March 6, 2019

In today’s digest read how DNA polymerase and number of rounds of amplification in PCR affect 16S rRNA gene sequence data, how urinary microbiota changes after Cesarean delivery, how diverse is microbial community of thermal pools in Kamchatka (Russia), and more. Enjoy!

General microbiome

Toward multiomics-based next-generation diagnostics for precision medicine – Qi Wang – Personalized Medicine

Pregnancy and early life

*Alterations in the Urinary Microbiota Are Associated With Cesarean Delivery
Fengping Liu – Frontiers in Microbiology

Antimicrobial susceptibility and serotype distribution of Streptococcus agalactiae recto-vaginal colonizing isolates from pregnant women at a tertiary hospital in Pretoria, South Africa: an observational descriptive study letter – Mohamed Said – bioRxiv

Gut microbiome

Interplay between the human gut microbiome and host metabolism – Alessia Visconti – bioRxiv

A decrease in iron availability to human gut microbiome reduces the growth of potentially pathogenic gut bacteria; an in vitro colonic fermentation study – Bhavika A Parmanand – The Journal of Nutritional Biochemistry

Volatile organic compounds emitted from faeces as a biomarker for colorectal cancer – Ashley Bond – Alimentary Pharmacology and Therapeutics

Animal experiments

Loading ceftriaxone, vancomycin, and Bifidobacteria bifidum TMC3115 to neonatal mice could differently and consequently affect intestinal microbiota and immunity in adulthood – RuYue Cheng – Scientific Reports

Probiotics/Prebiotics

Prebiotics from acorn and sago prevent high-fat-diet-induced insulin resistance via microbiome–gut–brain axis modulation – Shokouh Ahmadi – The Journal of Nutritional Biochemistry

Viruses

A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data – Umberto Rosani – Viruses

Untargeted metabolomics analysis of the upper respiratory tract of ferrets following influenza A virus infection and oseltamivir treatment – David J. Beale – Metabolomics

Techniques

*The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data – Marc A Sze & Patrick D Schloss – bioRxiv

Utilisation of Ambient Laser Desorption Ionisation Mass Spectrometry (ALDI-MS) Improves Lipid-Based Microbial Species Level Identification – Simon J. S. Cameron – Scientific Reports

Animal microbiome

Characterization of the otic bacterial microbiota in dogs with otitis externa compared to healthy individuals – Juraj Korbelik – Veterinary Dermatology

Water and extremophile microbiome

*Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia – Laetitia G. E. Wilkins – Scientific Reports

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March 4, 2019

Human Microbiome

Polyamines and microbiota in bicuspid and tricuspid aortic valve aortopathy – Amalia Forte – Journal of Molecular and Cellular Cardiology

Targeting the Gut Microbiota to Investigate the Mechanism of Lactulose in Negating the Effects of a High-Salt Diet on Hypertension – Zheng Zhang – Molecular Nutrition and Food Research

Food allergy: could the gut microbiota hold the key? – Supinda Bunyavanich – Nature Reviews Gastroenterology & Hepatology

The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases – Mathias L. Richard – Nature Reviews Gastroenterology & Hepatology

Type VI Secretion Systems and the Gut Microbiota –  Michael J. Coyne – Microbiology Spectrum

Autism Spectrum Disorders and the Gut Microbiota – Antonella Fattorusso – Nutrients

New Approaches to Detect Biosynthetic Gene Clusters in the Environment – Ray Chen – Medicines

Impact of microbiota on central nervous system and neurological diseases: the gut-brain axis – Qianquan Ma – Journal of Neuroinflammation

Dysregulated Lung Commensal Bacteria Drive Interleukin-17B Production to Promote Pulmonary Fibrosis through Their Outer Membrane Vesicles – Daping Yang – Immunity

Altered gut microbiome after bariatric surgery and its association with metabolic benefits: A systematic review – Naomi K. Davies – Surgery for Obesity and Related Diseases

Trimethylamine N-oxide, Mediterranean diet, and nutrition in healthy, normal-weight adults: also a matter of sex? – Luigi Barrea – Nutrition

The composition of the pulmonary microbiota in sarcoidosis – an observational study – André Becker – Respiratory Research

Emerging trends and research foci in gastrointestinal microbiome – Xiaoquan Huang – Journal of Translational Medicine

Updates on Clostridioides (Clostridium) difficile Infection With Emphasis on Long-Term Care – Eddie Grace –  The Senior Care Pharmacist

 

Animal Microbiome

Host genetics and diet composition interact to modulate gut microbiota and predisposition to metabolic syndrome in spontaneously hypertensive stroke-prone rats – Arashdeep Singh – The FASEB Journal

Comparative effects of n-hexane and methanol extracts of elecampane (Inula helenium L.) rhizome on growth performance, carcass traits, feed digestibility, intestinal antioxidant status and ileal microbiota in broiler chickens – Mirza-Ebrahim Abolfathi – Archives of Animal Nutrition

Comparison of the Gut Microbiota Composition between the Wild and Captive Tibetan Wild Ass (Equus kiang) – Hongmei Gao – Journal of Applied Microbiology

Consumption of drinking water N-Nitrosamines mixture alters gut microbiome and increases the obesity risk in young male rats – Jianqiang Zhu – Environmental Pollution

Modularity and predicted functions of the global sponge-microbiome network – Miguel Lurgi – Nature Communications

Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice – Kara D. McGaughey – Scientific Report

Loading ceftriaxone, vancomycin, and Bifidobacteria bifidum TMC3115 to neonatal mice could differently and consequently affect intestinal microbiota and immunity in adulthood – RuYue Cheng – Scientific Report

Dietary Protein Intake Level Modulates Mucosal Healing and Mucosa-Adherent Microbiota in Mouse Model of Colitis – Sandra Vidal-Lletjós – Nutrients

Farm stage, bird age and body site dominantly affect the quantity, taxonomic composition, and dynamics of respiratory and gut microbiota of commercial layer chickens – John M. Ngunjiri – Applied and Environmental Microbiology

Development and Function of the Intestinal Microbiome and Potential Implications for Pig Production – Tanya L. Nowland – Animals

Green Coffee Extract Improves Cardiometabolic Parameters and Modulates Gut Microbiota in High-Fat-Diet-Fed ApoE-/- Mice – Erika Caro-Gómez – Nutrients

Dysbiosis of the Gut Microbiota on the Inflammatory Background due to Lack of Suppressor of Cytokine Signalling-1 in Mice – Y. Gendo – Inflammatory Intestinal Diseases

 

Beneficial Microbes and Compounds

Prebiotic supplementation of in vitro faecal fermentations inhibits proteolysis by gut bacteria and host diet shapes gut bacterial metabolism and response to intervention – Xuedan Wang – Applied and Environmental Microbiology

Probiotics and Colon Cancer – Lorenzo Drago – Microorganisms

The Therapeutic Implications of the Gut Microbiome and Probiotics in Patients with NAFLD – Brandon J. Perumpail – Diseases

Cranberry Polyphenols: Natural Weapons against Dental Caries – Nebu Philip – Dentistry Journal

Dietary Components That May Influence the Disturbed Gut Microbiota in Chronic Kidney Disease – Denise Mafra – Nutrients

Liposomal Irinotecan for Treatment of Colorectal Cancer in a Preclinical Model – Jiao-Ren Huang – Cancers

Effects of acupuncture in treating insomnia due to spleen-stomach disharmony syndrome and its influence on intestinal microbiome: Study protocol for a randomized controlled trial –  Ya-ru Huangfu – Journal of Integrative Medicine

Patient perception and approval of faecal microbiota transplantation (FMT) as an alternative treatment option for obesity – F. Gundling – Obesity Science and Practice

 

Water Microbiome

Bacterial release from pipe biofilm in a full-scale drinking water distribution system – Sandy Chan – npj Biofilms and Microbiomes

 

Plant Microbiome

The tea leaf microbiome shows specific responses to chemical pesticides and biocontrol applications – Tomislav Cernava – Science of The Total Environment

Algae bacteria interactions that balance the planktonic microbiome – Emilio Cirri – New Phytologist

 

Bioinformatics

VERA: agent-based modeling transmission of antibiotic resistance between human pathogens and gut microbiota – Oksana E Glushchenko – Bioinformatics

CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis – Tony J. Lam – The CRISPR Journal

 

Other

Impact of primary carbon sources on microbiome shaping and biotransformation of pharmaceuticals and personal care products – Karen Rossmassler – Biodegradation

GrgA as a potential target of selective antichlamydials – Huirong Zhang – PLoS ONE

Quenching by sodium thiosulfate does not influence 16S rRNA gene sequencing profiles of reclaimed water from three sites in the Mid-Atlantic, United States – Sarah M.Allard – Environmental Research

March 1, 2019

Human Microbiome

The human microbiome in health and disease: hype or hope – Gwen Falony – Acta Clinica Belgica

Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities – Daniel Rodríguez Amor – Life

Influence of Crohn’s disease related polymorphisms in innate immune function on ileal microbiome – Ellen Li – PLoS ONE

Interactions between gut microbiota and non-alcoholic liver disease: the role of microbiota-derived metabolites – Kyongbum Lee – Pharmacological Research

Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection – Benjamin H Mullish – Gut

Fecal microbiota dynamics and its relation with disease course in Crohn’s disease – Gianluca Galazzo – Journal of Crohn’s and Colitis

Associations Between Gut Microbiota and Alzheimer’s Disease: Current Evidences and Future Therapeutic and Diagnostic Perspectives – Liang Shen – Journal of Alzheimer’s Disease

Western diet regulates immune status and the response to LPS-driven sepsis independent of diet-associated microbiome – Brooke A. Napier – PNAS

The Human Fecal Microbiota Metabolizes Foodborne Heterocyclic Aromatic Amines by Reuterin Conjugation and Further Transformations – Falco Beer – Molecular Nutrition and Food Research

Clinical Review on the Utility of Fecal Microbiota Transplantation in Immunocompromised Patients – Hamzah Abu-Sbeih – Current Gastroenterology Reports

Cellular and Molecular Therapeutic Targets in Inflammatory Bowel Disease-Focusing on Intestinal Barrier Function – Ida Schoultz – Cells

Can Gut Microbiota and Lifestyle Help Us in the Handling of Anorexia Nervosa Patients? – Vanessa Mendez-Figueroa – Microorganisms

Impact of the Gastro-Intestinal Bacterial Microbiome on Helicobacter-Associated Diseases – Maxime Pichon – Healthcare

Influence of short-term changes in dietary sulfur on the relative abundances of intestinal sulfate-reducing bacteria – Allison Dostal Webster – Gut Microbes

Fecal microbiota transplantation research output from 2004 to 2017: a bibliometric analysis – Yan Li – PeerJ

Conjunctival microbiome changes associated with fungal keratitis: metagenomic analysis – C. Ge – International Journal of Ophthalmology

Gut Microbiota and Chronic Constipation: A Review and Update – Toshifumi Ohkusa – Frontiers in Medicine

An altered fecal microbiota profile in patients with non-alcoholic fatty liver disease (NAFLD) associated with obesity – E. Nistal – The Spanish Journal of Gastroenterology

Paternal Programming of Liver Function and Lipid Profile Induced by a Paternal Pre-Conceptional Unhealthy Diet: Potential Association with Altered Gut Microbiome Composition – X. Zhang – Kidney and Blood Pressure Research

Tryptophan Metabolism and Related Pathways in Psychoneuroimmunology: The Impact of Nutrition and Lifestyle – J. M. Gostner – Neuropsychobiology

The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa – Jochen Seitz – Frontiers in Endocrinology

Sperm Microbiota and Its Impact on Semen Parameters – David Baud – Frontiers in Microbiology

A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016 – NIH Human Microbiome Portfolio Analysis Team – Microbiome

 

Microbiome and Cancer

Impact of chemotherapy on the association between fear of cancer recurrence and the gut microbiota in breast cancer survivors – Ryo Okubo – Brain, Behavior, and Immunity

Bugs, drugs, and cancer: can the microbiome be a potential therapeutic target for cancer management? – Biying Chen – Drug Discovery Today

 

Early Childhood Microbiome

Crosstalk Between the Microbiome and Gestational Immunity in Autism-Related Disorders – Matt J. Paysour – DNA and Cell Biology

Cohort profile: The LoewenKIDS Study – life-course perspective on infections, the microbiome and the development of the immune system in early childhood – Cornelia Gottschick – International Journal of Epidemiology

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month – Nina Iszatt – Microbiome

 

Animal Microbiome

Convergence, constraint and the potential for mutualism between ants and gut microbes – Elizabeth G. Pringle – Molecular Ecology

Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy – Martin Schwarzer – Frontiers in Immunology

Fto Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice via Alterations in Gut Microbiota – Lijuan Sun – Theranostics

 

Beneficial Bugs, Foods and Compounds

Re-purposing is needed for beneficial bugs, not for the drugs – Hari Ram – International Microbiology

Probiotic mixture of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 attenuates hippocampal apoptosis induced by lipopolysaccharide in rats – Ghazaleh Mohammadi – International Microbiology

The Use of Probiotic Therapy to Modulate the Gut Microbiota and Dendritic Cell Responses in Inflammatory Bowel Diseases – Pablo Alagón Fernández del Campo – Medical Sciences

Dietary fibers as emerging nutritional factors against diabetes: focus on the involvement of gut microbiota – Vemana Gowd – Critical Reviews in Biotechnology

Gut microbiota, a new frontier to understand traditional Chinese medicines – Wuwen Feng – Pharmacological Research

Fructooligosaccharides Ameliorating Cognitive Deficits and Neurodegeneration in APP/PS1 Transgenic Mice through Modulating Gut Microbiota – Jing Sun – Journal of Agricultural and Food Chemistry

Short-chain fatty acid delivery: assessing exogenous administration of the microbiome metabolite acetate in mice – Tyler B. Shubitowski – Physiological Reports

Dietary intake of whole strawberry inhibited colonic inflammation in dextran sulfate sodium-treated mice via restoring immune homeostasis and alleviating gut microbiota dysbiosis – Yanhui Han – Journal of Agricultural and Food Chemistry

Ganoderma lucidum polysaccharide improves rat DSS-induced colitis by altering cecal microbiota and gene expression of colonic epithelial cells – Jinli Xie –  Food & Nutrition Research

In Vitro Infant Faecal Fermentation of Low Viscosity Barley β-Glucan and Its Acid Hydrolyzed Derivatives: Evaluation of Their Potential as Novel Prebiotics – Ka-Lung Lam – Molecules

Role of intestinal microecology in the regulation of energy metabolism by dietary polyphenols and their metabolites – Shaoling Lin – Food & Nutrition Research

Neuroprotection of Fasting Mimicking Diet on MPTP-Induced Parkinson’s Disease Mice via Gut Microbiota and Metabolites – Zhi-Lan Zhou – Neurotherapeutics

Refined versus Extra Virgin Olive Oil High-Fat Diet Impact on Intestinal Microbiota of Mice and Its Relation to Different Physiological Variables – Nieves Martínez – Microorganisms

Engineered and wild-type L. lactis promote anti-inflammatory cytokine signalling in inflammatory bowel disease patient’s mucosa – Saša Simčič – World Journal of Microbiology and Biotechnology

Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro – Olaf Perdijk – Frontiers in Immunology

 

Built Environments

Man-made microbial resistances in built environments – Alexander Mahnert – Nature Communications

House dust microbiome and human health risks – Yifan Shan – International Microbiology

Microbiomes of China’s Space Station During Assembly, Integration, and Test Operations – Ying Zhang – Microbial Ecology

 

Environmental and Plant Microbiome

Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses – Cesar A. Pérez-Fernández – International Microbiology

Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils – Zhi-Bo Zhao – Microbiome

The deep continental subsurface: the dark biosphere – Cristina Escudero – International Microbiology

 

Bioinformatics

Batch effects correction for microbiome data with Dirichlet-multinomial regression – Zhenwei Dai – Bioinformatics

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon – Anna Cuscó – F1000Research

 

Methods

Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis – Xiaoxiao Sun – PeerJ

In Vitro Methods to Study Colon Release: State of the Art and An Outlook on New Strategies for Better In-Vitro Biorelevant Release Media – Marie Wahlgren – Pharmaceutics

 

February 23, 2019

Highlights: Today’s digest has articles on microbes associated with infants, vagina, gut, water and many more.

Events and jobs

Postdoctoral Researcher in mathematical modelling of the impact of host restriction on the transmission of bacteria – Amsterdam – Closing date: February 28, 2019

Pregnancy and early life

A role for the microbiome in mother–infant interaction and perinatal depression – Amanda Sanders – The International Review of Psychiatry

Multi-site human microbiome

Surgical site infections and the microbiome: An updated perspective – Richard P. Wenzel – Infection Control & Hospital Epidemiology

Human vaginal microbiome

The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls – Baris Ata – Scientific Reports

Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions – Cameron Klein – mBio

Human nearly-sterile sites 

Microbiome-based body fluid identification of samples exposed to indoor conditions – Akos Dobay – FSI Genetics

Human gut microbiome

Arabinoxylan oligosaccharides and polyunsaturated fatty acid effects on gut microbiota and metabolic markers in overweight individuals with signs of metabolic syndrome: a randomized cross-over trial – Louise Kjølbæk – Clinical Nutrition

The human microbiota and infection prevention – R. Araos – Infection Control & Hospital Epidemiology

Gut pathobionts as triggers for liver diseases – Peter Fickert – Nature Microbiology

Man and the Microbiome: A New Theory of Everything? – Mary I. Butler –  Annual Review of Clinical Psychology

Is it true that gut microbiota is considered as panacea in cancer therapy? – Amir Salek Farrokhi –  Journal of Cellular Physiology

Composition of gut microbiota in patients with toxigenic Clostridioides (Clostridium) difficile: Comparison between subgroups according to clinical criteria and toxin gene load – Sung-Hee Han – PLoS ONE

Effects of dietary fat on gut microbiota and faecal metabolites, and their relationship with cardiometabolic risk factors: a 6-month randomised controlled-feeding trial – Yi Wan – Gut

The Intestinal Microbiome, Plasma Metabolome and Liver Transcriptome‐ A Conspiracy Driving Hepatic Steatosis – Wajahat Z Mehal – Hepatology

A possible link between polyunsaturated fatty acids and uremic toxins from the gut microbiota in hemodialysis patients: A hypothesis – Julie Ann Kemp – Hemodialysis International 

Animal experiments 

Alterations of the mice gut microbiome via Schistosoma japonicum ova-induced granuloma – Yanqing Zhao – Frontiers in Microbiology

The functional repertoire encoded within the native microbiome of the model nematode Caenorhabditis elegans – Johannes Zimmermann – bioRxiv

Helminth-Based Product and the Microbiome of Mice with Lupus – Hadar Neuman – mSystems

Gut microbiota regulates lacteal integrity by inducing VEGF-C in intestinal villus macrophages. – SH Suh – EMBO Reports

Animal microbiome

Gut Microbiome Analysis In Adult Tropical Gars (Atractosteus tropicus) – Roberto Mendez-Perez – bioRxiv

Moderate plant water stress improves larval development, and impacts immunity and gut microbiota of a specialist herbivore – Elena Rosa -PLoS ONE

Plant, root, and soil microbiome

Chinese white truffles shape the ectomycorrhizal microbial communities of Corylus avellana – Mei Yang – Annals of Microbiology

Narrow safety margin in the phyllosphere during thermal extremes – Sylvain Pincebourde – PNAS

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles – Antoine P. Pagé – PLoS ONE

Water and extremophile microbiome 

Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California – Sabah Ul-Hasan – PLoS ONE

Editorial: Thermophilic and Halophilic Extremophiles in Eurasian Environments – Hongchen Jiang – Frontiers in Microbiology

Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay – Caitlin Petro – bioRxiv

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O – Ömer K. Coskun – The ISME Journal

Bacterial community pattern along the sediment seafloor of the Arctic fjorden (Kongsfjorden, Svalbard) – Xiao-Mei Fang – Antonie van Leeuwenhoek

Sources and selection of snow-specific microbial communities in a Greenlandic sea ice snow cover – Lorrie Maccario – Scientific Reports

Bacterial community composition shaped by water chemistry and geographic distance in an anthropogenically disturbed river – Peng Wang – Science of The Total Environment

Built environment 

Cell factories converting lactate and acetate to butyrate: Clostridium butyricum and microbial communities from dark fermentation bioreactors – Anna Detman – Microbial Cell Factories

Phages and viruses

Discovery of several thousand highly diverse circular DNA viruses – Michael J Tisza – bioRxiv

Techniques

Spatial metabolomics of in situ, host-microbe interactions – Benedikt K Geier – bioRxiv

Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass – Vincent Caruso – mSystems

 

 

February 19, 2019

Highlights: Microbial colonization in infants, prokaryotes of oxygen depleted water in Bay of Bengal, biodegradation of petroleum hydrocarbons, microbial communities across a range of saline soils, trait based approaches in wastewater treatment bioreactors to understand the changes in bacterial community composition. You can also read a handful of career based news in today’s non-microbe picks. 

General microbiome

Petroleum Microbiology Under Extreme Conditions – Oluwadara Oluwaseun Alegbeleye –Microbial Action on Hydrocarbons

Pregnancy and early life

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms – Matthew R Olm – Microbiome

Review: Establishment of an ideal gut microbiota to boost healthy growth of neonates – Thi Thanh Binh Nguyen – Critical Reviews in Microbiology

Necrotizing Enterocolitis Pathophysiology: How Microbiome Data Alter Our Understanding – Christina S. Kim MD – Clinics in Perinatology

Human skin microbiome

Rapid discrimination of fungal strains isolated from human skin based on microbial volatile organic profiles – Joao Raul Belinato – Journal of Chromatography B

Human gut microbiome

A pilot study on clinicopathological features and intestinal microflora changes in colorectal cancer patients born over a nine-year period encompassing three years before and after the Great Chinese famine – Jiante Li – Cancer Epidemiology

Animal experiments 

Ameliorating gut microenvironment through staphylococcal nuclease-mediated intestinal NETs degradation for prevention of type 1 diabetes in NOD mice – Yixuan Liang – Life Sciences

Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus – Johan S. Sáenz – Microbiome

Animal microbiome 

Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, nutrient digestibility, fecal fermentative end-products, fecal microbial populations, immune function, and diet palatability in adult dogs – Ching-Yen Lin – Journal of Animal Science

Bacterial community analysis for investigating bacterial transfer from tonsils to the pig carcass – Anne Mette Jakobsen – International Journal of Food Microbiology

Plant, root, and soil microbiome

Spatial distribution of prokaryotic communities in hypersaline soils – Blanca Vera-Gargallo – Scientific Reports

Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from ‘Concord’ Grape Vineyards – Ricky W. Lewis – Microbial Ecology

Dynamics of soil microbial communities following vegetation succession in a karst mountain ecosystem, Southwest China – Chang Zhao – Scientific Reports

Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants – Clarisse Brígido – MDPI

Robust archaeal and bacterial communities inhabit shallow subsurface sediments of the Bonneville Salt Flats – Julia M. McGonigle – bioRxiv

Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies – Tengxiang Lian – PeerJ

Alteration of Crop Rotation in Continuous Pinellia ternate Cropping Soils Profiled via ITS Amplicon Sequencing – Zhigui He – Letters in Applied Microbiology

Assessment of the Diversity of Fungal Community Composition Associated With Vachellia pachyceras and Its Rhizosphere Soil From Kuwait Desert – Majda K. Suleiman – Frontiers in Microbiology

Water and extremophile microbiome 

Prokaryotic Diversity in Oxygen Depleted Waters of the Bay of Bengal Inferred Using Culture-Dependent and -Independent Methods – Genevieve L. Fernandes – Indian Journal of Microbiology

Enrichment of anaerobic heterotrophic thermophiles from four Azorean hot springs revealed different community composition and genera abundances using recalcitrant substrates – Marcel Suleiman – Extremophiles 

Microbial Consortia and Biodegradation of Petroleum Hydrocarbons in Marine Environments – J. Paniagua-Michel – Microbial Action on Hydrocarbons

Built environment 

Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance – Ezequiel Santillan – bioRxiv

Non-Microbiology picks

To move research from quantity to quality, go beyond good intentions – Nature

How business-savvy scientists can find success in the risky start-up world – Nature

A disadvantaged background doesn’t have to be a barrier to success – Nature

Announcing the 2019 ScientistAtWork photo competition – Nature

Huge variations in US postdoc salaries point to undervalued workforce – Nature

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

 

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