Did you ever wonder about vitamin B12 role in microbiome organization and function? using a chemical probe mimic of vitamin B12, the authors reveal a light- and B12-dependent DNA regulator and predict that organismal interdependencies for B12 may be critical to microbiome stability and overall function. On the extremophiles front, a study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the salt-secreting desert tree Tamarix aphylla. An interesting paper reinforced linkages between the colonization of the foodborne pathogen E. coli O157:H7 in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders. And as for future generations, if you want to get your kids or students excited about microbiology, try an interactive tool created by Stanford bioengineers: the 3D printed microscope powered by your smartphone.
February 1, 2017
General Microbiome
Microbial Partnerships of Pathogenic Oomycetes-M Larousse-PLoS Pathogens
Biocontrol of Virulent Ralstonia solanacearum isolates by an Indigenous Bacillus cereus-H Mandal-Journal of Agricultural Technology
Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities-P Rubbens-PLoS ONE
Assessment of Metabolic changes in Mycobacterium smegmatis wild type and alr mutant strains: evidence for a new pathway of D-alanine biosynthesis.-DD Marshall-Journal of Proteome Research
Invasions of Host-Associated Microbiome Networks-CL Murall-Advances in Ecological Research
Review: Microbiome engineering: Current applications and its future.-JL Foo-Biotechnology Journal
Review: Microbes and Mental Health: A Review.-R Rieder-Brain, Behavior, and Immunity
Temporal dynamics of microbial communities in microcosms in response to pollutants-Shuo Jiao-Molecular Ecology
Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system-Zhou Li-Environmental Microbiology
Pregnancy and Early Life
Helicobacter pylori infection is associated with an altered gastric microbiota in children-KM Brawner-Mucosal Immunology
Multi-site Human Microbiome
Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity-MW Hall-npj Biofilms and Microbiomes
Human Respiratory Microbiome
Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants-BD Wagner-PLoS ONE
Metagenomic Analysis of Airborne Bacterial Community and Diversity in Seoul, Korea, during December 2014, Asian Dust Event-Seho Cha-PLoS ONE
Human Skin Microbiome
Review: The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals.-Rodrigues Hoffman A-Veterinary Dermatology
Human Nearly Sterile Sites
Impact of the Microbiota and Gastric Disease Development by Helicobacter pylori-Teresa Alarcon-Molecular Pathogenesis and Signal Transduction by Helicobacter pylori
Blood microbiota as a potential noninvasive diagnostic biomarker for liver fibrosis in severely obese patients: Choose carefully-Zongxin Ling-Heptatology
Epidemiological investigation of Candida species causing bloodstream infection in paediatric small bowel transplant recipients-Mallory J. Suhr-Mycoses
Human Gut Microbiome
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease-Timothy R. Sampson-Cell
The Intestinal Microbiome, the Immune System and Spondyloarthropathy-ME Costello-Next-Generation Therapies and Technologies for Immune-Mediated Inflammatory Diseases
Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations-ND Chu-PLoS ONE
The development and role of microbial-host interactions in gut mucosal immune development-CR Stokes-Journal of Animal Science and Biotechnology
Pd-237 The Microbiome of the Colonic Mucosal-luminal Interface in Crohn’s Disease Patients in Endoscopic Remission-J Jacobs-Inflammatory Bowel Diseases
Progress with treating the microbial dysbiosis associated with irritable bowel syndrome.-JS Pearson-Current Opinion in Gastroenterology
Fecal microbiota transplantation for gastrointestinal disorders.-T Malikowski-Current Opinion in Gastroenterology
The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect?-J Dore-Therapie
Review: Clostridium difficile colitis: A clinical review.-GK Ong-American Journal of Surgery
Biotransformation of Total Saponins in Siraitia Fructus by Human Intestinal Microbiota of Normal and Type 2 Diabetic Patients:Comprehensive Metabolites Identification and Metabolic Profile Elucidation Using LC-Q-TOF/MS.-G Zhou-Journal of Agricultural Food Chemistry
Colonic Absorption of Low-Molecular-Weight Metabolites Influenced by the Intestinal Microbiome: A Pilot Study-Mitsuharu Matsumoto-PLoS ONE
Blood Trimethylamine-N-Oxide Originates from Microbiota Mediated Breakdown of Phosphatidylcholine and Absorption from Small Intestine-Wolfgang Stremmel-PLoS ONE
Animal Experiments
P-327 Prolonged Restraint Stressor Exposure in Outbred Cd-1 Mice Impacts Microbiota, Colonic Inflammation, and Short Chain Fatty Acids in Colonic Inflammation-R Maltz-Inflammatory Bowel Diseases
EGCG Prevents High Fat Diet-Induced Changes in Gut Microbiota, Decreases of DNA Strand Breaks, and Changes in Expression and DNA Methylation of Dnmt1 and MLH1 in C57BL/6J Male Mice.-M Remely-Oxidative Medicine and Cellular Longevity
Bovine milk oligosaccharides decrease gut permeability and improve inflammation and microbial dysbiosis in diet-induced obese mice.-G Boudry-Journal of Dairy Science
The Association of Specific Constituents of the Fecal Microbiota with Immune-Mediated Brain Disease in Dogs-Nick D. Jeffery-PLoS ONE
Animal Microbiome
Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate-KR Amato-Microbial Ecology
Two biomass preparation methods provide insights into studying microbial communities of intestinal mucosa in grass carp (Ctenopharyngodon idellus)-NT Tran-Aquaculture Research
Changes in the Bacteriome of Honey Bees Associated with the Parasite Varroa destructor, and Pathogens Nosema-J Hubert-Invertebrate Microbiology
Characterization of faecal microbial communities of dairy cows fed diets containing ensiled Moringa oleifera fodder.-J Sun-Scientific Reports
Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine-Rahat Zaheer-PLoS ONE
Plant, Root and Soil Microbiome
Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere-JI Bravo-Genome Announcements
Draft Genome Sequence of Plant Growth–Promoting Micrococcus luteus Strain K39 Isolated from Cyperus conglomeratus in Saudi Arabia-Feras F. Lafi-Genome Announcements
Community structure, species variation, and functional characterization of rhizosphere-associated bacteria of different winter wheat (Triticum aestivum) cultivars-AK Mahoney-Frontiers in Plant Science
Draft Genome Sequence of Flavobacterium johnsoniae CI04, an Isolate from the Soybean Rhizosphere-JI Bravo-Genome Announcements
Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem-G Rodriguez-Caballero-Science of the Total Environment
Plant Growth Promoting Activity of Pink Pigmented Facultative Methylotroph-Methylobacterium extorquens MM2 on Lycopersicon esculentum L.-P Subhaswaraj-Journal of Applied Biology and Biotechnology
… Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens Strain CREA-C16 Isolated from Pea (Pisum sativum L.) Rhizosphere-N D’Agostino-Genome Announcements
Microbial species and functional diversity in rice rhizosphere of high-yield special ecological areas.-P LiYuan-Journal of Agricultural Resources and Environment
Translocation of Bacillus thuringiensis in Phaseolus vulgaris tissues and vertical transmission in Arabidopsis thaliana-R Garcia-Suarez-Journal of Applied Microbiology
Community Structures of Arbuscular Mycorrhizal Fungi in Soils and Plant Roots Inhabiting Abandoned Mines of Korea-H Park-Mycobiology
Fungal diversity in soils across a gradient of preserved Brazilian Cerrado-ASF de Araujo-Journal of Microbiology
Thesis: Potential risk factors associated with the microbiota of grass roots in the Kimberley region of Western Australia-B Achemedei
Soil Microbial Communities in Natural and Managed Cloud Montane Forests-EH Chang-Forests
Functional Genes That Distinguish Maize Phyllosphere Metagenomes in Drought and Well-Watered Conditions-Barbara A Methe-bioRxiv
Effects of jasmonic acid signalling on the wheat microbiome differ between body sites.-H Liu-Scientific Reports
Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities.-X Zhou-Scientific Reports
Water and Extremophile Microbiome
Production and Characterization of Organic Solvent-Tolerant Cellulase from Bacillus amyloliquefaciens AK9 Isolated from Hot Spring-M Irfan-Applied Biochemistry and Biotechnology
Significant seasonal variations of microbial community in an acid mine drainage lake in Anhui Province, China-C Hao-Environmental Pollution
Bacterial Community Structure and Functional Potential in the Northeastern Chukchi Sea-KM McFarlin-Continental Shelf Research
Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis-NI Won-International Journal of Environmental Research and Public Health
Radiative energy budgets of phototrophic surface-associated microbial communities and their photosynthetic efficiency under diffuse and collimated light-M Lichtenberg-bioRxiv
Anaerobic Dechlorination of Tetrachlorobisphenol A in River Sediment and Associated Changes in Bacterial Communities-J Zhang-Water, Air & Soil Pollution
Microbial community changes in methanogenic granules during the transition from mesophilic to thermophilic conditions.-X Zhu-Applied Microbial Biotechnology
The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem.-AS Wymore-Microbial Ecology
Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls-Petra Pop Ristova-PLoS ONE
Probiotics/Prebiotics
Toward a Personalized Approach in Prebiotics Research-M Dey-Nutrients
Phages and Viruses
Novel Temperate Phages of Salmonella enterica subsp. salamae and subsp. diarizonae and Their Activity against Pathogenic S. enterica subsp. enterica Isolates-Lenka Mikalova-PLoS ONE
Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea-Jinik Hwang-PLoS ONE
Bioinformatics
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks-S Prigent-PLoS Computational Biology
P-310 Yi Characterizing Gut Metagenome Variation with Host Contamination Using Nanopore Sequencing-J Wang-Inflammatory Bowel Diseases
MetaTopics: an integration tool to analyze microbial community profile by topic model-J Yan-BMC Genomics
Discovery of C-Glycosylpyranonaphthoquinones in Streptomyces sp. MBT76 by a Combined NMR-Based Metabolomics and Bioinformatics Workflow-C Wu-Journal of Natural Products
Next-generation sequencing approaches for improvement of lactic acid bacteria-fermented plant-based beverages-Jordyn Bergsveinson-AIMS Microbiology
Microbes in the News
Seres plots path back from phase 2 microbiome blowup-FierceBiotech
Which foods can improve your gut bacteria?-BBC News
Branding BIOHM, The Tesla Of Probiotics-Forbes
For A Healthier Mind, Trust Your Gut-GOOD Magazine
Fecal Transplants May Improve Autism By Targeting Gut Bacteria-Huffington Post
Are prebiotics or probiotics effective against dermatitis?-EurekAlert
Dynamic duo could quickly identify deadly bacteria in hospitals-New Atlas
Bacteria in estuaries have genes for antibiotic resistance-Phys.Org
January 31, 2017
Todays picks include nice reviews on microbiome engineering, and one on skin microbiomes in humans and animals. Biodegredation of mononitrophenol isomers by a tailor-made microbial consortium. Quite a lot of microbiome news – from autism to inflammatory bowel disease.
Events and jobs
Microbiome Scientist Job – Merck – Cambridge, MA
General microbiome
Review: Microbiome engineering: Current applications and its future – Jee Loon Foo – Biotechnology Journal
Simultaneous biodegradation of three mononitrophenol isomers by a tailor-made microbial consortium immobilized in sequential batch reactors – H. Fu – Letters in Applied Microbiology
Human skin microbiome
Review: The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals – Aline Rodrigues Hoffmann – Veterinary Dermatology
Animal experiments
A metagenomic study of the preventive effect of Lactobacillus rhamnosus GG on intestinal polyp formation in ApcMin/+ mice – Y. Ni – Journal of Applied Microbiology
Water and extremophile microbiome
Biofilms for Monitoring Presence of Microsporidia in Environmental Water – Joseph A. Moss – Journal of Eukaryotic Microbiology
Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy – Sandra Gran-Stadniczeñko – Journal of Eukaryotic Microbiology
Bioinformatics
Preprint: In-Depth Resistome Analysis by Targeted Metagenomics – Val F Lanza – bioRxiv
Microbes in the news
Could Fecal Microbiota Transplant Benefit Autistic Children? – MPR
Premature birth risk linked to bacteria in vagina and cervix – Catharine Paddock – MNT
New evidence of how gut microbes affect Inflammatory Bowel Disease – Kate Sweeney – BuisnessWeekly
Boost your immunity with foods that are alive – Rachel Yan – 9News
Rebalancing gut microbiome lengthens survival in mouse model of ALS – ScienceDaily
Carbohydrate That Promotes Biofilm May Be Key to Treating Pseudomonas Infections – Magdalena Kegel – CysticFibrosisNewsToday
January 30, 2017
General microbiome
Commentary: The AGA’s Fecal Microbiota Transplantation National Registry: An important step toward understanding risks and benefits of microbiota therapeutics – Colleen R. Kelly – Gastroenterology
Review: Microbes and Mental Health: A Review – Ryan Rieder – Brain, Behavior, and Immunity
Review: The role of divalent metals for infectious diseases susceptibility and outcome – Guenter Weiss – Clinical Microbiology and Infection
Human gut microbiome
Effects of Acarbose on the Gut Microbiota of Prediabetic Patients: A Randomized, Double-blind, Controlled Crossover Trial – Xiuying Zhang – Diabetes Therapy
Clinical Commentary: More Than a Gut Feeling: The Implications of the Gut Microbiota in Psychiatry – Pochu Ho – Biological Psychiatry
Animal experiments
Target Intestinal Microbiota to Alleviate Disease Progression in Amyotrophic Lateral Sclerosis – Yong-guo Zhang – Clinical Therapeutics
Commensal Bacteria at the Crossroad between Cholestrol Homeostasis and Chronic Inflammation in Atherosclerosis – Kazuyuki Kasahara – Journal of Lipid Research
Bovine milk oligosaccharides decrease gut permeability and improve inflammation and microbial dysbiosis in diet-induced obese mice – Gaelle Boudry – Journal of Dairy Science
Broad spectrum antibiotic enrofloxacin modulates contact sensitivity through gut microbiota in a murine model – Anna Strzepa – Journal of Allergy and Clinical Immunology
Effects of subchronic oral toxic metal exposure on the intestinal microbiota of mice -Qixiao Zhai – Science Bulletin
In vitro fermentation of key dietary compounds with rumen fluid: A genome-centric perspective – Stefano Campanaro – Science of the Total Environment
Cow, yak, and camel milk diets differentially modulated the systemic immunity and fecal microbiota of rats – Wen Yongping – Science Bulletin
Animal microbiome
The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential – Ciro Cesar Rossi – Veterinary Microbiology
Effects of daidzein on performance, serum metabolites, nutrient digestibility, and fecal bacterial community in bull calves – X.H. Zhao – Animal Feed Science and Technology
Plant microbiome
Marchantia liverworts as a proxy to plants basal microbiomes – Luis David Alcaraz – bioRxiv
Water and extremophile microbiome
Microbial succession in biofilms growing on artificial substratum in subtropical freshwater aquaculture ponds – Zhifei Li – FEMS Microbiology Letters
Model communities hint to promiscuous metabolic linkages between ubiquitous free-living freshwater bacteria – Sarahi L Garcia – bioRxiv
Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy – William J. Brazelton – PeerJ
Food microbiology
Beneficial effects of legumes in gut health – Alfonso Clemente – Current Opinion in Food Science
Probiotics / prebiotics
Impact of ageing and a synbiotic on the immune response to seasonal influenza vaccination; a randomised controlled trial – Sumaia Enani – Clinical Nutrition
Antivirulence Properties of Probiotics in Combating Microbial Pathogenesis – M. Surendran Nair – Advances in Applied Microbiology
Bioinformatics
MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data – B Fosso – Bioinformatics
Linclust: clustering protein sequences in linear time – Martin Steinegger – bioRxiv
Techniques
Chapter 3: Best practices for germ-free derivation and gnotobiotic zebrafish husbandry – E. Melancon – Methods in Cell Biology
Chapter 10: Modeling intestinal disorders using zebrafish – X. Zhao – Methods in Cell Biology
A novel LCMSMS method for quantitative measurement of short-chain fatty acids in human stool derivatized with 12C- and 13C-labelled aniline – James Chun Yip Chan – Journal of Pharmaceutical and Biomedical Analysis
Newly Isolated Strains
Actinomyces bouchesdurhonensis sp. nov. and Actinomyces mediterranea sp. nov., isolated from Human Stomach and Duodenum – Morgane Mailhe – Human Microbiome Journal
Peptoniphilus duodeni sp. nov., a new bacterial species identified in human duodenum – Morgane Mailhe – Human Microbiome Journal
Bacteroides bouchesdurhonensis sp. nov., a new bacterium isolated from the human gut – Sokhna Ndongo – Human Microbiome Journal
Microbes in the news
What Even is Kombucha, Anyway? – Anthony Rivas – BuzzFeed
Preventing Biofilm and Bacteria in Dental Operatory Tubing – Tech Featured
Non-Microbiology picks
The State of Systems Genetics in 2017 – Nitin S. Baliga – Cell Systems
Trump’s Immigration Ban Is Already Harming American Science – Ed Yong – The Atlantic
Geneticist launches bid for US Senate – Sara Reardon – Nature
January 29, 2017
A post on fecal transplats, the gut microbiome of cranes, fungal diversity of soils, and much more.
Events and Jobs
Assistant Professor of Microbiology, Immunology & Tropical Medicine at George Washington University
General microbiome
The Stromal Intervention: Regulation of Immunity and Inflammation at the Epithelial-Mesenchymal Barrier – Roni Nowarski – Cell
Effect of adsorbants on in vitro biohydrogenation of 22:6n-3 by mixed cultures of rumen microorganisms – Marlene Escobar – Animal
Pregnancy and early life
Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants – Brandie D. Wagner – PLoS One
Mode of Delivery and Its Influence on the Acquisition of Streptococcus mutans in Infants – Ritu G. Ubeja – International Journal of Clinical Pediatric Dentistry
Human gut microbiome
Blood Trimethylamine-N-Oxide Originates from Microbiota Mediated Breakdown of Phosphatidylcholine and Absorption from Small Intestine – Wolfgang Stremmel – PLoS One
Challenges in Fecal Donor Selection and Screening for Fecal Microbiota Transplantation: A Review – Michael H. Woodworth – Gut Microbes
Animal experiments
Peptostreptococcus anaerobius Induces Intracellular Cholesterol Biosynthesis in Colon Cells to Induce Proliferation and Causes Dysplasia in Mice – Ho Tsoi – Journal of AGA Institute: Gastroenterology Special Issure
Animal microbiome
The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China – Guanghong Zhao – Wiley
Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters – Hooman Derakhashani – Frontiers in Microbiology
Effect of antibiotic on survival and development of Spodoptera litura (Lepidoptera: Noctuidae) and its gut microbial diversity – Abhinay Thakur – Bullitin of Entomological Research
Plant, root, and soil microbiome
Fungal diversity in soils across a gradient of preserved Brazilian Cerrado – Ademir Sergio Ferreira de Araujo – Journal of Microbiology
Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction – Stephanie G. Hays – Journal of Biomedical Engineering
Translocation of Bacillus thuringiensis in Phaseolus vulgaris tissues and vertical transmission in Arabidopsis thaliana – Rosalina García-Suárez – Journal of Applied Microbiology
Transport Capabilities of Environmental Pseudomonads for Sulfur Compounds – Sarah Zerbs – Protein Science
Water and extremophile microbiome
Molecular-biological sensing in aquatic environments: recent developments and emerging capabilities – Jonathan S McQuillan – Current Opinion in Biotechnology
Probiotics / prebiotics
Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept – Vera Slomka – Wiley
Microbes in the news
Rebalancing gut microbiome lengthens survival in mouse model of ALS
What We’ve Learned From Studying Microbiomes
Microbiota Transfer Therapy Could Help Children With Autism
Bacteria’s sneaky way to spread by getting you to eat more
Studies show prevalence of multi-drug resistant bacteria in China
Researchers discover molecule that could fight ‘superbug’ bacteria
Microbes on the market
Bacteria Hysteria
SHOCKING: You won’t BELIEVE how many GERMS are on your hands
January 28, 2017
Among todays picks; Microbiota Transfer Therapy improves gastrointestinal and autism symptoms. Primate microbiota is linked to degree of host sociality. Identifying microbial community changes in space and time opens a door to predicting ecosystem level functioning. Native soil microbes help native plants compete with exotics. Metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.
Events and jobs
Postdoctoral fellowships in microbiome/neuroscience – Northwestern University
Medical Lab Technician in Microbiology – Medical University of South Carolina
Microbiology Technologist – CK Group, Surrey
General microbiome
Predicting the structure and function of coalesced microbial communities –Pawel Sierocinski – bioRxiv
Multi-site human microbiome
Frozen: Thawing and Its Effect on the Postmortem Microbiome in Two Pediatric Cases – Jennifer L. Pechal – Journal of Forensic Sciences
Human vaginal microbiome
Appreciable uncertainty regarding benefits and risks in the treatment of bacterial vaginosis to prevent preterm birth – Thor Haahr -Acta Obstetricia et Gynecologica Scandinavica
Human gut microbiome
Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study – Dae-Wook Kang – Microbiome
Dysregulation of Systemic and Mucosal Humoral Responses to Microbial and Food Antigens as a Factor Contributing to Microbial Translocation and Chronic Inflammation in HIV-1 Infection. – Zdenek Hel – PLOS PATHOGENS
Impact of the Microbiota and Gastric Disease Development by Helicobacter pylori. – Teresa Alarcón – Current Topics in Microbiology and Immunology
Helicobacter pylori-Induced Changes in Gastric Acid Secretion and Upper Gastrointestinal Disease. – Adam J. Smolka – Current Topics in Microbiology and Immunology
Sleepy, circadian disrupted and sick: Could intestinal microbiota play an important role in shift worker health? – Amy C. Reynolds – Molecular Metabolism
Oxidation During Digestion of Meat: Interactions with the Diet and Helicobacter pylori Gastritis, and Implications on Human Health – Thomas Van Hecke – Comprehensive Reviews in Food Science and Food Safety
Glucosinolate and Desulfo-glucosinolate Metabolism by a Selection of Human Gut Bacteria. – Vijitra Luang-In – Current Microbiology
Animal experiments
Species-specific immunity to Helicobacter suis – Iris Bosschem – Helicobacter
Animal microbiome
The Association of Specific Constituents of the Fecal Microbiota with Immune-Mediated Brain Disease in Dogs. – Nick D. Jeffery – PLOS ONE
Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate. – Katherine R. Amato – Microbial Ecology
Plant, root, and soil microbiome
Antimicrobial Activities of Some Actinomycetes Isolated from Different Rhizospheric Soils in Tunisia. – Ines Trabelsi – Current Microbiology
Native plants fare better against an introduced competitor with native microbes and lower nitrogen availability. – W. Gaya Shivega – AoB PLANTS
Identity of biocrust species and microbial communities drive the response of soil multifunctionality to simulated global change – Yu-Rong Liu – Soil Biology and Biochemistry
Distinct roles for soil fungal and bacterial communities associated with the suppression of vanilla Fusarium wilt disease – Wu Xiong – Soil Biology and Biochemistry
Prolonged exposure does not increase soil microbial community response to warming along geothermal gradients – Dajana Radujkovic – bioRxiv
Water and extremophile microbiome
Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism – Emily B. Graham – Frontiers in Microbiology
Copper toxicity response influences mesotrophic Synechococcus community structure – Rhona K. Stuart – Environmental Microbiology
Identification and bioactive potential of marine microorganisms from selected Florida coastal areas – Anna Christensen – MicrobiologyOpen
Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico) – Estelle Couradeau –
Biogeosciences
Techniques
Review: Mining for CRISPR–Cas – Ashley York – Nature Reviews Microbiology
Data Mining Techniques Applied to Hydrogen Lactose Breath Test – Cristina Rubio-Escudero – PLOS ONE
Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations – Nathaniel D. Chu – PLOS ONE
Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils – Kai Antweiler – Microbial Biotechnology
Molecular beacons to identify gifted microbes for genome mining – Richard H Baltz – The Journal of Antibiotics
Phages and viruses
Fecal virome of healthy chickens reveals a large diversity of the eukaryote viral community, including novel circular single-stranded DNA viruses – Diane Lima – Journal of General Virology
Studies on the Virome of the Entomopathogenic Fungus Beauveria bassiana Reveal Novel dsRNA Elements and Mild Hypervirulence – Ioly Kotta-Loizou – PLOS PATHOGENS
Microbes in the news
Microbiome Science Could Bring a Revolution in Medical Care – Lois Parshley – NBC NEWS
Is showering everyday bad for you? New research says yes – Sarah Young – The INDEPENDENT
Rapidly identifying life-threatening bacteria in hospitals – Phys.org
Bacteria May Be Altering Your Brain To Suppress Your Appetite When You’re Sick – Josh Davis – IFL Science
Stanford Medicine and uBiome Investigate Relationship Between Gut Bacteria and Diabetes – Julie Taylor – Prweb
Microbes in the news
*Pathogen-Mediated Inhibition of Anorexia Promotes Host Survival and Transmission – Sheila Rao – Cell
- Media: Why salmonella doesn’t want you to poop out – Helen Thompson – ScienceNews
Microbes on the market
Global Human Microbiome Market Is Expected to Witness a Steady Growth By 2020 – MedGadget
Daily Dog Diet Significantly Influences Canine Gut Microbiome, Report Says – Kalyan Kumar – Tech Times
Pete’s non-microbiology picks
Terrestrial discharges mediate trophic shifts and enhance methylmercury accumulation in estuarine biota – Sofi Jonsson – Science Advances
- Media: New mercury threat to oceans from climate change – Matt McGrath – BBC News
January 27, 2016
Reviews on prenatal bacterial microbiota, mycobiome in the lower respiratory tract and interesting articles on association of HPV infection with vaginal microbiota; prebiotic and bioactive milk fraction improving NREM sleep.
General microbiome
Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data – Kelly M. Robinson – Microbiome
Pregnancy and early life
*Review: Does a prenatal bacterial microbiota exist? – M Hornef -Mucosal Immunology
Human respiratory microbiome
*Review: Mycobiome in the Lower Respiratory Tract – A Clinical Perspective – Robert Krause- Frontiers in microbiology
Human vaginal microbiome
*Association of HPV infection and clearance with cervicovaginal immunology and the vaginal microbiota – B Shannon – Mucosal Immunology
Human gut microbiome
Review: Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle – Gina P. Rodriguez-Castaño – Frontiers in Genetics
Helicobacter pylori infection is associated with an altered gastric microbiota in children – K M Brawner – Mucosal Immunology
*Colonic Absorption of Low-Molecular-Weight Metabolites Influenced by the Intestinal Microbiome: A Pilot Study – Mitsuharu Matsumoto – PLoS One
Review: Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle – Gina P. Rodriguez-Castaño – Frontiers in Genetics
Animal experiments
Effect of Lactobacillus Strains on Intestinal Microflora and Mucosa Immunity in Escherichia coli O157:H7-Induced Diarrhea in Mice – Xin Bian – Current Microbiology
Modulation of gut microbiota and increase in fecal water content in mice induced by administration of Lactobacillus kefiranofaciens DN1 -Dana Jeong – Food & Function
Plant, root, and soil microbiome
Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland – Theresa A. McHugh- Environmental Microbiology
Water and extremophile microbiome
Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls – Petra Pop Ristova – PLoS One
Probiotics / prebiotics
*Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity – Robert S Thompson – Frontiers in Behavioral Neuroscience
Changes in the Gut Microbiota After Early Administration of Oral Synbiotics to Young Infants in India – DS Chandel -Journal of Pediatric Gastroenterology Nutrition
Techniques
Home-made cost effective preservation buffer is a better alternative to commercial preservation methods for microbiome research – Sebastian Menke- Frontiers in microbiology
Furosemide enhances the sensitivity of urinary metabolomics for assessment of kidney function – Isaie Sibomana – Metabolomics
Impact of sample processing on human airways microbial metagenomes – Lutz Wiehlmann – Journal of Biotechnology
Microbes in the news
Scientists develop new flu vaccines for dogs
New Insight Describes Connection between Salmonella Infection and Appetite Loss
Anitha’s non-microbiology picks
Tiny Satellites to Make Big Contributions to Science
First report of metallic hydrogen on earth – Hydrogen turned into metal in stunning act of alchemy that could revolutionise technology and spaceflight
Storify of the Human Microbiome Congress
(Crossposting from the NPJ Biofilms and Microbiome Community website)
This week I visited the Human Microbiome Congress in San Diego, where Kisaco Research brought together a splendid group of academic and industry researchers, who talked about their latest research. I really enjoyed listening to all these great speakers, and wanted to share this great event with the rest of the world, so I live-tweeted all the talks from my Twitter account @MicrobiomDigest. In case you missed it, here is a Storify with all my ~400 tweets. So grab a beer (or a kombucha) and some popcorn, and enjoy.
Storify of the Human Microbiome Congress in San Diego
We also held a 500WomenScientists meeting organized by Jessica Metcalf (who tweeted the first photo below).

And uBiome was represented at the poster session too! This was the first time I ordered a fabric poster, and it was great. Arrived folded up at my house (sort of like a t-shirt), and fitted easily in my luggage. I could have done a slightly better job ironing it (which is how you get rid of the wrinkles) but it was so much easier than traveling with a glossy print in a big tube. I ordered my poster at MakeSigns; poster + shipping (3 days after ordering) was $120. Recommended!

January 26, 2017
Environmental ecology review presents how microbial life strategy concepts are applied in complex microbial communities. Two interesting model systems are described in the techniques section, plus potentially scalable workflow for the preparation of high potency Akkermansia muciniphila cells for therapeutic interventions. The importance of understanding the role of the microbiome in preventing complications after organ transplant and surgeries are discussed in two reviews. Another study shows that proton pump inhibitors used to prevent gastric ulcers were associated with distinct gut microbiota signatures. For faster wound healing, try some saliva. A study shows the beneficial effects of saliva on wound healing in human epidermal keratinocytes and on the attenuation of intracellular Staph. aureus infection.
Pregnancy and early life
Assessment of the synbiotic properties of human milk oligosaccharides and Bifidobacterium longum subsp. infantis in vitro and in humanised mice – S Musilova- Beneficial Microbes
Multi-site human microbiome
Review: Infection in Organ Transplantation – Jay A. Fishman – American Journal of Transplantation
Review: The gut microbiome and the mechanism of surgical infection – J.C. Alverdy – The British Journal of Surgery
Human Oral Microbiome
Salivary mucins promote the coexistence of competing oral bacterial species – Erica Shapiro Frenke- The ISME Journal
Human skin microbiome
Saliva induces expression of antimicrobial peptides and promotes intracellular killing of bacteria in keratinocytes by epidermal growth factor receptor transactivation – T. Mohanty – British Journal of Dermatology
Human gut microbiome
The influence of proton pump inhibitors and other commonly used medication on the gut microbiota – Floris Imhann – Gut Microbes
Animal experiments
Review: Understanding host-microbial interactions in rumen: searching the best opportunity for microbiota manipulation – Nilusha Malmuthuge – Journal of Animal Science and Technology
Plant, root, and soil microbiome
Review: Revisiting life strategy concepts in environmental microbial ecology – Adrian Ho- FEMS Microbiology Ecology
Diclofop-methyl affects microbial rhizosphere community and induces systemic acquired resistance in rice – Si Chen – Journal of Environmental Sciences
Food microbiology
Review: Human pathogens in plant biofilms: Formation, physiology, and detection – Eduardo Ximenes – Biotechnology and Bioengineering
Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork -Koji Yahara – Environmental Microbiology
Digestive fate of dietary carrageenan: Evidence of interference with digestive proteolysis and disruption of gut epithelial function – Lulu Fahoum – Molecular Nutrition Food Research
Bioinformatics
It’s a big data problem: researchers from the University of California, San Diego and the J.C. Venter Institute used machine learning to teach a computer to learn to distinguish between healthy and unhealthy gut microbiomes. The new approach shows promise for predicting related health issues and providing guidance for therapy development. More from the press
Techniques
Preparation and preservation of viable Akkermansia muciniphila cells for therapeutic interventions – JP Ouwerkerk -Beneficial Microbes
Evaluation of colonization resistance in stool of human donors using ex vivo, in vitro and in vivo assays – MF Galvão – Beneficial Microbes
Improving metabolite production in microbial co-cultures using a spatially constrained hydrogel – Matthew J. Smith – Biotechnology and Bioengineering
Microbes in the news
CRISPR research institute expands into agriculture, microbiology
Dog obesity, a growing problem, may be managed through diet and exercise and- microbiology
Every surfer knows you should stay out of the water for 72 hours after it rains. Public health officials issued an advisory for all Los Angeles County beaches, cautioning swimmers and surfers to stay away from areas near storm drains, creeks and rivers. But when the waves show – some surfers just can’t help themselves.
January 25, 2017
Joint opinion on measures by the EU to reduce antimicrobial agents in animal husbandry, diet changes the gut microbiome of dogs, and synthetic chemicals might drive global climate change.
Jobs
PhD Position: THE ROLE OF THE GUT MICROBIOME IN LIVER DISEASE: DEVELOPMENT Of BIOINFORMATIC APPROACHES TO IDENTIFY, CHARACTERISE AND ANALYSE THE GUT VIROME – KU Leuven
Postdoctoral Research Scientist, Microbiology, School of Natural Sciences, NUI Galway
Microbiology Supervisor – Clinical Pathology Laboratories, Inc
General microbiology and policy
Artificial bacteria: A semisynthetic organism engineered for the stable expansion of the genetic alphabet – Yorke Zhang – PNAS
- Press: First step to ‘designer life’: Biologists breed bacteria with lab-made DNA, adding two extra, artificial letters – Ben Guarino – Washington Post
Policy opinions: EMA and EFSA Joint Scientific Opinion on measures to reduce the need to use antimicrobial agents in animal husbandry in the European Union, and the resulting impacts on food safety (RONAFA) – CVMP and BIOHAZ – EFSA Journal
Acid-suppression medications and bacterial gastroenteritis: a population-based cohort study – Wei Li – british journal of clinical pharmacology
Animal experiments
Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions – Qinghong Li – mBio
- Press: Study shows how a dog’s diet shapes its gut microbiome – Phys.org
Water and extremophile microbiome
Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality – Elvina Lee – PLoS One
Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing – Mathis Hjort Hjelmsø – PLoS One
Phages and viruses
FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems – Luis Jose Rene Arredondo-Hernandez – PLoS One
The Complete Genome Sequence of a Second Distinct Betabaculovirus from the True Armyworm, Mythimna unipuncta – Robert L. Harrison – PLoS One
Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand – Achiraya Siriphap – PLoS One
Bioinformatics
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective – Not Only Size Matters! – John Vollmers – PLoS One
Microbes in the news
Study: Babies’ Microbiomes Indifferent to Mode of Delivery – Kerry Grens – The Scientist
About FishTaco: Microbiome as complex as previously thought – Julian Harris – PHG Foundation
Auckland’s water shock: Bacteria levels ‘dangerously high’ – NZ Herald
For healthier buildings, just add bacteria? – Ed Yong – Ted
Xin’s non-microbiology pick
Synthetic chemicals as agents of global change – Emily S Bernhardt – Frontiers in Ecology and the Environment