Category Archives: Water microbiome

August 2, 2018

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In today’s Microbiome Digest you can read about: the connection of mother’s microbiota and development of psychiatric disorders by M.G. Codagnone; pulmonary microbiome by A.N. Costa; microbiome and allergic diseases by M.Pascal; olfactory communication via microbiota in birds by O. Maraci; global topsoil microbiome by M. Bahram and many more. Enjoy your hot summer read!

Pregnancy and early life

Review: Programming Bugs: Microbiota and the Developmental Origins of Brain Health and Disease – Martin G.Codagnone – Biological Psychiatry

Human respiratory microbiome

The pulmonary microbiome: challenges of a new paradigm – André Nathan Costa – Jornal Brasileiro de Pneumologia

Oral microbiology

Are the mutans streptococci still considered relevant to understanding the microbial etiology of dental caries? – Jeffrey A. Banas – BMC Oral Health

Predicting oral malodour based on the microbiota in saliva samples using a deep learning approach – Yoshio Nakano – BMC Oral Health

Human skin microbiome

The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome – Kang Kang – Cell Reports

Human gut microbiome

Alterations in the Gut Microbiota of Rats Chronically Exposed to Volatilized Cocaine and Its Active Adulterants Caffeine and Phenacetin – Cecilia Scorza – Neurotoxicity Research

Origination, change, and modulation of geriatric disease-related gut microbiota during life – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens – Alexandra E. Livanos – PLOS One

Minireview: Microbiome and Allergic Diseases – Mariona Pascal – Frontiers in Immunology / Mucosal Immunity

Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy – Xingming Deng – Frontiers in Microbiology / Antimicrobials, Resistance and Chemotherapy

Moxibustion treatment modulates the gut microbiota and immune function in a dextran sulphate sodium-induced colitis rat model – Qin Qi – World Journal of Gastroenterology

Helicobacter pylori in human health and disease: Mechanisms for local gastric and systemic effects – Denisse Bravo – World Journal of Gastroenterology

Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species – Valentina Laclare McEneany – The ISME Journal

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance – Aspen T. Reese – mBio

Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs – Celeste Alexander – British Journal of Nutrition

Standardization of gut microbiota analysis: Variability in samples taken at different times from single case and the effect of the freezing the sample – F. Saglam – International Journal of Infectious Diseases

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size – Emily C. Hoedt – The ISME journal

Animal experiments 

A Polysaccharide Isolated from Dictyophora indusiata Promotes Recovery from Antibiotic-Driven Intestinal Dysbiosis and Improves Gut Epithelial Barrier Function in a Mouse Model – Sadia Kanwal – Nutrients

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis – Simon Ghaly – Scientific Reports

Treatment with camu camu (Myrciaria dubia) prevents obesity by altering the gut microbiota and increasing energy expenditure in diet-induced obese mice – Fernando F Anhê – Gut Microbiota

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures – Matej Medvecky – BMC Genomics

Addition of arabinoxylan and mixed linkage glucans in porcine diets affects the large intestinal bacterial populations – John B. Gorham – European Journal of Nutrition

Animal microbiome 

A prokaryotic-eukaryotic relation in the fat body of Bombus terrestris – Anneleen Parmentier – Environmental Microbiology Reports

Olfactory Communication via Microbiota: What Is Known in Birds? – Öncü Maraci – Genes

Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta) – Alexandria Creasy – Viruses

Plant, root, and soil microbiome

Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field – Pranitha S. Pandit – Antonie van Leeuwenhoek

Long-term effects of untreated wastewater on soil bacterial communities – Tianlin Shen – Science of The Total Environment

Minireview: Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation – Sara Correa-García – Microbial Biotechnology

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana Fusarium wilt disease by reshaping the soil microbiome – Zongzhuan Shen – Biology and Fertility of Soils

Structure and function of the global topsoil microbiome – Mohammad Bahram – Nature

Globally rising soil heterotrophic respiration over recent decades – Ben Bond-Lamberty – Nature

Water and extremophile microbiome

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current – Flavia Flaviani – Frontiers in Microbiology / Aquatic Microbiology

Evaluation of biomethane potential of waste algal biomass collected from eutrophied lake: effect of source of inocula, co-substrate, and VS loading – Pushpendar Kumar – Journal of Applied Phycology

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria – Xiufeng Ma – Environmental Microbiology

Increased biofilm formation due to high-temperature adaptation in marine Roseobacter – Alyssa G. Kent – Nature Microbiology

Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms – Frank Unfried – The ISME Journal

The anchoring effect—long-term dormancy and genetic population structure – Lisa Sundqvist – The ISME Journal

Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments – Stefan Spring – Environmental Microbiology

The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients – Julia M. Otte – Environmental Microbiology

Temporal and spatial dynamics in microbial community composition within a temperate stream network – Norman Hassell – Environmental Microbiology

Diel dynamics and coupling of heterotrophic prokaryotes and dissolved organic matter in epipelagic and mesopelagic waters of the central Red Sea – Francisca C. García – Environmental Microbiology

Probiotics / prebiotics

The effects of a multispecies probiotic on migraine and markers of intestinal permeability–results of a randomized placebo-controlled study – N M de Roos – European Journal of Clinical Nutrition

Phages and viruses

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis – Tanmoy Chakraborty – Virulence

Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race – Amelia McKitterick – bioRxiv

Bioinformatics

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea – Johannes Alneberg – Scientific Data

Bacteria & Art

The Beautiful World of Bacteria

 

July 30, 2018

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Today’s digest features the microbiomes of a XVIII century mummy (Krásna Hôrka, Slovakia), an interesting initiative out of Belgium (Disbiome, a database of microbiota-disease associations), exciting news from Kamagata lab about improved culturing of environmental samples, promising findings on gut bacteria byproduct that protects against Salmonella, and much more. Happy reading!

Human microbiome

*Disbiome database: linking the microbiome to disease – Yorick Janssens – BMC Microbiol.

*The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment – Lucia Kraková – Environ Microbiol.

Gut microbiome

*A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection – Amanda Jacobson – Cell Host & Microbe

Simulation and modeling of dietary changes in the infant gut microbiome – Daniel Medina – FEMS Microbiol Ecol.

Human gut bacteria as potent class I histone deacetylase inhibitors in vitro through production of butyric acid and valeric acid – Samantha Yuille – PLoS One

Review: An update on the role of gut microbiota in chronic inflammatory diseases, and potential therapeutic targets – Bobbi Laing – Expert Rev Gastroenterol Hepatol.

A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode – Annamaria Painold – Bipolar Disord.

Review: The Gut-Brain Axis, the Human Gut Microbiota and Their Integration in the Development of Obesity – Edward Bliss – Front Physiol.

Fungal dysbiosis in cirrhosis – Jasmohan S Bajaj – Hepatology

Urinary tract microbiome

The bacterial microbiota in first-void urine from men with and without idiopathic urethritis – Maria Frølund – PLoS One

Lung microbiome

Lower respiratory tract microbial composition was diversified in Pseudomonas aeruginosa ventilator-associated pneumonia patients – Xiaoling Qi – Respir Res.

Plant microbiome

Bacterial community assemblages in the rhizosphere soil, root endosphere and cyst of soybean cyst nematode-suppressive soil challenged with nematodes – Muzammil Hussain – FEMS Microbiology Ecology

Exploring plant-microbe interactions of the rhizobacteria Bacillus subtilis and Bacillus mycoides by use of the CRISPR-Cas9 system – Yanglei Yi – Environ Microbiol.

Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling – Garcia Joshua – Front Microbiol.

Water microbiome

Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater – Roland Wilhelm – Environ Microbiol.

Techniques

*Isolation of Previously Uncultured Slow-growing Bacteria by Using a Simple Modification in Preparation of Agar Media – Souichiro Kato – Applied and Environmental Microbiology

Review: The role of the gut microbiota on animal model reproducibility – Patricia Turner – Animal Model Exp.

Review: Environmental enrichment and mouse models: Current perspectives – Kathryn Bayn – Animal Model Exp.

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface – Marta Calatayud Arroyo – J Vis Exp.

Bioprinting microbial communities to examine interspecies interactions in
time and space – William Frederick Hynes – Biomed. Phys. Eng. Express

July 28, 2018

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Have a good weekend! For this Saturday, we have more than 60 articles! 

Including: A set of reviews about mother, delivery and neonate microbiome; relationship between microbiome and cancer and Alzheimer; microbiome in primate models, reviews about pathogens and more…

 

Human and General Microbiome

Review: Gut Mycobiota and Fungal Metabolites in Human Homeostasis – Izabella Mogilnicka – Current Drug Targets

Review: Dietary Protein and Muscle in Aging People: The Potential Role of the Gut Microbiome – Mary Ni Lochlainn – Nutrients

Review: The interplay between neutrophils and microbiota in cancer – Carolyne K. Smith – Journal of Leukocyte Biology

Review: Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut – Siavash Atashgahi – Frontiers in Physiology

Review: Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How? – Sharon Y. Geerlings – Microorganisms

Review: Considering gut microbiota disturbance in the management of Helicobacter pylori infection – Loris R. Lopetuso – Expert Review of Gastroenterology & Hepatology

Microbiome Analyses for Toxicological Studies – Jacquelynn Benjamino – Current Protocols in Toxicology

Editorial: Caesarean-Section and Neonatal Gut Microbiome: Short and Long Term Effects and New Targets for Early Prevention – Giannattasio A. – Annals of Nutrition and Metabolism

Review: C-section and the Neonatal Gut Microbiome Acquisition: Consequences for Future Health – Arboleya S. – Annals of Nutrition and Metabolism

Review: Birth Mode-Related Differences in Gut Microbiota Colonization and Immune System Development – Francino M.P.  – Annals of Nutrition and Metabolism

Review: Intervention for Dysbiosis in Children Born by C-Section – Francavilla R. – Annals of Nutrition and Metabolism

Review: Gut Microbiota Composition in Healthy Japanese Infants and Young Adults Born by C-Section – Nagpal R. – Annals of Nutrition and Metabolism

Review: Dysbiosis in Children Born by Caesarean Section – Salas Garcia M.C. – Annals of Nutrition and Metabolism

 

Human Gut

Association between Alzheimer’s Disease and Oral and Gut Microbiota: Are Pore Forming Proteins the Missing Link? – Aguayo, Sebastian –  Journal of Alzheimer’s Disease

Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma – Zhigang Ren – Gut

A Multi-omic Association Study of Trimethylamine N-Oxide – Ohad Manor – Cell Reports

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults – Chad W. MacPherson – Scientific Reports

Cost-effectiveness analysis of ribotype-guided fecal microbiota transplantation in Chinese patients with severe Clostridium difficile infection – Minghuan Jiang – PLoS ONE

Microbiota Quality and Mitochondrial Activity Link with Occurrence of Muscle Cramps in Hemodialysis Patients using Citrate Dialysate: A Pilot Study – Durand P.-Y. – Blood Purification

Gut microbiota, dietary intakes and intestinal permeability reflected by serum zonulin in women – S. Mörkl – European Journal of Nutrition

Analysis of the Enteric Microbiome: First Tentative Steps Towards a Comprehensive Work-up of Prostate Cancer? – Ilaria Cavarretta – European Urology

 

Human Respiratory Tract

Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients – Georgios D. Kitsios – Frontiers in Microbiology

Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients – Laura Iaffaldano – Scientific Reports

 

Newborn and Mother Microbiome

Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study – Naruaki Imoto – Journal of Perinatology

 

Human Urinary/Reproductive Tract

Endocervical and vaginal microbiota in South African adolescents with asymptomatic Chlamydia trachomatis infection – Christina Balle – Scientific Reports

Introduction: Microbes in the female reproductive function, do they matter? – Carlos Simon – Fertility and Sterility

 

Human Skin

Relations between epidermal barrier dysregulation and staphylococci-dominated microbiome dysbiosis in atopic dermatitis – Can Altunbulakli – Atopic Dermatitis Research

 

Animal Microbiome / Animal Experiments

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – Scientific Reports

Diarrhea-Associated Intestinal Microbiota in Captive Sichuan Golden Snub-Nosed Monkeys (Rhinopithecus roxellana) – Hui Zhu – Microbes and Environments

An orally administered oral pathobiont and commensal have comparable and innocuous systemic effects in germ-free mice – Keisuke Sato – Journal of Periodontal Disease

Effects of dietary tryptophan supplementation in the acetic acid-induced colitis mouse model – Shuai Chen – Food and Nutrition

Early-life stress leads to sex-dependent changes in pubertal timing in rats that are reversed by a probiotic formulation – Caitlin S. M. Cowan – Developmental Psychobiology

A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway – Emilie U. Andersen-Ranberg – Microorganisms

Gut microbiota influences Alzheimer’s disease pathogenesis by regulating acetate in Drosophila model – Yan Kong – Future Microbiology

Elevated Seawater Temperatures Decrease Microbial Diversity in the Gut of Mytilus coruscus – Yi-Feng Li – Frontiers in Physiology

Microbiome-metabolomics Analysis of the Impacts of Long-term Dietary Advanced Glycation End Products Consumption on the C57BL/6 Mouse Fecal Microbiota and Metabolite Perturbation – Wanting Qu – Journal of Agricultural and Food Chemistry

Papio spp. Colon microbiome and its link to obesity in pregnancy – XuanJi Li – Journal of Medical Primatology

Combination of Aronia, Red Ginseng, Shiitake Mushroom and Nattokinase Potentiated Insulin Secretion and Reduced Insulin Resistance with Improving Gut Microbiome Dysbiosis in Insulin Deficient Type 2 Diabetic Rats – Hye Jeong Yang – Nutrients

Short and long-term effects of a synbiotic on clinical signs, the fecal microbiome, and metabolomic profiles in healthy research cats receiving clindamycin: a randomized, controlled trial – Jacqueline C. Whittemore​ – PeerJ

Lactobacillus plantarum ZDY04 exhibits a strain-specific property of lowering TMAO via the modulation of gut microbiota in mice – Liang Qiu – Food and Function

Diet induced maternal obesity affects offspring gut microbiota and persists into young adulthood – Yanjie Guo – Food and Function

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity – Xue-Song Zhang – eLife

Clostridium butyricum Attenuates Chronic Unpredictable Mild Stress-Induced Depressive-Like Behavior in Mice via the Gut-Brain Axis – Jing Sun – Journal of Agricultural and Food Chemistry

 

Food Microbiome

Analysis of Fish Commonly Sold in Local Supermarkets Reveals the Presence of Pathogenic and Multidrug-Resistant Bacterial Communities – Ama Okyere – Microbiology Insights

Short communication: Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE – Vesna Milanović – International Journal of Food Microbiology

Acyl-homoserine-lactones receptor LuxR of Shewanella baltica involved in the development of microbiota and spoilage of refrigerated shrimp – Jinxin Jie – Journal of Food Science and Technology

 

Beneficial Microbes and Compounds

Review: Probiotics against airway allergy: host factors to consider – Irina Spacova – Disease Model and Mechanisms

Abundance of gut Prevotella at baseline and metabolic response to barley prebiotics – Jonna Sandberg – European Journal of Nutrition

Letter: Effect of Metformin or Chinese Herbal Formula in Patients with Type 2 Diabetes Mellitus and Hyperlipidemia: A Reassessment – Venu Gopal Jonnalagadda – mBio

Coreopsis Tinctoria Modulates Lipid Metabolism by Decreasing Low-Density Lipoprotein and Improving Gut Microbiota – Ren Z. – Cellular Physiology and Biochemistry

 

Pathogen Research

Review: Recent insights into Shigella – Stephen Baker – Current Opinion in Infectious Diseases

Review: Cholera: recent updates – Ana A. Weil – Current Opinion in Infectious Diseases

 

Soil and Plant Microbiome

Microbial community assembly differs across minerals in a rhizosphere microcosm – Thea Whitman – Environmental Microbiology

Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome – Eric J. N. Helfrich – Nature Microbiology

Vineyard under-vine floor management alters soil microbial composition, while the fruit microbiome shows no corresponding shifts – Ming-Yi Chou – Scientific Reports

 

Methods

Methodology: A two-stage microbial association mapping framework with advanced FDR control – Jiyuan Hu – Microbiome

A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods – Jyotsna Talreja Wassan – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Generalized Linear Models with Linear Constraints for Microbiome Compositional Data – Jiarui Lu – Biometrics

Analyzing differences between microbiome communities using mixture distributions – Konstantin Shestopaloff – Statistics in Medicine

Pathomimetic modeling of human intestinal diseases and underlying host-gut microbiome interactions in a gut-on-a-chip – Woojung Shin – Methods in Cell Biology

 

Other

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems – Magdalena Calusinska – Biotechnology for Biofuels

 

July 27, 2018

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Diversity and stability of the oyster microbiota, earthworm gut bacteria contribute to silicon acquisition by maize, metabolic function and composition of the gut microbiota regulated by IgA, a review on engineering live biotherapeutics.

General microbiome

Review: Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity – Tanel Ozdemir – Cell Systems

Pre-print: Fungal chromatin mapping identifies BasR, as the regulatory node of bacteria-induced fungal secondary metabolism – Juliane Fischer – bioRxiv

Multi-site human microbiome

Review: The Gut Microbiome as a Major Regulator of the Gut-Skin Axis – Iman Salem – Frontiers in Microbiology

Human respiratory microbiome

Identifying aerosolized cyanobacteria in the human respiratory tract: A proposed mechanism for cyanotoxin-associated diseases – Dominic N Facciponte – Science of the Total Environment

Human skin microbiome

Minor taxa in human skin microbiome contribute to the personal identification – Hikaru Watanabe – PLOS ONE

Animal experiments

Intestinal Microbiota Disruption Reduces Regulatory T Cells and Increases Respiratory Viral Infection Mortality Through Increased IFNγ Production – Mitchell H Grayson – Frontiers in Immunology

IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria – Akira Nakajima – Journal of Experimental Medicine

Animal microbiome

Fecal bacterial communities from Mediterranean loggerhead sea turtles (Caretta caretta) – Elena Biagi – Environmental Microbiology Reports

Pre-print: Diversity and stability of microbiota are key factors associated to healthy and diseased Crassostrea gigas oysters – Camille Clerissi – bioRxiv

Plant, root, and soil microbiome

Earthworm gut bacteria increase silicon bioavailability and acquisition by maize – Lin Hu – Soil Biology and Biochemistry

Digging mammals contribute to rhizosphere fungal community composition and seedling growth – Shannon J Dundas – Biodiversity and Conservation

Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard – Bowen Liang – Microbiological Research

Water and extremophile microbiome

Microbiome functioning depends on individual and interactive effects of the environment and community structure – Chloé Orland – The ISME Journal

Microbes in space

Pre-print: Water quality and microbial load: a double-threshold identification procedure intended for space applications – Stefano Amalfitano – bioRxiv

Food microbiology

A low FODMAP diet is associated with changes in the microbiota and reduction in breath hydrogen but not colonic volume in healthy subjects – Tim J Sloan – PLOS ONE

Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE – Vesna Milanović – International Journal of Food Microbiology

Probiotics/prebiotics

Review: Adipose tissue inflammation and metabolic syndrome. The proactive role of probiotics – Sebastian Torres – European Journal of Nutrition

Techniques

Recognizing the reagent microbiome – Marcus C de Goffau – Nature Microbiology

More microbes

Metabolically engineered Corynebacterium glutamicum for bio-based production of chemicals, fuels, materials, and healthcare products – Judith Becker – Metabolic Engineering

Pre-print: A dual motif mediates outer-membrane translocation and packing of glycosidases into Bacteroides Outer Membrane Vesicles – Ezequiel Valguarnera – bioRxiv

The outer membrane is an essential load-bearing element in Gram-negative bacteria – Enrique R Rojas – Nature

Microbes in the news

Viruses cooperate to defeat bacteria – Aude Bernheim – Nature

July 26, 2018

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Altered intestinal phage populations in murine colitis, degradation of aromatic compounds by the wheat rhizosphere, barley products change the gut microbiota composition of rats.

General microbiome

Defining microbiome function – Jonathan L Klassen – Nature Microbiology

Electroactive microorganisms and microbial consortia – Enrico Marsili – Bioelectrochemistry

Humanome Versus Microbiome: Games of Dominance and Pan-Biosurveillance in the Omics Universe – Manousos E Kambouris – OMICS: A Journal of Integrative Biology

Human respiratory microbiome

The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens – Sophie Edouard – European Journal of Clinical Microbiology & Infectious Diseases

Human oral microbiome

Paired analysis of the microbiota between surface tissue swabs and biopsies from pediatric patients undergoing adenotonsillectomy – James Johnston – International Journal of Pediatric Otorhinolaryngology

Bacterial endotoxins and microorganisms in the oral cavities of patients on cancer therapy – J Mathews – Microbial Pathogenesis

Human gut microbiome

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface – Marta Calatayud Arroyo – Journal of Visualized Experiments

Altered gut microbiota profile in patients with generalized anxiety disorder – Hai-yin Jiang – Journal of Psychiatric Research

Animal experiments

Beneficial changes of gut microbiota and metabolism in weaned rats with Lactobacillus acidophilus NCFM and Bifidobacterium lactis Bi-07 supplementation – Mengxia Wang – Journal of Functional Foods

Diammonium Glycyrrhizinate Protects against Non-Alcoholic Fatty Liver Disease in mice through modulation of gut microbiota and restoring intestinal barrier – Yun Li – Molecular Pharmaceuticals

Animal microbiome

Altering the Gut Microbiome of Cattle: Considerations of Host-Microbiome Interactions for Persistent Microbiome Manipulation – Brooke A Clemmons – Microbial Ecology

Plant, root, and soil microbiome

Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest – Julia C Haas – Soil Biology and Biochemistry

Diversity and Co-occurrence Patterns of Soil Bacterial and Fungal Communities in Seven Intercropping Systems – Sen Li – Frontiers in Microbiology

Metatranscriptome Analysis Deciphers Multifunctional Genes and Enzymes Linked With the Degradation of Aromatic Compounds and Pesticides in the Wheat Rhizosphere – Dhananjaya P Singh – Frontiers in Microbiology

Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population – Lucas Dantas Lopes – Environmental Microbiology

Water and extremophile microbiome

Comparative microbial communities in tidal flats sediment on Incheon, South Korea – Hye Jin Choi – The Journal of General and Applied Microbiology

Food microbiology

Fucoidan alleviates dyslipidemia and modulates gut microbiota in high-fat diet-induced mice – Min Liu – Journal of Functional Foods

Polyphenolic derivatives from mango (Mangifera Indica L.) modulate fecal microbiome, short-chain fatty acids production and the HDAC1/AMPK/LC3 axis in rats with DSS-induced colitis – Hyemee Kim – Journal of Functional Foods

Jaboticaba berry peel intake increases short chain fatty acids production and prevent hepatic steatosis in mice fed high-fat diet – Ângela Giovana Batista – Journal of Functional Foods

Bioavailability of Isoflavone Metabolites After Korean Fermented Soybean Paste (Doenjang) Ingestion in Estrogen‐Deficient Rats – Da-Hye Lee – Journal of Food Science

Barley Products of Different Fibre Composition Selectively Change Microbiota Composition in Rats – Cristina Teixeira – Molecular Nutrition & Food Research

Probiotics/prebiotics

A soy-based probiotic drink modulates the microbiota and reduces body weight gain in diet-induced obese mice – Juliana de Carvalho Marchesin – Journal of Functional Foods

Probiotics in cystic fibrosis patients: A double blind crossover placebo controlled study: Pilot study from the ESPGHAN Working Group on Pancreas/CF – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Probiotics in Pediatric Gastroenterology: Emerging Indications – Elena Scarpato – Journal of Clinical Gastroenterology

Phages and viruses

Murine colitis reveals a disease-associated bacteriophage community – Breck A Duerkop – Nature Microbiology

Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins – Alexander P Hynes – Nature Communications

Bioinformatics

A marginalized two-part Beta regression model for microbiome compositional data – Haitao Chai – PLOS Computational Biology

Metabolomics

Simultaneous HS-SPME GC-MS determination of short chain fatty acids, trimethylamine and trimethylamine N-oxide for gut microbiota metabolic profile – Jessica Fiori – Talanta

Techniques

Balances: a New Perspective for Microbiome Analysis – J Rivera-Pinto – mSystems

Coupling magnetic-nanoparticle mediated isolation (MMI) and stable isotope probing (SIP) for identifying and isolating the active microbes involved in phenanthrene degradation in wastewater with higher resolution and accuracy – Jibing Li – Water Research

July 25, 2018

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Today’s digest consists of opinion paper from European MyNewGut project, review article on gut microbiota dysbiosis, and meta-analysis to find association between antibiotic associated microbiota perturbation and childhood obesity. Also includes application of contraceptive rings and probiotic capsules to increase vaginal lactobacilli, and how preprint publishing could create confusion in public journalism!

General microbiome

Towards microbiome-informed dietary recommendations for promoting metabolic and mental health: Opinion papers of the MyNewGut project – Yolanda Sanz – Clinical Nutrition

Review: The gut microbiota: A new target in the management of alcohol dependence? – Sophie Leclercq – Alcohol

Review: Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery – Michael Kriss – Current Opinion in Microbiology

Review: Environmental factors, gut microbiota, and colorectal cancer prevention – Mingyang Song – Clinical Gastroenterology and Hepatology

Review: The association between antibiotic use in infancy and childhood overweight or obesity: a systematic review and meta-analysis – SA Miller – Obesity Reviews

Multi-site human microbiome

Unique subgingival microbiota associated with periodontitis in cirrhosis patients – Anders Jensen – Scientific Reports

Human respiratory microbiome

A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota – Katrina Kalantar – bioRxiv

Human vaginal microbiome

Contraceptive rings promote vaginal lactobacilli in a high bacterial vaginosis prevalence population: A randomised, open-label longitudinal study in Rwandan women – Tania Crucitti – PlosOne

Comparative phase I randomized open-label pilot clinical trial of Gynophilus® (Lcr regenerans®) immediate release capsules versus slow release muco-adhesive tablets – Caroline Dausset – European Journal of Clinical Microbiology and Infectious Diseases

Human gut microbiome

Association Between Intestinal Microbiota Collected at Hospital Admission and Outcomes of Patients with Cirrhosis – Jasmohan S Bajaj – Clinical Gastroenterology and Hepatology

Animal experiments

Butyrate regulates inflammatory cytokine expression without affecting oxidative respiration in primary astrocytes from spontaneously hypertensive rats – Tao Yang – Physiological Reports

Plant, root, and soil microbiome

Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA – Katerina Papp – The ISME Journal

Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil – Gylaine VT Tchakounte – Microbiological Research

Water and extremophile microbiome

Effects of mercury addition on microbial community composition and nitrate removal inside permeable reactive barriers – Kenly Hiller-Bittrolff – Environmental Pollution

Food microbiology

Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems – Clemence Defois – Scientific Reports

Polyol-producing lactic acid bacteria isolated from sourdough and their application to reduce sugar in a quinoa-based milk substitute – Stephanie Jeske – International Journal of Food Microbiology

Probiotics / prebiotics

Probiotics in cystic fibrosis patients: A double blind crossover placebo controlled study: Pilot study from the ESPGHAN Working Group on Pancreas/CF – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Phages and viruses

Parvovirus Minute Virus of Mice Interacts with Sites of Cellular DNA Damage to Establish and Amplify its Lytic Infection – Kinjal Majumder – eLife

Techniques

Review: The evolving interface between synthetic biology and functional metagenomics – Eric Van der Helm – Nature Chemical Biology

Targeted analysis of microbial-generated phenolic acid metabolites derived from grape flavanols by gas chromatography-triple quadrupole mass spectrometry – Eileen Carry – Journal of Pharmaceutical and Biomedical Analysis

Science, publishing, and career 

Preprints could promote confusion and distortion – Nature News

‘Science-adjacent’ conferences and why they matter – Nature News

Tulika’s non-microbiology picks

Metformin inhibits gluconeogenesis via a redox-dependent mechanism in vivo – Anila K Madiraju – Nature Medicine

 

23 July, 2018

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Today’s digest includes exciting Microbiome events and brilliant papers on animal microbiomes. Lastly, research exploring the war on gluten.

Events

Microbiome X Regulation 1 Panel discussion on navigating the FDA

Introduction to the 4th International Symposium on Gluten-Free Cereal Products and Beverages.

General Microbiome

Antibiotic Scars Left on the Gut Microbiota from the Stringent Response. Yi H. Trends in Microbiology

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Hua ZS. Nature Communications

Genomic Characterization of Sulphite Reducing Bacteria Isolated From the Dairy Production Chain.Doyle CJ. Frontiers in Microbiology.

How Microbial Aggregates Protect against Nanoparticle Toxicity.Tang J. Trends in Biotechnology.

Inhibition of microbial spoilage of grass carp (Ctenopharyngodon idellus) fillets with a chitosan-based coating during refrigerated storage. Yu D. International Journal of Food Microbiology

Gut Microbiome

The gut microbiome and irritable bowel syndrome. Menees S. F1000Research

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism.Zarrinpar A. Nature Communications

Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Zhang X. Nature Communications

Techniques

A rapid PCR-based method to discriminate Macrococcus caseolyticus and Macrococcus canis from closely-related Staphylococcus species based on the ctaC gene sequence. Mazhar S. Journal of Microbiological Methods

MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification. Vervier K. Methods in Molecular Biology

Soil, Water, and Air Microbiome

Influence of new agromining cropping systems on soil bacterial diversity and the physico-chemical characteristics of an ultramafic soil. Saad RF. Science of the Total Environment

<i>Pseudomonas chlororaphis</i> produces multiple R-tailocin particles that broaden the killing spectrum and contribute to persistence in rhizosphere communities.Dorosky RJ. Applied and Environmental Microbiology

REVIEW: Microbial diversity and biogeography in Arctic soils.Malard LA. Environmental Microbiology Reports.

Impact of brine and antiscalants on reef-building corals in the Gulf of Aqaba – Potential effects from desalination plants.Petersen KL. Water Research

Mapping the Bacterial Community in Digboi Oil Refinery, India by High-Throughput Sequencing Approach. Dasgupta A.  Current Microbiology.

Chemical-, site-, and taxa-dependent benthic community health in coastal areas of the Bohai Sea and northern Yellow Sea: A sediment quality triad approach. Khim JS. Science of the Total Environment.

Animal Experiments and Microbiome

Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda. Zeng Y. Frontiers in Microbiology

REVIEW:The gut microbiota of wild rodents: Challenges and opportunities. Viney M. Laboratory Animals

Genome-wide association studies of inflammatory bowel disease in German shepherd dogs. Peiravan A. PLoS One.

Effects of Rodent Diet Choice and Fiber Type on Data Interpretation of Gut Microbiome and Metabolic Disease Research.Pellizzon MA. Current Protocols in Toxicology

Non-Microbiology Hot Pick

The war on gluten. Servick K. Science.

 

 

July 20, 2018

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Happy Friday! Today’s digest includes the bacterial diversity of bat guano, cyanobacterial blooms in oil-contaminated sediments, and the shrimp gut microbiome. Also, an NPR interview with astrophysicist Adam Frank about how to be a savvy consumer of science news.

Pregnancy and early life

Maternal peripartum antibiotic exposure and the risk of postpartum depression – Jordan R. Murphy – Research in Nursing and Health

Review: Breast milk, formula, the microbiome and overweight – Elisabetta Mueller – Nature Reviews Endocrinology

Human vaginal microbiome

Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome – Somaieh Afiuni-Zadeh – Scientific Reports

Human gut microbiome

Review: The Gut Microbiota and Healthy Aging: A Mini-Review – Sangkyu Kim – Gerontology

Animal experiments

Western diet feeding influences gut microbiota profiles in apoE knockout mice – Baoning Liu – Lipids in Health and Disease

Animal microbiome

Bacterial diversity of bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines: A first report on the metagenome of Philippine bat guano – Marian P. De Leon – PLoS One

Disease outbreak accompanies the dispersive structure of shrimp gut bacterial community with a simple core microbiota – Zhiyuan Yao – AMB Express

In ovo microbial communities: a potential mechanism for the initial acquisition of gut microbiota among oviparous birds and lizards – Brian K. Trevelline – Biology Letters

Plant, root, and soil microbiome

Plant diversity and density predict belowground diversity and function in an early successional alpine ecosystem – Dorota L. Porazinska – Ecology

Water and extremophile microbiome

Cyanobacterial blooms in oil-contaminated subtidal sediments revealed by integrated approaches – Cuixiao Xie – Environmental Microbiology Reports

ddPCR applied on archived Continuous Plankton Recorder samples reveals long-term occurrence of class 1 integrons and a sulphonamide resistance gene in marine plankton communities – Andrea Di Cesare – Environmental Microbiology Reports

Structure of Microbial Communities of the Sediments of Alkaline Transbaikalia Lakes with Different Salinity – S. V. Zaitseva – Microbiology

Diversity of Heterotrophic Halophilic Bacteria Isolated from Coastal Solar Salterns, Bulgaria and Their Ability to Synthesize Bioactive Molecules with Biotechnological Impact – I. Boyadzhieva – Microbiology

Diversity of Prokaryotes in Planktonic Communities of Saline Sol-Iletsk lakes (Orenburg Oblast, Russia) – E. A. Selivanova – Microbiology

Pre-Print: Genetic evidence for two carbon fixation pathways in symbiotic and free-living bacteria: The Calvin-Benson-Bassham cycle and the reverse tricarboxylic acid cycle – Maxim Rubin Blum – BioRxiv

Science, publishing, and career

Track the fate of postdocs to help the next generation of scientists – Nature

How To Be A Savvy Consumer Of Science News – NPR’s All Things Considered

Non-microbiology picks

Jupiter has 10 more moons we didn’t know about — and they’re weird – Nature

July 19, 2018

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An all-around Digest today features newly discovered Wolbachia in Anopheles mosquitoes that can lead to probiotic therapy for malaria, a novel mechanism for the plants to control rhizosphere microbiota, growth and defense, and fascinating art produced entirely by microbes. Enjoy!

General microbiology

Review: Large noncoding RNAs in bacteria – Kimberly A. Harris & Ronald R. Breaker – Microbiology spectrum

Bioremediation and microbial metabolism of benzo(a)pyrene – E M Ostrem Loss & J H Yu – Molecular Microbiology

Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses – Fábio Campioni et al. – Scientific Reports

Preprint: Host adaptation and convergent evolution increases antibiotic resistance without loss of virulence in a major human pathogen – Alicia Fajardo-Lubian et al. – bioRxiv

Pregnancy and early life

Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester – María Florencia Zacarías et al. – PLoS One

Mini-Review: Antibiotics and lactation: An overview of relative infant doses and a systematic assessment of clinical studies – J.J. van Wattum et al. – Basic & Clinical Pharmacology & Toxicology

Human respiratory microbiome

Characterisation of the nasal microbiota in granulomatosis with polyangiitis – Rennie L Rhee et al. – Annals of the Rheumatic Diseases

Human skin microbiome

Human skin commensals augment Staphylococcus aureus pathogenesis – Emma Boldock et al. – Nature Microbiology

Human oral microbiome

Unique subgingival microbiota associated with periodontitis in cirrhosis patients – Anders Jensen et al. – Scientific Reports

Human gut microbiome

ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages – Chris M Rands et al. – Environmental Microbiology

Review: Recent advances in probiotics as live biotherapeutics against gastrointestinal diseases – Kota RK et al. – Current Pharmaceutical Design

Review: Microbiota–Host Crosstalk: A Bridge Between Cardiovascular Risk Factors, Diet, and Cardiovascular Disease – Jacques Amar – American Journal of Hypertension

Human built environment microbiome

β-Lactam and Fluoroquinolone-Resistant Enterobacteriaceae Recovered from the Environment of Human and Veterinary Tertiary Care Hospitals – Dimitria A. Mathys et al. – Vector-Borne and Zoonotic Diseases

Metabolomics

Quantitative metabolomics comparison of traditional blood draws and TAP capillary blood collection – Alexis Catala et al. – Metabolomics

Functional genetic discovery of enzymes using full-scan mass spectrometry metabolomics – Amy A. Caudy et al. – Biochemistry and Cell Biology

Animal experiments

Dietary L-Arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut microbiota in Broiler Chickens Challenged by Clostridium perfringens – Beibei Zhang et al. – Frontiers in Microbiology

Dissertation: Recent Evolution of Host Genetic Control of Microbiota in Cichlid Fishes and Humans – Kaitlin Patricia Coyle – North Carolina State University

Mouse: Gut Microbiota-Stimulated Innate Lymphoid Cells Support b-Defensin 14 Expression in Pancreatic Endocrine Cells, Preventing Autoimmune Diabetes – Michela Miani et al. – Cell Metabolism

Mouse: In vitro probiotic properties of vaginal Lactobacillus fermentum MG901 and Lactobacillus plantarum MG989 against Candida albicans – Chang-Ho Kang et al. – European Journal of Obstetrics & Gynecology and Reproductive Biology

Betaine Improves Intestinal Functions by Enhancing Digestive Enzymes, Ameliorating Intestinal Morphology, and Enriching Intestinal Microbiota in High-salt stressed Rats – Haichao Wang et al. – Nutrients

The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract – Xiaoxi B. Lin et al. – The ISME Journal

Differences Between the Intestinal Lumen Microbiota of Aberrant Crypt Foci (ACF)-Bearing and Non-bearing Rats – Xiuli Xiao et al. – Digestive Diseases and Sciences

Mouse: A selective gut bacterial bile salt hydrolase alters host metabolism – Lina Yao et al. – eLife

Diabetes-Associated Alterations in the Cecal Microbiome and Metabolome are Independent of Diet or Environment in the UC Davis Type 2-Diabetes Mellitus Rat Model – Brian D. Piccolo et al. – American Journal of Physiology-Endocrinology and Metabolism

Animal microbiome

Effects of dietary energy levels on rumen bacterial community composition in Holstein heifers under the same forage to concentrate ratio condition – Yanliang Bi et al. – BMC Microbiology

The cecal microbiome of commercial broiler chickens varies significantly by season – Brian B Oakley et al. – Poultry Science

American beaver: Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome – Zachary Armstrong et al. – The ISME Journal

High Gut Microbiota Diversity Provides Lower Resistance against Infection by an Intestinal Parasite in Bumblebees – Kathrin Näpflin & Paul Schmid-Hempel – The American Naturalist

Effect of Dietary Fructooligosaccharide (FOS) Supplementation on Ileal Microbiota in Broiler Chickens – Yue Shang et al. – Poultry Science

Arrival date and microorganisms in barn swallows – Z. Al Rubaiee et al. – Journal of Avian Biology

* Preprint: Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa – Claire L Jeffries et al. – bioRxiv

Plant, root and soil microbiome

Metabolomics analysis of Cajanus cajan L. seedlings unravelled amelioration of stress induced responses to salinity after halopriming of seeds – Sabarni Biswas, Asok K. Biswas & Bratati De – Plant Signaling & Behavior

* Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota – Lingfei Hu et al. – Nature Communications

Water and extremophile microbiome

Abstract: Exploring the relative importance of surficial cyanobacteria communities versus physical, chemical and bioloigical processes at depth on sulfur cycling in two microbial mat environments – Maya Gomes et al. – Caltech Authors

Temperature driven changes in benthic microbial diversity influences biogeochemical cycling in coastal sediments – Natalie Hicks et al. – Frontiers in Microbiology

Resistance and Recovery of Methane-Oxidizing Communities depends on Stress Regime and History; a Microcosm Study – Henri van Kruistum et al. – Frontiers in Microbiology

Enterococci Concentrations in a Coastal Ecosystem are a Function of Fecal Source Input, Environmental Conditions, and Environmental Sources – Derek Rothenheber & Stephen Jones – Applied and Environmental Microbiology

Agulhas Current properties shape microbial community diversity and potential functionality – Sandra Phoma et al. – Scientific Reports

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N. Enke et al. – Nature Communications

Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assays – Manel Ben Abdallah et al. – Extremophiles

Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size – Laura Frère et al. – Environmental Pollution

Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative – Mark V. Brown et al. – Scientific Data

Microbes in space

The influence of bioregenerative life‐support system (BLSS) dietary structure and lifestyle on the gut microbiota: A 105‐day ground‐based space simulation in Lunar Palace 1 – Zikai Hao et al. – Environmental Microbiology

Probiotics, Prebiotics and Synbiotics

Harms Reporting in Randomized Controlled Trials of Interventions Aimed at Modifying Microbiota: A Systematic Review – Aïda Bafeta et al. – Annals of Internal Medicine

Lactobacillus acidophilus and Clostridium butyricum ameliorate colitis in murine by strengthening the gut barrier function and decreasing inflammatory factors – Y. Wang et al. – Beneficial Microbes

Technology

Review: Interkingdom microbial consortia mechanisms to guide biotechnological applications – Shu Zhang et al. – Microbial Biotechnology

Establishing a mucosal gut microbial community in vitro using an artificial simulator – LinShu Liu et al. – PLoS One

Bioinformatics

Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome – Jun Miyoshi et al. – PeerJ

Preprint: Macroecological relationships in the dynamics of gut microbiota – Brian W. Ji et al. – bioRxiv

Microbes in the news

Designer microbiomes – Alfie Gleeson & Abigail Sawyer – BioTechniques

* You need to see this award-winning artwork made entirely from microbes – Irish News

Disgusting Things You Never Knew Your Pets Are Bringing Into Your Home – Amanda Harding – Cheat Sheet

Scientific education

Preprint: Long term impact of intensive post graduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course – Sarah Ly et al. – bioRxiv

July 13, 2018

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Comparing affects of host physiology and diet on primate gut microbiomes, oral bacterial and fungal dysbiosis in people with HIV, contribution of non-fermentable dietary fiber to prevention of autoimmune neurological disease via the gut microbiota.

General microbiome

Tools for engineering coordinated system behaviour in synthetic microbial consortia – Nicolas Kylilis – Nature Communications

Human oral microbiome

Dysbiosis in the oral bacterial and fungal microbiome of HIV-infected subjects is associated with clinical and immunologic variables of HIV infection – Pranab K Mukherjee – PLOS ONE

Human gut microbiome

Dietary non-fermentable fiber prevents autoimmune neurological disease by changing gut metabolic and immune status – Kerstin Berer – Scientific Reports

Physiology and central carbon metabolism of the gut bacterium Prevotella copri – Thomas Franke – Molecular Microbiology

Chemotaxis of Escherichia coli to major hormones and polyamines present in human gut – Joana G Lopes – The ISME Journal

Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms – Omar Youssef – Digestive Diseases and Sciences

Animal experiments

Of Mice and Men . . . and Microbes: Conclusions and Cautions from a Murine Study of the Lung Microbiome and Microbiome-Immune Interactions – John E McGinniss – American Journal of Respiratory and Critical Care Medicine

Modulation of gut microbiota by mulberry fruit polysaccharide treatment of obese diabetic db/db mice – Chun Chen – Food & Function

Evidence for the Role of the Cecal Microbiome in Maintenance of Immune Regulation and Homeostasis – Preeti Chhabra – Annals of Surgery

Human Milk Fortification with Bovine Colostrum Is Superior to Formula‐Based Fortifiers to Prevent Gut Dysfunction, Necrotizing Enterocolitis, and Systemic Infection in Preterm Pigs – Jing Sun – Journal of Parenteral & Enteral Nutrition

Fecal Microbiota Transplantation Is Effective in Relieving Visceral Hypersensitivity in a Postinfectious Model – Tao Bai – BioMed Research International

Animal microbiome

First report of foregut microbial community in proboscis monkeys: Are diverse forests a reservoir for diverse microbiomes? – Takashi Hayakawa – Environmental Microbiology Reports

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes – Katherine R Amato – The ISME Journal

The composition of the perinatal intestinal microbiota in cattle – Mohammad Jaber Alipour – Scientific Reports

Metagenomic evaluation of the effects of storage conditions on the bacterial microbiota of oysters Crassostrea gasar (Adanson, 1757) – Antonio Ostrensky – Journal of Applied Microbiology

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus – Inga Reich – Scientific Reports

A Robust Noninvasive Approach to Study Gut Microbiota Structure of Amphibian Tadpoles by Feces – Xiaowei Song – Herpetology Research

Plant, root, and soil microbiome

Isolation and characterization of two phosphate-solubilizing fungi from rhizosphere soil of moso bamboo and their functional capacities when exposed to different phosphorus sources and pH environments – Yang Zhang – PLOS ONE

Water and extremophile microbiome

Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits – Yuchen Han – Scientific Reports

Food microbiology

Changes in Quality and Microbial Succession of Lightly Salted and Sugar-Salted Blunt Snout Bream (Megalobrama amblycephala) Fillets Stored at 4°C – Yan Li – Journal of Food Protection

Review: Novel approaches for Chemical and Microbiological shelf life extension of cereal crops – Marcus Schmidt – Critical Reviews in Food Science and Nutrition

Probiotics/prebiotics

The short-term impact of probiotic consumption on the oral cavity microbiome – Erik Dassi – Scientific Reports

Bioinformatics

The evolutionary signal in metagenome phyletic profiles predicts many gene functions – Vedrana Vidulin – Microbiome

More microbes

Pre-print: Listeria monocytogenes cell-to-cell spread in epithelia is heterogeneous and dominated by rare pioneer bacteria – Fabian E Ortega – bioRxiv

Microbes in the news

Gut microbiota: a new way to take your vitamins – João Carlos Gomes-Neto – Nature Reviews Gastroenterology & Hepatology