July 16, 2017

Events and jobs
Postdoctoral Fellow – Astrobiology – University of Florida

Microbiology Laboratory Manager – Cranleigh Scientific, Northamptonshire, England

Human respiratory microbiome
Review: Microbiome in chronic obstructive pulmonary disease – Eduard Monso – Annals of Translational Medicine

Monitoring clinical and microbiological evolution of a cystic fibrosis patient over 26 years: experience of a Brazilian CF Centre – Cassiana da Costa Ferreira Leite – BMC Pulmonary Medicine

Distal airway microbiome is associated with immunoregulatory myeloid cell responses in lung transplant recipients – Nirmal S. Sharma – The Journal of Heart and Lung Transplantation

Human oral microbiome
Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase Its Pathogenicity – E. Xiao – Cell Host and Microbe

Microbiome of peri-implantitis affected and healthy dental sites in patients with a history of chronic periodontitis – Danae Apatzidou – Archives of Oral Biology

Human gut microbiome
Review: Gut–CNS-Axis as Possibility to Modulate Inflammatory Disease Activity—Implications for Multiple Sclerosis – Ann-Katrin Fleck – International Journal of Molecular Sciences

Determination of certain bacterial groups in gut microbiota and endotoxin levels in patients with nonalcoholic steatohepatitis – Ceren Özkul – The Turkish Journal of Gastroenterology

Animal experiments
Meat and bone meal as partial replacement of fishmeal in diets for gilthead sea bream (Sparus aurata) juveniles: Diets digestibility, digestive function, and microbiota modulation – Sara Moutinho – Aquaculture

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease – Mohamed Zeineldin – Veterinary Microbiology

Animal microbiome
Effects of chromium(III) on enzyme activities and bacterial communities during swine manure composting – Yanan Yin – Bioresource Technology

Antimicrobial Activity of Actinobacteria Isolated From the Guts of Subterranean Termites – R. A. Arango – Environmental Entomology

Oral Disease and Microbiota in Free-roaming cats – Ana Whyte – Topics in Companion Animal Medicine

Plant, root, and soil microbiome
Investigating the durable effect of the hot water treatment used in nurseries on pathogenic fungi inhabiting grapevine wood and involved in Grapevine Trunk Diseases – Emilie Bruez – Crop Protection

Understanding the mycobiota of maize from the highlands of Guatemala, and implications for maize quality and safety – José Rodrigo Mendoza – Crop Protection

The uniqueness and biogeochemical cycling of plant root microbial communities in a floating treatment wetland – Hidetoshi Urakawa – Ecological Engineering

Water and extremophile microbiome
The Other Microeukaryotes of the Coral Reef Microbiome – T.D. Ainsworth – Trends in Microbiology

Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area – Stefan Thiele – Marine Genomics

Built environment
Stimulation effect of electric current density (ECD) on microbial community of a three dimensional particle electrode coupled with biological aerated filter reactor (TDE-BAF) – Yan Feng – BioResource Technology

Food microbiology
Review: Bacteriocin-Antimicrobial Synergy: A Medical and Food Perspective – Harsh Mathur – Frontiers in Microbiology

Review: Low FODMAP Diet in the Treatment of Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis – Dania Schumann – Nutrition

Macrophages treated with non-digestible polysaccharides reveal a transcriptionally unique phenotype – Yongfu Tang – Journal of Functional Foods

Microbial Ecology
Interplay between antibiotic efficacy and drug-induced lysis underlie enhanced biofilm formation at subinhibitory drug concentrations – Wen Yu – bioRxiv

A phylogenetic and evolutionary analysis of antimycin biosynthesis – Rebecca Joynt – bioRxiv

Probiotics / prebiotics
Review: Prenatal and postnatal administration of prebiotics and probiotics – Kristin Sohn – Seminars in Fetal and Neonatal Medicine

Techniques
Phototrophic microorganisms in the symbiotic communities of Baikal sponges: Diversity of psbA gene (encoding D1 protein of photosystem II) sequences – OV Kaluzhnaya – Mol Biol (Mosk)
Unfortunately, this article is in Russian and I cannot access the original. The abstract was interesting though, the goal of the study is to determine whether psbA sequences can be used as a marker for phototrophic organisms.

New sequences
Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics – F. Cadoret – New Microbes and New Infections

Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India – Sara Jones – Genome Announcements

Phoenicibacter massiliensis‘ gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman – M. Bilen – New Microbes and New Infections

Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: implications for drug discovery – Amine Namouchi – BMC Genomics

Microbes in the news 
** Mini-Metagenomics Leads to Microbial Discovery – Abby Olena – The Scientist
Refers to Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Brian Yu – ELife **

APC Microbiome Institute appoints Spinning Clock to Mind Your Microbes brief – Andy Black – The Drum
An app for kids to learn about the microbiome!

Microbial diversity: ‘key benchmark in the coming Third Wave cosmetic revolution’ – Lucy Whitehouse – Cosmetics Design

Novel bacterial physiology identified in the creation of biofilms – Science Daily

Physicists Just Found a Way to Spin Teeny Tiny Robot Motors With Bacteria – Gemma Conroy – Science Alert

New bacteria being developed for cheese may save industry $10m a year, researchers say – Melanie Vujkovic – ABC

Bacteria-infected mosquitoes are coming to Fresno – but it’s a good thing! – Bryant-Jon Anteola – Fresno Bee

BYU student overcomes flesh-eating bacteria to compete on ‘American Ninja Warrior’ – Braley Dodson – Daily Herald

Bacteria Actively Drive Development of Colorectal Cancer – Newswise
Looking at Streptococcus gallolyticus and its ability to promote colorectal cancer in cell culture, animal models, and human tissue.

Bacteria Hysteria
How surgeons can stop the spread of germs by operating NAKED instead of wearing surgical gowns – Colin Fernandez – Daily Mail

July 4, 2017

Happy 4th of July!

Events and jobs
Microbiology Team Lead – Bentleyville, PA

General microbiome
Host Microbiome Richness Predicts Resistance to Disturbance by Pathogenic Infection in a Vertebrate Host – Xavier A. Harrison – bioRxiv

Pregnancy and early life
Review: SALSA—A dance on a slippery floor with changing partners – M.P. Reichhardt – Molecular Immunology

Review: The Microbiome and Biomarkers for Necrotizing Enterocolitis: Are We Any Closer to Prediction? – Brigida Rusconi – Journal of Pediatrics

Human skin microbiome
Cutaneous Leishmaniasis Induces a Transmissible Dysbiotic Skin Microbiota that Promotes Skin Inflammation – Ciara Gimblet – Cell Host and Microbe

Human oral microbiome
Hydrogen sulfide exposure induces NLRP3 inflammasome-dependent IL-1β and IL-18 secretion in human mononuclear leukocytes in vitro – Amina Basic – Clinical and Experimental Dental Research

Human gut microbiome
Immunoregulatory effect of mast cells influenced by microbes in neurodegenerative diseases – Francesco Girolamo – Brain, Behavior, and Immunity

Review: Host Genetics and Gut Microbiome: Challenges and Perspectives – Alexander Kurilshikov – Trends in Immunology

Review: Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk – Derek V. Seidel – Seminars in Cancer Biology

Review: Extracellular vesicles in gastrointestinal cancer in conjunction with microbiota: On the border of Kingdoms – Natasha S. Barteneva – Biochimica et Biophysica Acta (BBA) – Reviews on Cancer

Microbial ecology
Small subsets of highly connected taxa predict compositional change in microbial communities – Cristina Herren – bioRxiv

Animal experiments
Effect of administration route and dose alteration on sulfadiazine-trimethoprim plasma and intestinal concentrations in pigs – Joren De Smet – International Journal of Antimicrobial Agents

Isomalto-oligosaccharides, a prebiotic, functionally augment green tea effects against high fat diet-induced metabolic alterations via preventing gut dysbacteriosis in mice – Dhirendra Pratap Singh – Pharmacological Research

6-Shogaol ameliorates injury to the intestinal mucosa and increases survival after high-dose abdominal irradiation – Jinhan Wang – Journal of Functional Foods

Total abdominal irradiation exposure impairs cognitive function involving miR-34a-5p/BDNF axis – Ming Cui – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

Bidirectional Brain-Gut Interactions and Chronic Pathological Changes after Traumatic Brain Injury in Mice – Elise L. Ma – Brain, Behavior, and Immunity

An increase in corn resistant starch decreases protein fermentation and modulates gut microbiota during in vitro cultivation of pig large intestinal inocula – Xiangyu He – Animal Nutrition

Animal microbiome
Natural products and morphogenic activity of γ-Proteobacteria associated with the marine hydroid polyp Hydractinia echinata – Huijuan Guo – Bioorganic and Medicinal Chemistry

Plant, root, and soil microbiome
Feedbacks between plant N demand and rhizosphere priming depend on type of mycorrhizal association – Benjamin N. Sulman – Ecology Letters

Cyanobacterial and rhizobial inoculation modulates the plant physiological attributes and nodule microbial communities of chickpea – Radha Prasanna – Archives of Microbiology

Probiotics / prebiotics
Development of Carboxymethyl Cellulose-Chitosan Hybrid Micro- and Macroparticles for Encapsulation of Probiotic Bacteria – P. Singh – Carbohydrate Polymers

Bioinformatics
Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants – Sherine Awad – bioRxiv

Techniques
Magic pools: parallel assessment of transposon delivery vectors in bacteria – Hualan Liu – bioRxiv

Imaging Bacterial Colonies and Phage–Bacterium Interaction at Sub-Nanometer Resolution Using Helium-Ion Microscopy – Miika Leppänen – Advanced BioSystems

Microbes in the news
Essays on health: microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman and Tarsh Bates – The Conversation

Modified sugar compound can clear intestinal colonization by UPEC – Irene Vacca – Nature Reviews Microbiology
Original paper: Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist – Caitlin N. Spaulding – Nature (June 14, 2017)

Human Emotions Really Are Affected by Gut Bacteria, New Study Suggests – Peter Dockrill – Science Alert
Original paper: Brain structure and response to emotional stimuli as related to gut microbial profiles in healthy women – Kirsten Tillisch – Psychosomatic Medicine (June 28, 2017)

Eliminating harmful bacteria from oil reservoirs – Newcastle University

Woman contracts flesh-eating bacteria in Fairhope – Allison Marlow – Gulf Coast News Today

Second LA Fitness also tests positive for Legionnaires’-causing bacteria – Kyle Arnold – Orlando Sentinel

Microbes on the market
EPS for DexCom, Inc. (DXCM) Expected At $-0.14; Profile of 6 Analysts Covering Seres Therapeutics (MCRB) – Clifton Ray – Herald KS

Using Microbiome Analytics to Improve Milk Safety – Joel Hans – RT Insights

Bacteria Hysteria
These terrifying photos show why you really should throw your old makeup away – Laura Capon – Cosmopolitan

Science, publishing, and career
Is the staggeringly profitable business of scientific publishing bad for science? – The Guardian
This sure made the round on Twitter a few days ago!

The vagueness problem in academic writing – The Thesis Whisperer

Laid Off From the Tenure Track – a Guest Post – The Professor is In
I read her book a while back and thought it was fantastic. Karen Kelsky’s blog focuses on academia in the humanities, but there are overlaps in science!

June 20, 2017

Great articles from bioRxiv today!

Events and jobs
Microbiology Clinical Laboratory Scientist OR Microbiology CLS Opening – KA Recruiting – San Francisco, CA

Acting QC Specialist: Microbiology – Johnson and Johnson – Cork, Ireland

Human vaginal microbiome
Effects of intrauterine contraception on the vaginal microbiota – Christine M. Bassis – Contraception

Human gut microbiome
**Environmental factors dominate over host genetics in shaping human gut microbiota composition – Daphna Rothschild – bioRxiv**

Review: Role of gut microbiota against calcium oxalate – Humaira Sadaf – Microbial Pathogenesis

Review: Glucocorticoids and gut bacteria: “The GALF Hypothesis” in the metagenomic era – David J. Morris – Steroids

Review: The microbiome-gut-brain axis: implications for schizophrenia and antipsychotic induced weight gain – S. Kanji – European Archives of Psychiatry and Clinical Neuroscience

Animal experiments
Glycaemic and insulinaemic responses of adult healthy warm-blooded mares following feeding with Jerusalem artichoke meal – M. Glatter – Animal Physiology and Animal Nutrition

Water and extremophile microbiome
Review: Phototrophic biofilms: diversity, ecology and applications – Asha Bharti – Journal of Applied Phycology

Built environment
Response of microbial community function to fluctuating geochemical conditions within a legacy radioactive waste trench environment – Xabier Vázquez-Campos – bioRxiv

Accelerating anodic biofilms formation and electron transfer in microbial fuel cells: Role of anionic biosurfactants and mechanism – Yunshu Zhang – Bioelectrochemistry

Food microbiology
Influence of food consumption patterns and Galician lifestyle on human gut microbiota – María Castro-Penalonga – Journal of Physiology and Biochemistry

Microbes in the news
Light-sensitive bacteria could save you during a heart attack – Jon Fingas – Engadget

Bacteria from hot springs solve mystery of metabolismBacteria from hot springs solve mystery of metabolism – Stockholm University – Science News

Common disease-causing bacteria can live airborne for 45 minutes, study shows – Queensland University of Technology – Science News

Meerkats Can Thank Bacteria for Their Signature Butt Scents – Elizabeth Preston – Discover

Microbes on the market
OptiBiotix Signs Major Supply Agreement For Its Microbiome Modulating Cholesterol-Reduction Probiotic – BioSpace

June 13, 2017

Excellent reviews across all sections, with many from the Nature Journals. Also, multiple articles on the tree of life and animal experiments.

General microbiome
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life – Supratim Mukherjee – Nature Biotechnology

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes – Violette Da Cunha – PLoS Genetics

Review: Natural Products and the Gene Cluster Revolution – Paul R. Jensen – Trends in Microbiology

Pregnancy and early life
Review: How nutrition and the maternal microbiota shape the neonatal immune system – Andrew J. MacPherson – Nature Reviews Immunology

Multi-site human microbiome
Review: Role of oral and gut microbiome in nitric oxide mediated colon motility – Miriam Y. Walker – Nitric Oxide

Human skin microbiome
Review: Chemical signaling in mosquito–host interactions: the role of human skin microbiota – William Takken – Current Opinion in Insect Science

Human oral microbiome
Reduced Susceptibility to Antiseptics Is Conferred by Heterologous Housekeeping Genes – Supathep Tansirichaiya – Microbial Drug Resistance

Human gut microbiome
*Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae – Derrick R. Samuelson – PLoS Pathogens

Review: Fungal dysbiosis: immunity and interactions at mucosal barriers – Ilian D. Iliev – Nature Reviews Immunology

Review: Transmission of the gut microbiota: spreading of health – Hilary P. Browne – Nature Reviews Microbiology

Editorial: Post-dieting weight gain: the role of persistent microbiome changes – Christoph A Thaiss – Future Microbiology

Animal experiments
*Thermoneutral housing exacerbates nonalcoholic fatty liver disease in mice and allows for sex-independent disease modeling – Daniel A. Giles – Nature Medicine

*Cold-induced conversion of cholesterol to bile acids in mice shapes the gut microbiome and promotes adaptive thermogenesis – A. Worthmann – Nature Medicine

Integrated Metagenomic Analyses of the Rumen Microbiome of Cattles Reveals Key Biological Mechanisms Associated with Methane Traits – Haiying Wang – Methods

Long-term multi-species Lactobacillus and Bifidobacterium dietary supplement enhances memory and changes regional brain metabolites in middle-aged rats – Caroline O’Hagan – Neurobiology of Learning and Memory

Soy compared with milk protein in a Western diet changes fecal microbiota and decreases hepatic steatosis in obese OLETF rats – Matthew R. Panasevich – Journal of Nutritional Biochemistry

Targeted metabolomics analysis of aromatic amino acids and their gut microbiota-host co-metabolites in rat serum and urine by liquid chromatography with tandem mass spectrometry – Yifeng Zeng – Journal of Separation Science

Effect of cocoa’s theobromine on intestinal microbiota of rats – Sandra Martin-Pelaez – Molecular Nutrition and Food Research

Water and extremophile microbiome
Review: Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems – Alan W. Decho – Frontiers in Microbiology

Review: Linking genes to microbial biogeochemical cycling: lessons from arsenic – Yong-Guan Zhu – Environmental Science and Technology

Food microbiology
Review: Extremozymes from metagenome: Potential applications in food processing – Mahejibin Khan – Critical Reviews in Food Science and Nutrition

Phages and viruses
Review: Interplay between viruses and bacterial microbiota in cancer development – Dariia Vyshenska – Seminars in Immunology

Bioinformatics
A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni – Journal of Microbiological Methods

Power and sample size calculations for high-throughput sequencing-based experiments – Chung-I Li – Briefings in Bioinformatics
Only a short section on microbiome.

Techniques
*A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis – Spencer R. Scott – Nature Microbiology

Body fluid prediction from microbial patterns for forensic application – Eirik Nataas Hanssen – Forensic Science International: Genetics

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinIONTM portable nanopore sequencer – Alfonso Benítez-Páez – GigaScience

Review: Phenotyping of gut microbiota: Focus on capillary electrophoresis – Manuel Ferrer – Electrophoresis

Review: Panacea in progress: CRISPR and the future of its biological research introduction – Michael Carroll – Microbiological Research

June 3, 2017

There were over 100 alerts today! Here are plenty of papers after the few light digests.

Events and jobs
Bioinformatics Scientist, Microbiome – Human Longevity, Inc, Greater San Diego Area

MSc position in Microbiology – Teagasc, London/Europe

General microbiome
Review: The multi-omics promise in context: from sequence to microbial isolate – Johanna Gutleben – Critical Reviews in Microbiology

Review: Symbiosis-inspired approaches to antibiotic discovery – Navid Adnani – Natural Product Reports

Pregnancy and early life
The Microbiome of Infants Recruited to a Randomised Placebo-controlled Probiotic Trial (PiPS Trial) – Michael Millar – EBioMedicine

Safety and tolerability of Bifidobacterium longum subspecies infantis EVC001 supplementation in healthy term breastfed infants: a phase I clinical trial – Jennifer T. Smilowitz – BMC Pediatrics

Human vaginal microbiome
Vaginal bacteria modify HIV tenofovir microbicide efficacy in African women – Nichole R. Klatt – Science

Changes in vaginal community state types reflect major shifts in the microbiome – J. Paul Brooks – Microbial Ecology in Health and Disease

Human gut microbiome
Chemoproteomic Profiling of Bile Acid Interacting Proteins – Shentian Zhuang – ACS Central Science

Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota – Tingting Chen – Scientific Reports

Vancomycin Taper and Risk of Failure of Fecal Microbiota Transplant in Patients With Recurrent Clostridium difficile Infection – Roberto L. Patron – Clinical Infectious Diseases

Surgically induced changes in gut microbiome and hedonic eating as related to weight loss: Preliminary findings in obese women undergoing bariatric surgery – Claudia P. Sanmiguel – Psychosomatic Medicine

Intestinal microbiota in patients with chronic hepatitis C with and without liver cirrhosis compared to healthy controls – Benjamin Heidrich – Liver International

Dimethyl fumarate reduces the risk of mycotoxins via improving intestinal barrier and microbiota – Ning Ma – Oncotarget

Optimized multiplex immunofluorescence single-cell analysis reveals tuft cell heterogeneity – Eliot T. McKinley – JCI Insight

Gut microbiota regulate hepatic von Willebrand Factor synthesis and arterial thrombus formation via Toll-like receptor-2 – Sven Jäckel – Blood

Review: Trust your gut – metformin and diabetes – Conor A. Bradley – Nature Reviews Endocrinology

Review: Gut microbiota: Inulin regulates endothelial function: a prebiotic smoking gun? – Francesca Fava – Nature Reviews Gastroenterology and Hepatology

Review: Gut Microbiota, Endocrine-Disrupting Chemicals, and the Diabetes Epidemic – Ganesan Velmurugan – Trends in Endocrinology and Metabolism

Review: Gut Microbiota and the Gut-Brain Axis: New Insights in the Pathophysiology of Metabolic Syndrome – de Clercq – Psychosomatic Medicine

Animal experiments
Genetic mouse models with intestinal-specific tight junction deletion resemble an ulcerative colitis phenotype – Wolfgang Stremmel – Journal of Crohn’s and Colitis

Deciphering the landscape of host barriers to Listeria monocytogenes infection – Ting Zhang – PNAS

Rifaximin exerts beneficial effects in PI-IBS mouse model beyond gut microbiota – Yu Jin – Journal of Gastroenterology and Hepatology

Farnesoid X Receptor Agonist Treatment Alters Bile Acid Metabolism but Exacerbates Liver Damage in a Piglet Model of Short-Bowel Syndrome – Prue M. Pereira-Fantini – Cellular and Molecular Gastroenterology and Hepatology

Faecal transplantation for the treatment of Clostridium difficile infection in a marmoset – Yumiko Yamazaki – BMC Veterinary Research

Effect of soybean husk supplementation on the fecal fermentation metabolites and microbiota of dogs – Htun Myint – Animal Science Journal

A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs – Kristin M. V. Herstad – BMC Veterinary Research

Animal microbiome
Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks – Georg Steinert – Scientific Reports

The feline skin microbiota: The bacteria inhabiting the skin of healthy and allergic cats – Caitlin E. Older – PLoS One

Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life – A. Schoster – BMC Veterinary Research

Cost-effective screening and isolation of xylano-cellulolytic positive microbes from termite gut and termitarium – Libin Mathew Varghese – 3 Biotech

Plant, root, and soil microbiome
Impact of metal stress on the production of secondary metabolites in Pteris vittata L. and associated rhizosphere bacterial communities – Hoang Nam Pham – Environmental Science and Pollution Research

High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism – Yun-Juan Bao – Journal of Environmental Sciences

Impact of microbial communities from tropical soils on the mobilization of trace metals during dissolution of cinnabar ore – Clarisse Balland-Bolou-Bi – Journal of Environmental Sciences

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition – Xingyu Ma – Molecular Ecology

Anthropogenic protection alters the microbiome in intertidal mangrove wetlands in Hainan Island – Juanli Yun – Applied Microbiology and Biotechnology

Water and extremophile microbiome
Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships – Justin R. Seymour – Nature Microbiology

Genetic characterization of periphyton communities associated with selenium bioconcentration and trophic transfer in a simple food chain – Vanessa Friesen – Environmental Science and Technology

Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora – Rachel M. Wright – Scientific Reports

Metabolic network analysis reveals microbial community interactions in anammox granules – Christopher E. Lawson – Nature Communications

Hot springs of Indian Himalayas: potential sources of microbial diversity and thermostable hydrolytic enzymes – Harmesh Sahay – 3 Biotech

High throughput sequencing of microbial eukaryotes in Lake Baikal reveals ecologically differentiated communities and novel evolutionary radiations – Zhenzhen Yi – FEMS Microbiology Ecology

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure – Xiao Ma – Environmental Science and Technology

Built environment
Evolution of microbial communities growing with carbon monoxide, hydrogen and carbon dioxide – Sofia Esquivel-Elizondo – FEMS Microbiology Ecology

Adaptation of microbial community of the anode biofilm in microbial fuel cells to temperature – Xiaoxue Mei – Bioelectrochemistry

Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer – Jesus D. Fernandez-Bayo – Journal of Environmental Sciences

Bacterial community structure transformed after thermophilically composting human waste in Haiti – Yvette M. Piceno – PLoS One

Food microbiology
Characterization of the peptide fraction from digested Parmigiano Reggiano cheese and its effect on growth of lactobacilli and bifidobacteria – Benedetta Bottari – International Journal of Food Microbiology

Impact of food grade and nano-TiO2 particles on a human intestinal community – William Dudefoi – Food and Chemical Toxicology

Probiotics / prebiotics
Probiotic yogurt and acidified milk similarly reduce postprandial inflammation and both alter the gut microbiota of healthy, young men – Kathryn J. Burton – British Journal of Nutrition

Phages and viruses
Phylogenetic Diversity of T4-Type Phages in Sediments from the Subtropical Pearl River Estuary – Maoqiu He – Frontiers in Microbiology

Bacteriophage-prokaryote dynamics and interaction within anaerobic digestion processes across time and space – Junyu Zhang – Microbiome

Bioinformatics
Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities – Jonathan L. Golob – BMC Bioinformatics

Techniques
Review: Capturing the genetic makeup of the active microbiome in situ – Esther Singer – ISME

Novel Co-Culture Plate Enables Growth Dynamic-Based Assessment Of Contact-Independent Microbial Interactions – Thomas J. Moutinho Jr. – bioRxiv

Optimization of high-yielding protocol for DNA extraction from the forest rhizosphere microbes – Sadam D. V. Satyanarayana – 3 Biotech

DNA metabarcoding to assess indoor fungal communities: Electrostatic dust collectors and Illumina sequencing – Steffi Rocchi – Journal of Microbiological Methods

Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets – Blair Lawley – PeerJ

Microbes in the news
Unhealthy vagina microbiome can make HIV drugs less effective – Bob Roehr – New Scientist
Article featured above!

Gut microbiota and melanoma treatment responses – Caroline Robert and Franck Carbonnel – OUPblog

Biologists examine biofilm as part of port field studies – Sandor Gyarmati – Delta Optimist

Bacteria used as factories to produce cancer drugs – Phys.Org

Boffins find evidence of strange uranium-producing bacteria lurking underground – Katyanna Quach – The Reigster

Man dies from flesh-eating bacteria after swimming with new tattoo – MSN

Microbes on the market
Why Should we be Excited about the Emerging Microbiome Field? – Antonio – LabBioTech

May 22, 2017

Events and jobs
Microscopist Asbestos/Microbiology – EMSL Analytical, Seattle, WA

Technician (Microbiology Team) – AsureQuality (AQ), Christchurch, Canterbury, New Zealand

Laboratory Technician I (Microbiology & Genetics) – IDEXX, Columbia, MO, US

Associate Scientist Molecular Microbiology – CheckMark Labrecruitment, South Holland

Human respiratory microbiome
Review: Infection-mediated asthma: etiology, mechanisms and treatment options, with focus on Chlamydia pneumoniae and macrolides – Wilmore C. Webley – Respiratory Research

Human gut microbiome
Review: The bidirectional gut-brain-microbiota axis as a potential nexus between traumatic brain injury, inflammation, and disease – Mark Sundman – Brain, Behavior, and Immunity

Clinical Trial Watch: ‘Targeting the gut-liver axis in liver disease’ – Reiner Wiest – Journal of Hepatology

Gluten-degrading bacteria are present in the human small intestine of healthy volunteers and celiac patients – Alexandra R. Herran – Research in Microbiology

The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans – Lloyd S. Robinson – Journal of Biological Chemistry

Plant, root, and soil microbiome
Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation – José A. Siles A. Siles – Scientific Reports

Review: Evolutionary Ecology of Multitrophic Interactions between Plants, Insect Herbivores and Entomopathogens – Ikkei Shikano – Journal of Chemical Ecology

Pseudomonas chlororaphis produces two distinct R-tailocins that contribute to bacterial competition in biofilms and on roots – Robert J. Dorosky – Applied and Environmental Microbiology

Water and extremophile microbiome
Review: A multiomics approach to study the microbiome response to phytoplankton blooms – Liyan Song – Applied Microbiology and Biotechnology

Antibiotics/probiotics/prebiotics
The Resistome Of Important Human Pathogens – Christian Munck – bioRxiv

Phages and viruses
Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer – Marie Touchon – Current Opinion in Microbiology
Part of a themed issue on MGE-HGT in prokaryotes

Bioinformatics
StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees – Märt Roosaare – PeerJ

Microbes in the news
Bacteria could lead to cleaner methane power – Jon Fingas – Engadget

Luminous bacteria will help to measure radioactivity – Siberian Federal University – EurekAlert!

A ‘Superbug’ Fungus Is Spreading Across The US – Kristen V. Brown – Gizmodo

Research shows that gut bacteria tells their hosts what to eat – Cordis News

Indian researchers use a novel route to kill TB bacteria – R. Prasad – The Hindu

Bacteria Hysteria
Cash is even grosser than you knew: Dangerous bacteria survive on paper money, study finds – James Dennin – AOL

May 8, 2017

First, a job opportunity in my PI’s lab: please forward or apply! Papers today are spread over multiple topics, with more in soil and water, and an emphasis on ecological ideas for the general microbiome.

Events and jobs
Bioinformatics Research Associate – Harvard T.H. Chan School of Public Health

General microbiome
Perspective: Multi-stability and the origin of microbial community types – Didier Gonze – ISME

Microbial consortia at steady supply – Thibaud Taillefumier – eLife

Human oral microbiome
Natural Competence Is Common among Clinical Isolates of Veillonella parvula and Is Useful for Genetic Manipulation of This Key Member of the Oral Microbiome – Steven Knapp – Frontiers in Cellular and Infection Microbiology

Human gut microbiome
Opinion: What happened to Koch’s Postulates in Diarrhea? – Shamima Sultana – Environmental Microbiology

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics – Sonny T.M. Lee – Microbiome

Animal experiments
TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome – Robert D. Stedtfeld – FEMS Microbiology Ecology

A Metagenomics Investigation of Carbohydrate-Active Enzymes along the Gastrointestinal Tract of Saudi Sheep – Saad Al-Masaudi – Frontiers in Microbiology

Plant, root, and soil microbiome
Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances – Bingxin Li – Science of the Total Environment

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations – Yunfu Gu – PLoS One

Soil microbial community composition in tallgrass prairie restorations converge with remnants across a 27-year chronosequence – Nicholas A. Barber – Environmental Microbiology

Arbuscular and Ectomycorrhizal Fungi Associated with the Invasive Brazilian Pepper Tree (Schinus terebinthifolius) and Two Native Plants in South Florida – Karim Dawkins – Frontiers in Microbiology

Water and extremophile microbiome
Differential responses of marine, mesohaline, and oligohaline bacterial communities to the addition of terrigenous carbon – DPR Herlemann – Environmental Microbiology

Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia – Hauke F. Kegler – Frontiers in Microbiology

Built environment
Long-term successional dynamics of microbial association networks in anaerobic digestion processes – Linwei Wu – Water Research

Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition – A. Anisa Cokro – Water Research

Probiotics / prebiotics
Review: Effectiveness of Probiotic, Prebiotic, and Synbiotic Therapies in Reducing Postoperative Complications: A Systematic Review and Network Meta-analysis – Nongyao Kasatpibal – Clinical Infectious Diseases

Review: Effect of Probiotics on Metabolic Outcomes in Pregnant Women with Gestational Diabetes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials – Bonnie L. Taylor – Nutrients

Techniques
Rapid Pathogen Identification in Bacterial Pneumonia Using Real-time Metagenomics – Kathryn M Pendleton – American Journal of Respiratory and Critical Care Medicine

The Type of Forage Substrate Preparation Included as Substrate in a RUSITEC System Affects the Ruminal Microbiota and Fermentation Characteristics – Andrea C. Duarte – Frontiers in Microbiology

Microbes in the news
Gold processing bacteria help to recycle electronics – Tim Sandle – Digital Journal

Continued exposure to bacteria from decomposing bodies took its toll on workers – Mahesh Avadhuta – Deccan Chronicle

Bacteria Hysteria
Rob Mancini: Why do folks insist on providing bad food safety advice? – Ben Chapman – BarfBlog