Gut Microbiota: A Population-Based Retrospective Cross-Sectional Study – Hee-Yong Yoon – Journal of Clinical Medicine

Data-driven multiple-level analysis of gut-microbiome-immune-joint interactions in rheumatoid arthritis – QuanQiu Wang – BMC Genomics

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes – J. Alfredo Blakeley-Ruiz – BMC Microbiome

Role of the Gut Microbiome in Autism Spectrum Disorders – Joby Pulikkan – Reviews on Biomarker Studies in Psychiatric and Neurodegenerative Disorders

Faecal microbiota transplantation in Australia: bogged down in regulatory uncertainty – Samuel P. Costello – Internal Medicine Journal

Animal experiments

Characterization of oral microbiota in marmosets: Feasibility of using the marmoset as a human oral disease model – Sachiko Takehara – PLoS One

The Effect of Multispecies Probiotic Supplementation on Iron Status in Rats – Katazyna Skrypnik – Biological Trace Element Research

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples – Susakul Palakawong Na Ayudthaya – Current Microbiology

Animal microbiome

A Diverse Microbial Community Supports Larval Development and Survivorship of the Asian Tiger Mosquito (Diptera: Culicidae) – Nicholas V Travanty – Journal of Medical Entomology

Plant, root, and soil microbiome

Belowground biota responses to maize biochar addition to the soil of a Mediterranean vineyard – Pilar Andrés – Science of The Total Environment

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining – Markus Gastauer – Scientific Data

Probiotics / prebiotics

Infant Complementary Feeding of Prebiotics for the Microbiome and Immunity – Starin McKeen – Nutrients

Techniques

Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis – James B. Thissen – PLoS One

Microbes in the news

Tube pollution: Could bacteria create clean air on the London Underground?

Ed’s non-microbiology picks

Adjunctive vitamin D in tuberculosis treatment: meta-analysis of individual participant data – David A. Jolliffe – European Respiratory Journal

Physical activity protects against depression

Want Healthier Eating Habits? Start with a workout

GMO Cassava Can Provide Iron, Zinc To Malnourished African Children

February 13, 2019

Today’s digest features a study on leaf-associated microbiomes of grafted tomato plants, study that reveals the chemical “fingerprint” and contribution of Parasutterella to host health, and Everything Hertz podcast with episode “Promiscuous expertise”. Happy reading/listening!

Gut microbiome

A new genomic blueprint of the human gut microbiota – Alexandre Almeida – Nature

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana – Matthew E. B. Hansen – Genome Biology

Disturbance of trace element and gut microbiota profiles as indicators of autism spectrum disorder: A pilot study of Chinese children – Qixiao Zhai – Environmental Research

*Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota – Tingting Ju – The ISME Journal

Extensive transmission of microbes along the gastrointestinal tract – Thomas Sebastian Benedikt Schmidt – eLife

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota – Andres Aranda-Diaz – bioRxiv

Skin microbiome

Review: Microbiosis in pathogenesis and intervention of atopic dermatitis – Jianhua Dou – International Immunopharmacology

Plant/root/soil microbiome

*Leaf-associated microbiomes of grafted tomato plants – Hirokazu Toju – Scientific Reports

Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment – Jarosław Grządziel and Anna Gałązka – Frontiers in Microbiology

Podcast

*Episode 77: Promiscuous expertise – Dan Quintana and James Heathers – Everything Hertz [A great episode about scientists who claim to be a public authority on topics outside their area of expertise!]

February 8, 2019

Happy Friday! Today’s digest includes the sea cucumber gut microbiome, bacterial diversity of volcano steam vents, and the impacts of arsenic and antimony on microbes in river sediment. Enjoy!

Human gut microbiome

Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels – Lokmer – PLoS ONE

Age-associated Impairment of the Mucus Barrier Function is Associated with Profound Changes in Microbiota and Immunity – Sovran – Scientific Reports

A single alcohol binge impacts on neutrophil function without changes in gut barrier function and gut microbiome composition in healthy volunteers – Stadlbauer – PLoS ONE

Animal experiments

TGFβ/BMP immune signaling affects abundance and function of C. elegans gut commensals – Berg – Nature Communications

Animal microbiome

Distinct microbiotas of anatomical gut regions display idiosyncratic seasonal variation in an avian folivore – Drovetski – Animal Microbiome

Characterization of the intestinal microbiota of the sea cucumber Holothuria glaberrima – Pagán-Jiménez – PLoS ONE

Dynamic distribution of gallbladder microbiota in rabbit at different ages and health states – Xing – PLoS ONE

Dietary-induced modulation of the hindgut microbiota is related to behavioral responses during stressful events in horses – Destrez – Physiology & Behavior

Review: Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts – O’Brien – mBio

Plant, root, and soil microbiome

Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems – Jiao – Microbiome

The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome – Shi -Microbiome

Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.) – Cernava – Microbiome

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon – Suárez-Moo – PLoS ONE

Characterization of iron-metabolizing communities in soils contaminated by acid mine drainage from an abandoned coal mine in Southwest China – Gao – Environmental Science and Pollution Research

Water and extremophile microbiome

Impacts of Arsenic and Antimony Co-Contamination on Sedimentary Microbial Communities in Rivers with Different Pollution Gradients – Sun – Microbial Ecology

The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes – Souza Brito – Extremophiles

Food microbiology

Spent coffee grounds extract rich in manooligosaccharides promote a healthier gut microbial community in a dose dependent manner – Pérez-Burillo – Journal of Agricultural and Food Chemistry

Impact of routine sanitation on the microbiomes in a fresh produce processing facility – Gu – International Journal of Food Microbiology

February 1, 2019

Today’s digest is quite diverse: the respiratory microbiome networks in cystic fibrosis patients, ketogenic diet effects on the gut microbiota in children with severe epilepsy, and insect-associated Streptomyces (spoiler: inhibit antimicrobial-resistant pathogens more than soil Streptomyces). Happy reading!

General microbiome

Minireview: The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases – A H Bishop – FEMS Microbiology Letters

Transforming medicine with the microbiome – Niv Zmora – Science Translational Medicine

Gut microbiome

Gut intraepithelial T cells calibrate metabolism and accelerate cardiovascular disease – Shun He – Nature

*The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy – Marie Lindefeldt – npj Biofilms and Microbiomes

Vaginal microbiome

Association between vaginal washing and vaginal bacterial concentrations – Michelle C. Sabo – PlosOne

Skin microbiome

Investigation of the Skin Microbiome: Swabs vs Biopsies – S. Prast‐Nielsen – British Journal of Dermatology

Oral microbiome

Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents – A. Esberg – Scientific Reports

Respiratory microbiome

*Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations – Mehdi Layeghifard – npj Biofilms and Microbiomes

Plant/root/soil microbiome

Effects of long-term fertilization on soil organic carbon mineralization and microbial community structure – Zhen Guo – PlosOne

Water microbiome

Functional screening for triclosan resistance in a wastewater metagenome and isolates of Escherichia coli and Enterococcus spp. from a large Canadian healthcare region – Andrew Camero – PlosOne

Animal experiments

Cream Cheese-Derived Lactococcus chungangensis CAU 28 Modulates the Gut Microbiota and Alleviates Atopic Dermatitis in BALB/c Mice – Jong-Hwa Kim – Scientific Reports

Animal Microbiome

*The antimicrobial potential of Streptomyces from insect microbiomes – Marc G. Chevrette – Nature Communications

January 31, 2019

Today’s digest covers articles describing sphingolipids in host-microbiome interaction, unique microbiome and metabolome of Indian population, selection and stabilization of soil microbiome and effect of probiotics on early sepsis in patients and immune response in childrenEnjoy reading!

General microbiome

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview – Partho Sen – Metabolites

Altered composition and function of intestinal microbiota in autism spectrum disorders: a systematic review – Feitong Liu – Translational Psychiatry

Sphingolipids in host–microbial interactions – Stacey L. Heaver – Current Opinion in Microbiology

Pregnancy and early life

Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children – Shilu Mathew – Scientific Reports

Pathways linking caesarean delivery to early health in a dual burden context: Immune development and the gut microbiome in infants and children from Galápagos, Ecuador – Amanda L. Thompson – American Journal of Human Biology

Human gut microbiome

The vagino-cervical microbiome as a woman’s life history – Zhuye Jie – BioRxiv

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers – Nielson T. Baxter – mBio

The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches – D.B. Dhakan – Gigascience

Animal experiments

Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats – Suzana Stanisavljević – Scientific Reports

Intestinal epithelial N-acylphosphatidylethanolamine phospholipase D links dietary fat to metabolic adaptations in obesity and steatosis – Amandine Everard – Nature Communications

Mutual interplay between IL-17–producing γδT cells and microbiota orchestrates oral mucosal homeostasis – Anneke Wilharm – PNAS

Plant, root and soil microbiome

Selection, succession and stabilization of soil microbial consortia – Elias K. Zegeye – BioRxiv

Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow – Mohammad Ghashghavi – BioRxiv

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance – Sammy Frenk – Applied and Environmental Microbiology

Water and extremophiles microbiome

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity – Aleksei A. Korzhenkov – Microbiome

Antibiotic disturbance affects aquatic microbial community composition and foodweb interactions but not community resilience – Ester M. Eckert – Molecular Ecology

 Phages and viruses

Megaphages infect Prevotella and variants are widespread in gut microbiomes – Audra E. Devoto – Nature Microbiology

Probiotics / prebiotics

Dysbiosis in early sepsis can be modulated by a multispecies probiotic: a randomised controlled pilot trial – V. Stadlbauer – Beneficial Microbes

Lactobacillus plantarum IS-10506 supplementation increases faecal sIgA and immune response in children younger than two years – P.D. Kusumo – Beneficial Microbes

Supplementation with Lactobacillus kefiranofaciens ZW3 from Tibetan Kefir improves depression-like behavior in stressed mice by modulating the gut microbiota – Ye Sun – Food and Function

Non-microbiology picks

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping – Helmuth Gehart – Cell

January 25, 2019

General microbiome

A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples – A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples – Chao Zhang – Frontiers in Microbiology

Review: Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment – Muneer Ahmad Malla – Frontiers in Immunology

The microbiome and its relevance in complex wounds – Francesco Drago – European Journal of Dermatology

Commentary: A Link between the Gut and Bone: Bone Health Impacted by Changes in Gut Microbiota – Larry J.Suva – The American Journal of Pathology

Pregnancy and early life

Feeding intolerance alters the gut microbiota of preterm infants – Zhenya Yuan – PLOS ONE

Multi-site human microbiome

Review: A correlation between intestinal microbiota dysbiosis and osteoarthritis – Marta AnnaSzychlinska – Heliyon

Human respiratory microbiome

A survey of fungal microbiota in airways of healthy volunteer subjects from Puglia (Apulia), Italy – Giovanna Elisiana Carpagnano – BMC Infectious Diseases

The Association Between Disease Severity and Microbiome in Chronic Rhinosinusitis – Darren Rom – The Laryngoscope

Review: Microbiota and asthma: Clinical implications – Konstantinos Katsoulis – Respiratory Medicine

Human oral microbiology

Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children – Nezar Noor Al-Hebshi – Journal of Oral Microbiology

Periodontal pathogens are a risk factor of oral cavity squamous cell carcinoma, independent of tobacco and alcohol and human papillomavirus – Ian Ganly – International Journal of Cancer

Human gut microbiome

Review: Role of diet and gut microbiota on colorectal cancer immunomodulation – Carolina Vieira De Almeida – World Journal of Gastroenterology

Review: Targeting obesity management through gut microbiota modulation by herbal products: A systematic review – Hanieh-SadatEjtahed – Complementary Therapies in Medicine

Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility – Vasudevan Dinakaran – Frontiers in Microbiology

Animal experiments

Fecal microbiota changes associated with dehorning and castration stress primarily affects light-weight dairy calves – Raies A. Mir – PLOS ONE

Advanced Age Impairs Intestinal Antimicrobial Peptide Response and Worsens Fecal Microbiome Dysbiosis Following Burn Injury in Mice – Elizabeth G Wheatley – Shock

Effects of drought‐stressed temperate forage legumes on the degradation and the rumen microbial community in vitro – Susanne Riede – Journal of Animal Physiology and Animal Nutrition

Bacillus amyloliquefaciens ameliorates Dextran Sulfate Sodium-Induced Colitis by Improving Gut Microbial Dysbiosis in Mice Model – Guangtian Cao – Frontiers in Microbiology

Bacillus subtilis 29784 induces a shift in broiler gut microbiome toward butyrate-producing bacteria and improves intestinal histomorphology and animal performance – Vincent Jacquier – Poultry Science

Green Tea Polyphenols Modify the Gut Microbiome in db/db Mice as Co‐abundance Groups Correlating with the Blood Glucose Lowering Effect – Tingting Chen – Molecular Nutrition and Food Research

Influence of Porphyromonas gingivalis in gut microbiota of streptozotocin‐induced diabetic mice – Anri Ohtsu – Oral diseases

Plant, root, and soil microbiome

Nanopore Sequencing as a Surveillance Tool for Plant Pathogens in Plant and Insect Tissues – Aline Bronzato Badial – Plant Disease

Rhizosphere Microbiomes from Root Knot Nematode Non-infested Plants Suppress Nematode Infection – Dongmei Zhou – Microbial Ecology

Water and extremophile microbiome

Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations – Natàlia Corcoll – Frontiers in Microbiology

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity – Nicola Vitulo – Frontiers in Microbiology

Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation – Jian-liLiu – Environmental Pollution

Long- and short-chain AHLs affect AOA and AOB microbial community composition and ammonia oxidation rate in activated sludge – Jie Gao – Journal of Environmental Sciences

Food microbiology

Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization – Javier Alonso‐del‐Real – Environmental Microbiology

Phages and viruses

Commentary : Going Viral: a Novel Role for Bacteriophage in Colorectal Cancer – Scott A. Handley – mBio