Category Archives: Human respiratory

August 9, 2018

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Horizontal gene transfer in microbiomes, metabolic study of the microbiota isolated from the camel rumen, a review on the bacteriophage virome in IBD.

General microbiome

Review: Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives – Rafael Pinilla-Redondo – Plasmid

Review: Learning from bacterial competition in the host to develop antimicrobials – Manuela Raffatellu – Nature Medicine

Pregnancy and early life

Early life colonization of the human gut: microbes matter everywhere – Katri Korpela – Current Opinion in Microbiology

Human respiratory microbiome

Determinants of the Nasal Microbiome: Pilot Study of Effects of Intranasal Medication Use – Vijay R Ramakrishnan – Allergy & Rhinology

Human skin microbiome

Sensitive scalp is associated with excessive sebum and perturbed microbiome – Li Ma – Journal of Cosmetic Dermatology

Animal experiments

Effects of host genetics and environmental conditions on fecal microbiota composition of pigs – Tereza Kubasova – PLOS ONE

Animal microbiome

A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation – Javad Gharechahi – Biotechnology for Biofuels

Plant, root, and soil microbiome

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota – Allen Van Deynze – PLOS Biology

Brazilian Ironstone Plant Communities as Reservoirs of Culturable Bacteria With Diverse Biotechnological Potential – Washington L Caneschi – Frontiers in Microbiology

Water and extremophile microbiome

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change – Trine Markussen – Environmental Microbiology

Pre-print: Resource diversity structures aquatic bacterial communities – Mario E Muscarella – bioRxiv

Pre-print: Modular assembly of polysaccharide-degrading microbial communities in the ocean – Tim N Enke – bioRxiv

Food microbiology

Review: Bakery yeasts, a new model for studies in ecology and evolution – Belen Carbonetto – Yeast

Inferences from inventories of microbes in ecological vineyard settings – Hans-Josef Schroers – International Journal of Environmental Quality

Phages and viruses

Review: Bacteriophage virome in IBD – Clemens Thoma – Nature Reviews Gastroenterology and Hepatology

Bioinformatics

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis – Simon A Hardwick – Nature Communications

August 7, 2018

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Today’s Digest features a lot of soil and plant microbiome articles. Highlights include an opinion piece on hypothesis-driven microbiome research, a study on the spread of MCR-3 colistin resistance in China, and a consortium of bacteria to protect plants from pathogents.

General microbiology

** Are microbiome studies ready for hypothesis-driven research? – Anupriya Tripathi et al. – Current Opinion in Microbiology

Mitracarpus frigidus: A promising antifungal in the treatment of vulvovaginal candidiasis – Lara M. Campos et al. – Industrial Crops and Products

Isolation, growth, enzyme assay and identification via 16S rRNA full sequencing of cellulolytic microbes from Nepal for biofuel production – Binayak Raj Pandey et al. – Renewable Energy

Review (Uncorrected Proof): From hairballs to hypotheses – biological insights from microbial networks – Lisa Röttjers & Karoline Faust – FEMS Microbiology Reviews

Review: Barriers and opportunities in bio-based production of hydrocarbons – Yongjin J. Zhou, Eduard J. Kerkhoven & Jens Nielsen – Nature Energy

Antibiotic resistance

** Spread of MCR-3 Colistin Resistance in China: An Epidemiological, Genomic and Mechanistic Study – Yongchang Xu et al. – EBioMedicine

Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize – Qing-Lin Chen et al. – Science of The Total Environment

Carbapenem resistance in bacteria isolated from soil and water environments in Algeria – Katia DJENADI et al. – Journal of Global Antimicrobial Resistance

Human respiratory microbiome

Prospective study of timing and pattern of bacteria and viruses in the nasopharyngeal microbiome in a birth cohort – J.L.Mathew et al. – International Journal of Infectious Diseases

Human gut microbiome

Population changes of colon lumen microbiota in patients with chronic hepatitis C – A. Sydorchuk et al. – International Journal of Infectious Diseases

Multi-site human microbiome

Metagenomics of pigmented and cholesterol gallstones: the putative role of bacteria – S. H. Kose et al. – Scientific Reports

Food microbiology

Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process – Louise Vermote et al. – International Dairy Journal

Exploring core functional microbiota responsible for the production of volatile flavour during the traditional brewing of Wuyi Hong Qu glutinous rice wine – Zi-Rui Huang et al. – Food Microbiology

Review: Spoilage yeasts: What are the sources of contamination of foods and beverages? – A. Hernández et al. – International Journal of Food Microbiology

Animal experiments

Consumption of virgin coconut oil in Wistar rats increases saturated fatty acids in the liver and adipose tissue, as well as adipose tissue inflammation – Marianade Moura e Dias et al. – Journal of Functional Foods

Experimental microbial dysbiosis does not promote disease progression in SIV-infected macaques – Alexandra M. Ortiz et al. – Nature Medicine

Animal microbiome

Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract – Nicole A. Lloyd, Sylvie Nazaret & TamarBarkay – Marine Pollution Bulletin

Inferences of gut bacterial diversity from next-generation sequencing of 16S rDNA in deep sea blind ray – Benthobatis moresbyi – Tina Kollannoor Johny et al. – Ecological Genetics and Genomics

Characterization of the fecal microbiota of healthy horses – Holly L. Stewart et al. – American Journal of Veterinary Research

Plant, root and soil microbiome

Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems – Madangchanok Imchen et al. – Scientific Reports

Structural development and assembly patterns of the root-associated microbiomes during phytoremediation – Yanmei Chen et al. – Science of The Total Environment

A Method for Collecting Atmospheric Microbial Samples From Set Altitudes for Use With Next-Generation Sequencing Techniques to Characterize Communities – Allison M Spring et al. – Air, Soil and Water Research

Plant-microbe interactions drive denitrification rates, dissolved nitrogen removal, and the abundance of denitrification genes in stormwater control measures – Natalie R Morse et al. – Environmental Science & Technology

Short- and long-term warming alters soil microbial community and relates to soil traits – Hongying Yu et al. – Applied Soil Ecology

Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils – Yuqian Tang et al. – Science of The Total Environment

Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil – Kunkun Fan et al. – Soil Biology and Biochemistry

Influence of biochars on the accessibility of organochlorine pesticides and microbial community in contaminated soils – Neelum Ali et al. – Science of The Total Environment

Structure and activity of soil microbial communities in three Mediterranean forests – Felicia Grosso et al. – Applied Soil Ecology

Species-associated differences in the below-ground microbiomes of wild and domesticated Setaria – Srinivasa R. Chaluvadi & Jeff Bennetzen – Frontiers in Plant Science

Review: Processes that determine the interplay of root exudation, methane emission and yield in rice agriculture – D. Maurer et al. – Plant Biology

** Nutrient-and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen – Maureen Berg & Britt Koskella – Current Biology

Network Analyses Can Advance Above-Belowground Ecology – Kelly S.Ramirez et al. – Trends in Plant Science

Minireview: Microbial anaerobic Fe(II) oxidation – ecology, mechanisms and environmental implications – C Bryce et al. – Environmental Microbiology

Phages and viruses

No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster – Mang Shi et al. – Proceedings B

Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms – Shaun T. Cross et al. – Viruses

Investigation of recombination-intense viral groups and their genes in the Earth’s virome – Jan P. Meier-Kolthoff et al. – Scientific Reports

Microbes in the news

Endophytes: Study Shows GMO Corn Has No Impact On Good Bacteria – Science 2.0

August 3, 2018

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Happy Friday! Today’s digest includes the axolotl microbiome, carbon processing in thawing permafrost, and esterases discovered in hot spring microbial mats. In addition, there’s a Nature career column discussing why it’s not a ‘failure’ to leave academia. Enjoy!

Multi-site human microbiome

Optimizing body fluid recognition from microbial taxonomic profiles – Eirik Nataas Hanssen – Forensic Science International

Human oral microbiome

Dysbiosis of the buccal mucosa microbiome in primary Sjögren’s syndrome patients – Taco A van der Meulen – Rheumatology

Human respiratory microbiome

Comparison of the upper and lower airway microbiota in children with chronic lung diseases – Bushra Ahmed – PLoS One

Human vaginal microbiome

Review: Case for a role of the microbiome in gynecologic cancers: Clinician’s perspective – Ismail Mert – Journal of Obstetrics and Gynecology Research

Human gut microbiome

Enhanced preservation of the human intestinal microbiota by ridinilazole, a novel Clostridium difficile-targeting antibacterial, compared to vancomycin – Cheleste M. Thorpe – PLoS One

Animal experiments

Euphorbia kansui fry-baked with vinegar modulates gut microbiota and reduces intestinal toxicity in rats – DongjingJiang – Journal of Ethnopharmacology

Animal microbiome

Experimentally induced metamorphosis in highly regenerative axolotl (ambystoma mexicanum) under constant diet restructures microbiota – Turan Demircan – Scientific Reports

Response of host–bacterial colonization in shrimp to developmental stage, environment and disease – Jinbo Xiong – Molecular Ecology

Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes – Quinn S. McFrederick – Microbial Ecology

Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea) – Pavel V. Shelyakin – Scientific Reports

Effect of dietary fat to starch content on fecal microbiota composition and activity in dogs – Sofia Schauf – Journal of Animal Science

Primer: The importance of being persistent: The first true resident gut symbiont in Drosophila – Dali Ma – PLoS Biology

Plant, root, and soil microbiome

Genome-centric view of carbon processing in thawing permafrost – Ben J. Woodcroft – Nature

Review: Uptake of bacteria into living plant cells, the unifying and distinct feature of the nitrogen-fixing root nodule symbiosis – Martin Parniske – Current Opinion in Plant Biology

Pre-print: Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon – Pablo de Jesus Suarez-Moo – bioRxiv

Water and extremophile microbiome

Discovery of a diverse set of esterases from hot spring microbial mat and sea sediment metagenomes – RaviRanjan – International Journal of Biological Macromolecules

Built environment

Microbial communities and functional genes of nitrogen cycling in an electrolysis augmented constructed wetland treating wastewater treatment plant effluent – Pengfei Zhang – Chemosphere

Science, publishing, and career

Why it is not a ‘failure’ to leave academia – Philipp Kruger – Nature

July 31, 2018

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Today’s Digest features a report that different types of tobacco products can cause oral microbial dysbiosis, an update on fecal microbiome transplant, and exploration into Westernization and evolution of gut microbiota. Enjoy reading!

General microbiology

Alterations of Salmonella Typhimurium Antibiotic Resistance under Environmental Pressure – Mengfei Peng et al. – Applied and Environmental Microbiology

Preprint: Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome – Tabitha Innocent et al. – bioRxiv

Human oral microbiome

Chicken or the Egg: Microbial Alterations in Biopsy Samples of Patients with Oral Potentially Malignant Disorders – Gabor Decsi et al. – Pathology & Oncology Research

** Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study – Yvonne Vallès et al. – Scientific Reports

Human respiratory microbiome

Decreased microbiome diversity in the HIV small airway epithelium – Stella Xu et al. – Respiratory Research

Human gut microbiome

Antibiotic Exposure and Reduced Short Chain Fatty Acid Production after Hematopoietic Stem Cell Transplant – Lindsey ERomick-Rosendale et al. – Biology of Blood and Marrow Transplantation

** Review: Fecal Microbiota Transplantation: Current Status in Treatment of GI and Liver Disease – Byron P.Vaughn et al. – Clinical Gastroenterology and Hepatology

The association between the incidence of intestinal graft-versus-host disease and antibiotic use after allogeneic hematopoietic stem cell transplantation – Daisuke Hidaka et al. – Clinical Transplantation

Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients – Carola Venturini et al. – Intensive Care Medicine Experimental

** Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization – Jacobo de la Cuesta-Zuluaga et al. – Scientific Reports

A diverse range of human gut bacteria have the potential to metabolise the dietary component gallic acid – María Esteban-Torres et al. – Applied and Environmental Microbiology

Metagenomic analysis of gut microbial communities from a Central Asian population – Almagul Kushugulova et al. – BMJ Open

Animal experiments

Early cellular responses of germ-free and specific-pathogen-free mice to Francisella tularensis infection – ZuzanaKrocova et al. – Microbial Pathogenesis

Rat: Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins – Cláudia Marques et al. – Scientific Reports

Mouse: Complementary intestinal mucosa and microbiota responses to caloric restriction – Kalina Duszka et al. – Scientific Reports

Greater Microbial Translocation and Vulnerability to Metabolic Disease in Healthy Aged Female Monkeys – Quentin N. Wilson et al. – Scientific Reports

Medicinal Mushrooms Supplements Alter Chicken Intestinal Microbiome – Janelle Robinson et al. – International Journal of Medicinal Mushrooms

Review: Standardization in host-microbiota interaction studies: challenges, gnotobiology as a tool, and perspective – Catherine Mooser et al. – Current Opinion in Microbiology

Animal microbiome

Review: Where in the serotonergic system does it go wrong? Unravelling the route by which the serotonergic system affects feather pecking in chickens – Elske N.de Haas & Jerine A.J.van der Eijk – Neuroscience & Biobehavioral Reviews

Exploring the pathology of an epidermal disease affecting a circum-Antarctic sea star – Laura Núñez-Pons et al. – Scientific Reports

Assessment of rumen microbiota from a large cattle cohort reveals the pan and core bacteriome contributing to varied phenotypes – Mingyuan Xue et al. – Applied and Environmental Microbiology

Preprint: Whole genome screen reveals a novel relationship between Wolbachia and Drosophila host translation – Yolande Grobler et al. – bioRxiv

Food microbiology

Dynamics and biodiversity of bacterial and yeast communities during the fermentation of cocoa beans – Jatziri Mota-Gutierrez et al. – Applied and Environmental Microbiology

Plant, root and soil microbiome

Alternate life history phases of a common seaweed have distinct microbial surface communities – Matthew A Lemay et al. – Molecular Ecology

Diversity of bacterial microbiota of coastal halophyte Limonium sinense and amelioration of salinity stress damage by symbiotic plant growth-promoting actinobacterium Glutamicibacter halophytocola KLBMP 5180 – Sheng Qin et al. – Applied and Environmental Microbiology

Bacterial microbiota protect an invasive bark beetle from a pine defensive compound – Chihang Cheng et al. – Microbiome

Structural inflexibility of the rhizosphere microbiome in mangrove plant Kandelia obovata under elevated CO2 – Panqing Yin et al. – Marine Environmental Research

Mutualistic fungus Phomopsis liquidambari increases root aerenchyma formation through auxin-mediated ethylene accumulation in rice (Oryza sativa L.) – Li-Yan Hu et al. – Plant Physiology and Biochemistry

Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient – Ming Ma et al. – Science of The Total Environment

Isolation and diversity of culturable rhizobacteria associated with economically important crops and uncultivated plants in Québec, Canada – Di Fan et al. – Systematic and Applied Microbiology

Phages and viruses

Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron – Yvan Bettarel et al. – Scientific Reports

Bioinformatics

Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity – Anton Bankevich & Pavel A.Pevzner – Cell Systems

Microbes in the news

Gut bacteria can protect against Salmonella infections – Press Trust of India – Business Standard

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

 

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