June 25, 2017

Lots of interesting pre-prints in this post that might be worth following! Also a blog post on some cool science art with kombucha, as well as a lot of articles on rhizosphere-microbe interactions.

Events and jobs

Research Opportunities in Molecular Microbiology – Washington University in St. Louis

PhD scholarship in Metagenomics analysis and systems biology – Danmarks Tekniske Universitet

General microbiome

Microbiome yarns: microbial forensics for auditing provenance in global food chains – Timmis et al. – Microbial Biotechnology

Adjuncts and alternatives in the time of antibiotic resistance and in-feed antibiotic bans – Brüssow – Microbial Biotechnology

Human gut microbiome

Bacteria facilitate viral co-infection of mammalian cells and promote genetic recombination – Erickson et al. – bioRXiv

Chemical transformation of xenobiotics by the human gut microbiota – Koppel et al. – Science

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer – Purcell et al. – bioRXiv

Animal microbiome

Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife – Thomas et al. – bioRXiv

 

Plant, root, and soil microbiome

Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore – Pangesti et al. – FEMS Microbiology Ecology

Bioelectrochemical approach for control of methane emission from wetlands – Liu et al. – Bioresource Technology

The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks – Duke et al. – BMC Genomics

Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer – Carro et al. – International Journal of Systematic and Evolutionary Microbiology

Synthesis and Secretion of Isoflavones by Field-Grown Soybean – Sugiyama et al. – Plant Cell Physiology

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage – Qiao et al. – Scientific Reports

Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth -Promoting Rhizobacterium with Antifungal Activity – Wang et al. – Genome Anouncements

Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species – Haruna et al. – Microbial Ecology

Phytoavailability of Cr in Silene vulgaris: The role of soil, plant genotype and bacterial rhizobiome – García-Gonzalez et al. – Ecotoxicology and Environmental Safety

Water and extremophile microbiome

Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs – Campbell et al. – Environmental Microbiology

Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters – Lesaulnier et al. – bioRXiv

Techniques

Rapid whole genome amplification and sequencing of low cell numbers in a bacteraemia model – Anscombe et al. – bioRXiv

Microbes in the news

Do Probiotics Really Work? – Ferris Jabr – Scientific American

Fungi and bacteria team up in dental plaque – Evans – LabRoots

Scientists spy on the secret inner life of bacteria – Saey – Science News

Biofilms: The eradication has begun – McGill University Health Centre – Science Daily

Bacteria and Mental Health: Gut Bacteria Linked to Bipolar Disorder – Villamil – Medical News Bulletin

The Kombucha Craze Steps into Art and the Science of the Microbiome – Fernández – Labiotech

Microbes on the market

Global Microbiome Drugs Industry Market Research Report 2017 – Medgadget

April 19, 2017

Exciting papers with locoregional effects of microbiota in a mouse model of colon carcinogenesis, maternal high fat diet detrimentally alterring epigenetic and gut microbiome pathways leading to fatty liver disease in mice.

Events and jobs

ASM Microbe 2017 : New Orleans

QC Microbiology Product Testing Associate – Experis : Irvine, CA
General microbiome

Review: Applying the design-build-test paradigm in microbiome engineering – Hoang Long Pham – Current Opinion in Biotechnology

Cohort Profile: African Collaborative Center for Microbiome and Genomics Research’s (ACCME) Human Papillomavirus (HPV) and Cervical Cancer Study – Sally N. Adebamowo – International Journal of Epidemiology

Review: Cultured microbes represent a substantial fraction of the human and mouse gut microbiota – Ilias Lagkouvardos – Gut Microbes

Human skin microbiome

A distinct cutaneous microbiota pofile in autoimmune bullous disease patients – Mor Miodovnika – Experimental Dermatology

Human gut microbiome

Review : A psychology of the human brain–gut–microbiome axis – Andrew P. Allen – Social and Personality Psychology Compass

Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs – Sean M P Bennet – Gut

Animal microbiome

Temporal changes in cutaneous bacterial communities of terrestrial- and aquatic- phase newts (Amphibia) – Joana Sabino-Pinto – Environmental Microbiology

The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa – Tomeu Viver – Environmental Microbiology

Studying the effect of administration route and treatment dose on the selection of enrofloxacin resistance in commensal Escherichia coli in broilers – Ilias Chantziaras -Journal of Antimicrobial Chemotherapy

The skin microbiome of the Common thresher shark (Alopias vulpinus) has low taxonomic and potential metabolic β-diversity – Michael P. Doane – Environmental Microbiology Reports

Animal experiments

Intestinal, extra-intestinal and systemic sequelae of Toxoplasma gondii induced acute ileitis in mice harboring a human gut microbiota – Eliane von Klitzing – PLOS ONE

Effects of the inclusion of a Bacillus direct-fed microbial on performance parameters, bone quality, recovered gut microflora, and intestinal morphology in broilers consuming a grower diet containing corn distillers dried grains with solubles – J. D. Latorre – Poultry Science

Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock – Shengyin Jiao – Journal of the Science of Food and Agriculture

*Locoregional effects of microbiota in a preclinical model of colon carcinogenesis – Sarah Tomkovich – Cancer Research

Selection of Cholesterol-Lowering Lactic Acid Bacteria and its Effects on Rats Fed with High-Cholesterol Diet – Yufang Liu – Current Microbiology

*Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations – Umesh D. Wankhade – PLOS ONE

Plant, root, and soil microbiome

Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion – Steven D Mamet- The ISME Journal

An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil – Masahito Hayatsu – The ISME Journal

Investigation of Arsenotrophic Microbiome in Arsenic-Affected Bangladesh Groundwater – Munawar Sultana – Groundwater

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses – Patricia Moya – Plos ONE

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii) – Qiang Li – Plos ONE

The ‘known’ genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils – Ian D. E. A. Lidbury – Microbiology Open

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations – M. S. Bray – Gebiology

Water and extremophile microbiome

Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats – Dimitry Y Sorokin – The ISME Journal

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system – Laura A Sauder – The ISME Journal

Minireview: Microbial ecology of mountain glacier ecosystems: Biodiversity, ecological connections, and implications of a warming climate – Scott Hotaling – Environmental Microbiology

Probiotics / prebiotics
Colonic gas homeostasis: Mechanisms of adaptation following HOST-G904 galactooligosaccharide use in humans – M. Mego – Neurogastroenterology and Motility

Techniques

Stochastically reduced communities—Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces – Jialan Cao – Engineering in Life Sciences

Protocol : Metagenomics and CAZyme Discovery – Benoit J. Kunath – Protein-Carbohydrate Interactions : Methods in Molecular Biology

The resident microflora of voided midstream urine of healthy controls: standard versus expanded urine culture protocols – L. Coorevits – European Journal of Clinical Microbiology & Infectious Diseases

Microbes in the news

Study finds amoeba ‘grazing,’ killing bacteria usually protected by film

How Bacteria-Laden Beetle Poop Is Killing American Squash and Melons

Glowing bacteria detect buried landmines

Science, publishing, and career

Saturday, Science Advocates Prepare for a Long March

Anitha’s non-microbiology picks

Research unlocks molecular key to animal evolution and disease

Cumulative culture can emerge from collective intelligence in animal groups – Takao Sasaki – Nature Communications

March 29, 2017

Today’s digest is chock-full of human gut studies related to disease, soil/plant and water/environmental studies, quite a lot of research on animal microbiomes and symbiotic microbes, as well as some discussion of techniques to improve various metagenomic applications.

Events and jobs

Scientist – Microbiology Development – BD (Becton, Dickinson and Company)

Microbiology Technical Manager – UKAS – W.Midlands

Multi-site human microbiome

Integration of microbiome and epigenome to decipher the pathogenesis of autoimmune diseases – Beidi Chen – Journal of Autoimmunity

Human respiratory microbiome

Integrating the microbiota of the respiratory tract with the unified airway model – Alissa S. Hanshew – Respiratory Medicine

The role of acute and chronic respiratory colonization and infections in the pathogenesis of COPD – Janice M. Leung – Respirology

Human nearly-sterile sites (blood, organs, brain)

* The blood DNA virome in 8,000 humans – Ahmed Moustafa – PLOS Pathogens

Human gut microbiome

Role of External and Environmental Factors in Drug Resistance Emergence: Gut Microbiota – Daniel Ryan – Drug Resistance in Bacteria, Fungi, Malaria, and Cancer

* Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiologic stress – J. Philip Karl – American Journal of Physiology-Gastrointestinal and Liver Physiology

Robust Microbiota-Based Diagnostics for Inflammatory Bowel Disease – A. Eck – Journal of Clinical Microbiology

Tackling the Antibiotic Resistance: The “Gut” Feeling – Richa Misra – Drug Resistance in Bacteria, Fungi, Malaria, and Cancer

Book Chapter – Human Gut Microbiota and Obesity During Development – Tomás Cerdó – Adiposity – Omics and Molecular Understanding

Fecal microbiota transplantation – methods of treatment of recurrent Clostridium difficile infections and other diseases – Juszczuk K – Postepy Hig Med Dosw (Online)

Gut Colonization by Methanogenic Archaea Is Associated with Organic Dairy Consumption in Children – van de Pol JA – Frontiers in Microbiology

Gut Microbiome in Chronic Kidney Disease – R. G. Armani – Current Hypertension Reports

Sex-dependent effects on gut microbiota regulate hepatic carcinogenic outcomes – Guoxiang Xie – Scientific Reports

Gut microbiome analysis of type 2 diabetic patients from the Chinese minority ethnic groups the Uygurs and Kazaks – Ye Wang – PLOS ONE

Animal experiments 

Stressor exposure has prolonged effects on colonic microbial community structure in Citrobacter rodentium-challenged mice – Jeffrey D. Galley – Scientific Reports

Engineered Resistant-Starch (ERS) Diet Shapes Colon Microbiota Profile in Parallel with the Retardation of Tumor Growth in In Vitro and In Vivo Pancreatic Cancer Models – Concetta Panebianco – Nutrients

Alcohol-related changes in the intestinal microbiome influence neutrophil infiltration, inflammation and steatosis in early alcoholic hepatitis in mice – Patrick P. Lowe  – PLOS ONE

Altered gut microbiome in a mouse model of Gulf War Illness causes neuroinflammation and intestinal injury via leaky gut and TLR4 activation – Firas Alhasson – PLOS ONE

Olive oil bioactives protect pigs against experimentally-induced chronic inflammation independently of alterations in gut microbiota – Martin Liehr – PLOS ONE

Animal microbiome

Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus – Eva Novakova – Frontiers in Microbiology

The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot – Devin B. Holman – BMC Microbiology

Fungal diversity and community structure in gut, mound and surrounding soil of fungus-cultivating termites – Huxley Mae Makonde – African Journal of Microbiology Research

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics – Lucas Moitinho-Silva – The ISME Journal (Microbial Ecology)

Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics – Francis C. Weng – Frontiers in Microbiology

Plant, root, and soil microbiome

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny – Aaron A. Jones – Frontiers in Microbiology

Defining the core citrus leaf- and root-associated microbiota: Factors associated with community structure and implications for managing Huanglongbing (Citrus greening) disease – Ryan A. Blaustein – American Society for Microbiology

The preservation of microbial DNA in archived soils of various genetic types – Ekaterina A. Ivanova – PLOS ONE

Unknown risks to soil biodiversity from commercial fungal inoculants – Miranda M. Hart – Nature Ecology and Evolution

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils – Li-Li Han – Scientific Reports

Relationship of microbial communities and suppressiveness of Trichoderma fortified composts for pepper seedlings infected by Phytophthora nicotianae – Margarita Ros – PLOS ONE

Metagenomic analyses of bacterial endophytes associated with the phyllosphere of a Bt maize cultivar and its isogenic parental line from South Africa – Ramadimetja A – World Journal of Microbiology and Biotechnology

Water and extremophile microbiome

* Characterization of culturable bacteria isolated from hot springs for plant growth promoting traits and effect on tomato (Lycopersicon esculentum) seedling – Kinjal Samir Patel – Comptes Rendus Biologies

* Microbial indicators as a diagnostic tool for assessing water quality and climate stress in coral reef ecosystems – Bettina Glasl – Marine Biology

Pre-print – Response Of Microbial Community Function To Fluctuating Geochemical Conditions Within A Legacy Radioactive Waste Trench Environment – Xabier Vázquez-Campos – bioRxiv

* Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers – Jason T. Payne – PLOS ONE

Food microbiology

Monitoring of the bacterial communities of bamboo shoots (Dendrocalamus latiflorus) during pickling process – Xuejuan Xia – International Journal of Food Science + Technology

Bioinformatics

Preprint – MIMIX: a Bayesian Mixed-Effects Model for Microbiome Data from Designed Experiments – Neal S. Grantham – arXiv

Techniques

Integrated Methodology to Characterize Microbial Populations and Functions across Small Spatial Scales in an Oil Production Facility – Christopher R. Marks – Routledge

Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media – Saara Sillanpää – American Society for Microbiology Journals

Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding – Matthieu Leray – PeerJ

Novel 16S rDNA primers revealed the diversity and habitats-related community structure of sphingomonads in 10 different niches – Yili Huang – Antonie van Leeuwenhoek

Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications – Ahsanuddin S – Journal of Biomolecular Techniques

Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches – Sepideh Lamei – PLOS ONE

Microbes in the news 

Bacteria, deadwood and climate change—forest floor as carbon sink

Basic microbiology research study unexpectedly uncovers practical findings for growers

Bacteria That Cause Human Diseases Found in Orca Blowholes

Bacteria Hysteria

Keep Your Phone Bacteria Free with PhoneSoap

Science, publishing, and career 

Behar, Finberg and Luzuriaga elected fellows of American Academy of Microbiology

Ed’s non-microbiology picks 

Spinach Leaf Transformed Into Beating Human Heart Tissue

Low Socioeconomic Status Affects Life Expectancy More Than Obesity

Caesarean sections and for-profit status of hospitals: systematic review and meta-analysis – Ilir Hoxha – BMJ Open

Work organization and mental health problems in PhD students – Katia Levecque – Research Policy

Influence of Anthropogenic Climate Change on Planetary Wave Resonance and Extreme Weather Events – Michael E. Mann – Scientific Reports

February 23, 2017

Today’s selection includes an interesting review on how bacteria keep their time. Long term ceftriaxon sodium usage alters gut microbiota and immune system. Clostridium perfringens toxin genes in the gut microbiota of autistic children. Taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. Enjoy!

General microbiome

Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status. – Akito Sakanaka – Scientific Reports

*Review: Timing the day: what makes bacterial clocks tick? – Carl Hirschie Johnson – Nature Reviews Microbiology

Human urinary microbiome

Review: The female urinary microbiota, urinary health and common urinary disorders. – Linda Brubaker – Annals of Translational Medicine

Review: Questions and challenges associated with studying the microbiome of the urinary tract – Yige Bao – Annals of Translational Medicine

Review: The association between bacteria and urinary stones. – Andrew L. Schwaderer – Annals of Translational Medicine

Human nearly-sterile sites 

The Conserved Phylogeny of Blood Microbiome – Malay Bhattacharyya – Molecular Phylogenetics and Evolution

Human gut microbiome

Review: The gut microbiome in human neurological disease: A review. – Helen Tremlett – Annals of Neurology

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wang – Microbial Pathogenesis

Review: Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome. – Hans C. Arora – Annals of Translational Medicine

*Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system. – Yanjie Guo – Scientific Reports

Note Elies Bik: This study was not performed in humans but in a horrible rat model that can only be qualified as torture. This does not test for depression but for extreme stress. Should not have performed. Proceed with extreme caution. Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics. – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Specific inulin-type fructan fibers protect against autoimmune diabetes by modulating gut immunity, barrier function and microbiota homeostasis. – Kang Chen – Molecular Nutrition and Food Research

Gut microbiota and oxalate homeostasis. – Marguerite Hatch – Annals of Translational Medicine

Tryptophan: A gut microbiota-derived metabolites regulating inflammation. – Lucie Etienne-Mesmin –  World Journal of Gastrointestestinal Pharmacology

*Detection of Clostridium perfringens toxin genes in the gut microbiota of autistic children. – Sydney M. Finegold – Anaerobe

Animal experiments

Butyrate restores HFD induced adaptations in brain function and metabolism in mid-adult obese mice – Ilse A. C. Arnoldussen – International Journal of Obesity

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. – Lucie Etienne-Mesmin – Gut

Animal microbiome

Individual Signatures Define Canine Skin Microbiota Composition and Variability. – Anna Cuscó – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬. – Ines Aline Aschenbrenner – Molecular Ecology

Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change. – Lin Li – Ecology and Evolution

Water and extremophile microbiome

*Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. – Etienne Yergeau – Scientific Reports

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. – Adrienne Narrowe – Environmental Microbiology

Food microbiology

Enhanced Control of Listeria monocytogenes by Enterococcus faecium KE82, a Multiple Enterocin–Producing Strain, in Different Milk Environments. – Elpinki Vandera – Journal of food protection

Probiotics / prebiotics

Review: Probiotics for prevention of urinary stones. – John C. Lieske – Annals of Translational Medicine

Review: Review of the mechanisms of probiotic actions in the prevention of colorectal cancer. – Sandra A. dos Reis – Nutrition Research

Phages and viruses

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses – Lisa Zeigler Allen – mSystems

Microbes in the news 

The Future Of Skin Care: Lotions That Feed Our Microbiome

Collapse of Aztec society linked to catastrophic salmonella outbreak

Smart’ bacteria remodel their genes to infect our intestines

Smallest CRISPR So Far Comes from Food Poisoning Bacteria

Anitha’s non-microbiology picks 

An epigenetics gold rush: new controls for gene expression

Scientists discover 7 ‘Earthlike’ planets orbiting a nearby star

January 11, 2017

Vaginal microbial  communities associated with HIV acquisition or protection, evolution and function of the appendix, microbes and bird evolution, soil microbes followed for 17 years, and bone microbiome and cause-of-death of an 18th century child.
Jobs

Faculty Position in Microbiome Research – National University of Singapore – Science Careers

Pregnancy and early life

The Role of Early Life Nutrition in the Establishment of Gastrointestinal Microbial Composition and Function – Erin C. Davis – Gut Microbes

Human vaginal microbiome

Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women – Christina Gosmann – Immunity

Diagnosis and microecological characteristics of aerobic vaginitis in outpatients based on preformed enzymes – Zhi-liang Wang – Taiwanese Journal of Obstetrics & Gynecology

Human respiratory microbiome

Review: The microbiome in mechanically ventilated patients – Yin, Yudong – Current Opinion in Infectious Diseases

Human gut microbiome

Morphological evolution of the mammalian cecum and cecal appendix – Heather F. Smith – Comptes Rendus Palevol

Exploring the Efficacy of Pooled Stools in Fecal Microbiota Transplantation for Microbiota-Associated Chronic Diseases – Abbas Kazerouni – PLOS ONE

Review: Role of Vitamin D in the Hygiene Hypothesis: The Interplay between Vitamin D, Vitamin D Receptors, Gut Microbiota, and Immune Response – Allison Clark – Frontiers in Immunology

Review: Bacterial Signaling to the Nervous System via Toxins and Metabolites – Nicole J. Yang – Journal of Molecular Biology

Animal experiments

Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior – Caleb Fischer – eLIFE

Gut Microbiota Mediates Protection Against Enteropathy Induced by Indomethacin – Xue Xiao – Scientific Reports

Faecal parameters as biomarkers of the equine hindgut microbial ecosystem under dietary change – P. Grimm – Animal

Characterisation of Early-Life Fecal Microbiota in Susceptible and Healthy Pigs to Post-Weaning Diarrhoea – Samir Dou – PLOS ONE

Animal microbiome

Metagenomic analysis of microbial community of a parasitoid wasp Megaphragma amalphitanum – A.V. Nedoluzhko – Genomics Data

* Review: Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history – Jessica K. Evans – Hormones and Behavior

Archaeology microbiome

The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing – Valeria D’Argenio – International Journal of Molecular Sciences

Plant, root, and soil microbiome

Phyllosphere Methylobacterium bacteria contain UVA-absorbing compounds – Shigenobu Yoshida – Journal of Photochemistry and Photobiology B: Biology

Major Crop Species Show Differential Balance between Root Morphological and Physiological Responses to Variable Phosphorus Supply – Yang Lyu – Frontiers in Plant Science

* Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change – Emma J. Sayer – Ecology and Evolution

Water and extremophile microbiome

Two microcrustaceans affect microbial and macroinvertebrate-driven litter breakdown – Sophie Chambord – Freshwater Biology

Biofilms Confer Resistance to Simulated Extra-terrestrial Geochemical Extremes – Adam H Stevens – bioRxiv Preprint

Bioinformatics, statistics, and metagenomics

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer – Aaron Weimann – mSystems

Structural zeros in high-dimensional data with applications to microbiome studies – Abhishek Kaul – Biostatistics

More microbiology

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response – Robert Heler – Molecular Cell

Press: Researchers Learn to Enhance Bacteria’s Ability to Form Genetic Memories – SciCasts

Microbes in the news
Meet Canada’s ‘poop lady’: “I got to know people up there very well over the years, said Girard, 28. – EurekAlert

A new year for our journal club! – Fiona Whelan – Human Microbiome Journal Club

Oral bacteria linked to preterm labor in Hawaiʻi – Desiree Uyeda – University of Hawai’i News

Mayo’s microbiome study targets diabetes – Brett Boese – Post Bulletin

MicrobEYEome: Liver Cancer Patients Have a Signature Microbiome – GastroEndo News

PresentationThe role of the microbiome in Porcine Reproductive & Respiratory Syndrome (PRRS) – Megan Niederwerder – YouTube

Based on the title this appears to be a good candidate for the “Overselling The Microbiome Award” by Jonathan Eisen: How Sexual Attraction Is Shaped by Gut Bacteria, Infectious Diseases, and Parasites – Kathleen McAuliffe – BigThink

Latest Dengue Update: Bacteria Strain That Stops Dengue Transmission In Mosquitoes Dies In Hot Environment – Minnow Blythe – Counsel Heal

Microbes on the market

Allergan (AGN) Enters Licensing Agreement with Assembly Biosciences (ASMB) to Obtain Worldwide Rights to GI Programs – StreetInsider

Ferring Partners with Intralytix to Develop Bacteriophage Treatments for Conditions Associated with the Microbiome and Drug-Resistant Bacteria – BusinessWire

La Roche-Posay Introduces Prebiotic Skincare Line – PR NewsWire

Indigo’s Preliminary Commercial Data Demonstrate Significant Yield Gains for Growers with Plant Microbiome Product – PR NewsWire

Bik’s non-microbiology picks

The Association of Hot Red Chili Pepper Consumption and Mortality: A Large Population-Based Cohort Study – Mustafa Chopan – PLOS ONE

January 4, 2017

Short-chain sugars and lactose intolerance, NEC and bile salts, gut microbiome in women with Polycystic Ovary Syndrome, Brucella in frogs. And since this is a quiet time on the microbiome literature front,  I also included some other interesting microbes in the news.

Pregnancy and early life

Fecal Bile Salts and the Development of Necrotizing Enterocolitis in Preterm Infants – Christian V. Hulzebos – PLOS ONE

Human respiratory microbiome

Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation – Linh Do Ngoc Nguyen – PLOS ONE

Human gut microbiome

Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals – M. Andrea Azcarate-Peril – PNAS

Alterations in Gut Microbiome Composition and Barrier Function Are Associated with Reproductive and Metabolic Defects in Women with Polycystic Ovary Syndrome (PCOS): A Pilot Study – Lisa Lindheim – PLOS ONE

Review: Modulation of alloimmune response by commensal gut microbiota and potential new avenues to influence the outcome of allogeneic transplantation by modification of the ‘gut culture’ – S. Kanangat – International Journal of Immunogenetics

Editorial: Gut Microbiota, Diet and Health. (We and our gut microbes) – Juan Carlos Espín – Molecular Nutrition & Food Research

Editorial: Hot Topics in 2017 – Gut Microbiota, Whole Grains and Health – Hans-Ulrich Humpf – Molecular Nutrition & Food Research

Microbiology of nearly sterile sites

Pseudomonas aeruginosa Microcolonies in Coronary Thrombi from Patients with ST-Segment Elevation Myocardial Infarction – Gorm Mørk Hansen – PLOS ONE

Animal microbiome

The Change of a Medically Important Genus: Worldwide Occurrence of Genetically Diverse Novel Brucella Species in Exotic Frogs – Holger C. Scholz – PLOS ONE

Synbiotics for Broiler Chickens—In Vitro Design and Evaluation of the Influence on Host and Selected Microbiota Populations following In Ovo Delivery – Aleksandra Dunislawska – PLOS ONE

Plant, root, and soil microbiome

Frontiers for research on the ecology of plant-pathogenic bacteria: fundamentals for sustainability. Challenges in Bacterial Molecular Plant Pathology – Cindy E. Morris – Molecular Plant Pathology

Water and extremophile microbiome

Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment – Christophe Leboulanger – PLOS ONE

Food microbiology

Crystal Ball: Exciting strain-level resolution studies of the food microbiome – Danilo Ercolini – Microbial Biotechnology

Viruses / phages / bioinformatics / metagenomics

Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data – Guillaume Carissimo – PLOS ONE

Microbial Ecology

Effects of Spatial Localization on Microbial Consortia Growth – Michael Venters – PLOS ONE

More microbiology / Microbes in the news

RelA Mutant Enterococcus faecium with Multiantibiotic Tolerance Arising in an Immunocompromised Host– Erin S. Honsa – mBio

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins – Benjamin J. Rauch – Cell

50 Years of Journal of Virology: Classic Spotlight, 1969 and 1970: Articles of Significant Interest Selected from the Journal of Virology Archives by the Editors – Journal of Virology

Research Highlight: Building a bacterial ribosome – Ashley York – Nature Reviews Microbiology

Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria – Nancy L. Burritt – PLOS ONE

Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian clock – Anna M Puszynska – bioRxiv

Microbiomes Move Standard Plate Count One Step Forward – Gregory Siragusa – Food Safety Tech

Bisphenol-A Linked to Endocrine Disorders in Pets, Humans – CBS Local

Microbes on the market

Alimentary discoveries produce a gut reaction among investors – Companies aim to exploit one of the 21st century’s big advances – Clive Cookson – Financial Times

Marina Biotech Granted European Claims Covering Bacteria Mediated Gene Silencing – Market Wired

A Bright Future for Bacteria – Betsy Davis – Pharma Elsevier

Synthetic Biologics to Present at the Biotech Showcase™ 2017 Conference – PR Newswire

Bacteria Hysteria

The Bacteria We’ve Got to Beat: Nasty germs lurk on cell phones, doorknobs, ketchup bottles — here’s how to fight ’em this flu season – Carleen Wild – Lifezette

January 3, 2017

Denture microbiome, insulin resistance and appendix microbiome in obesity, raw milk microbiome, subtropical forest soils, biofilms in drinking water systems, metabolomics of a Mediterranean diet, cell shape and biofilms.

Human oral microbiome

The Denture-Associated Oral Microbiome in Health and Stomatitis – Baochen Shi – mSphere

Commentary: A novel strategy for diagnosing viral versus bacterial infection: implications for oral diseases – Nataly Kravchenko-Balasha – Oral Diseases

Human gut microbiome

*  Insulin resistance is associated with specific gut microbiota in appendix samples from
morbidly obese patients – Isabel Moreno-Indias – American Journal of Translational Research

Microbiology of nearly sterile sites

Improving molecular diagnosis of neonatal septicaemia: Comparative evaluation of different protocols for extraction of bacterial and fungal DNA from blood samples – Gargi Dangre-Mudey – International Journal of Current Research in Medical Sciences

Animal microbiome

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study – Conor J. Doyle – Applied and Environmental Microbiology

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula – Maren Ziegler – Journal of Biogeography

Plant, root, and soil microbiome

Colonization and community structure of arbuscular mycorrhizal fungi in maize roots at different depths in the soil profile respond differently to phosphorus inputs on a long-term experimental site – Chao Wang – Mycorrhiza

Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal but not litter addition in a lowland tropical forest – Merlin Sheldrake – New Phytologist

Modeling of mineral nutrient uptake of spruce tree roots as affected by the ion dynamics in the rhizosphere: Upscaling of model results to field plot scale – H. Nietfeld – Ecological Modelling

Competition between rhizobia under different environmental conditions affects the nodulation of a legume – Zhao Jun Ji – Systematic and Applied Microbiology

 

Altered precipitation seasonality impacts the dominant fungal but rare bacterial taxa in subtropical forest soils – Qian Zhao – Biology and Fertility of Soils

Cultivable bacterial communities associated with roots of rose-scented geranium (Pelargonium graveolens) with the potential to contribute to plant growth – Thais Freitas da Silva – Applied Soil Ecology

Isolation of Soil and Endophytic Fungi from Rice (Oryza sativa L.) – Thianrat Leewijit – Journal of Agricultural Technology

Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition – A. Blaud – Advances in Agronomy

Book chapter: The Significance of Plant-Associated Microbial Rhizosphere for the Degradation of Xenobiotic Compounds – Durgesh Kumar Jaiswal – Plant Responses to Xenobiotics

Review: Plant Communication With Associated Microbiota in the Spermosphere, Rhizosphere and Phyllosphere – P. Lemanceau – Advances in Botanical Research

Review: Plant growth promoting Rhizobacteria: Biocontrol potential for pathogens – Roomina Mazhar – Pure Appl Biol

Water and extremophile microbiome

* Spatial and temporal analogies in microbial communities in natural drinking water biofilms – I. Douterelo – Science of The Total Environment

Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments – Rituja Saxena – Frontiers in Microbiology

Response of the microbial community to bioturbation by benthic macrofauna on intertidal flats – Hui Shen – Journal of Experimental Marine Biology and Ecology

Review: Biotechnological Applications of Marine Enzymes From Algae, Bacteria, Fungi, and Sponges – S. Parte – Advances in Food and Nutrition Research

Waste and pollution microbiology

Inhibitory effects of sodium azide on microbial growth in experimental resuspension of marine sediment – Cabrol Léa – Journal of Microbiological Methods

Effect of various chemical oxidation agents on soil microbial communities – Eva Kakosová – Chemical Engineering Journal

Shifts in microbial community structure and function in surface waters impacted by unconventional oil and gas wastewater revealed by metagenomics – N.L. Fahrenfeld – Science of the Total Environment

Changes in the microbial community during bioremediation of gasoline-contaminated soil – Aline Jaime Leal – Brazilian Journal of Microbiology

Performance and microbial communities of completely autotrophic denitrification in a bioelectrochemically-assisted constructed wetland system for nitrate removal – Dan Xu – Bioresource Technology

Screening selectively harnessed environmental microbial communities for biodegradation of polycyclic aromatic hydrocarbons in moving bed biofilm reactors – Marc A. Demeter – Bioresource Technology

Review: Resource recovery from wastewater by biological technologies: opportunities, challenges and prospects – Daniel Puyol – Frontiers in Microbiology

Fungi

A Review of the Ubiquity of Ascomycetes Filamentous Fungi in Relation to Their Economic and Medical Importance – Mary Augustina Egbuta – Advances in Microbiology

Phages

Editorial: Filamentous Bacteriophage in Bio/Nano/Technology, Bacterial Pathogenesis and Ecology – Jasna Rakonjac – Frontiers in Microbiology

Metabolomics

Adherence to a Mediterranean diet influences the fecal metabolic profile of microbial-derived phenolics in a Spanish cohort of middle-age and older people – Isabel Gutiérrez-Díaz – Journal of Agricultural and Food Chemistry

MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics – Adam Hunter – Metabolomics

More microbiology

* Cell morphology drives spatial patterning in microbial communities – William P. J. Smith – PNAS

Microbes in the news

A Gut Makeover for the New Year – Roni Caryn Rabin – The New York Times

Keys plan field trial for bacteria-infected mosquitoes – Associated Press

Salmonella bacteria threatens Mudumalai: cattle and elephants died – Times of India

How your gut’s circadian rhythm affects your whole body – Richard G. “Bugs” Stevens – The Conversation

Eat Dirt… It’s Good For You (So Are Worms) – Tanya Mead – The Alternative Daily