April 23, 2017

Water and extremophile microbiome

Size fractionated phytoplankton biomass and net metabolism along a tropical estuarine gradient – Sara Soria-Píriz – Limnology and Oceanography

Tropical mangrove swamp metagenome reveals unusual abundance of ecologically important microbes – Zahidah Ismail – Current Science


HirBin: high-resolution identification of differentially abundant functions in metagenomes – Tobias Österlund – BMC Genomics

Microbes in the news

Using elements of viruses, antibodies to fight resistant bacteria – Chris Dall – CIDRAP News

Lower Hutt officials investigate bacteria in water – Newshub

Stowaway Bacteria Could Be Even More Contagious in Space Than We Thought – Peter Dockrill – Science Alert

April 16, 2017

A post with an overgrowth of gut and skin microbiome papers. Talk about dysbiosis!


General microbiome

The ovarian cancer oncobiome – Sagarika Banerjee – Oncotarget

A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam – Saurav Das – Genomics Data

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

Microbiota and their affiliation with physiochemical characteristics of different subsurface petroleum reservoirs – Xiao-Xiao Li – International Biodeterioration & Biodegradation

Sampling, sequencing and the SAD – Sharon Bewick – Ecological Complexity

Pregnancy and early life

The Maternal Diet, Gut Bacteria, and Bacterial Metabolites during Pregnancy Influence Offspring Asthma – Lawrence E. K. Gray – Frontiers in Immunology

Deficiency Leads to Dysbiosis and Bacterial Translocation in the Newborn Intestine – Jason Fawley – Journal of Surgical Research

Human respiratory microbiome

The microbiome of the lung and its extracellular vesicles in nonsmokers, healthy smokers and COPD patients – Hyun Jung Kim – Experimental & Molecular Medicine

Human skin microbiome

The Molecular Revolution in Cutaneous Biology: Investigating the Skin Microbiome – Heidi H. Kong – Journal of Investigative Dermatology

Microbiome controls mast cell differentiation in the skin – Z. Wang – Journal of Investigative Dermatology

Inflammatory gene expression in keratinocytes is regulated by HDAC8 and HDAC9 and is modulated by metabolites from the microbiome – J. Sanford – Journal of Investigative Dermatology

Ultraviolet radiation alters the skin microbiome composition – H. Ahmed – Journal of Investigative Dermatology

Isolation and Identification of the follicular microbiome: Implications for acne research – Amanda Nelson – Journal of Investigative Dermatology

Role of the cutaneous microbiome in the pathogenesis of psoriasis – D. Yan – Journal of Investigative Dermatology

Skin microbiome and psoriasis: Staphylococcus induces robust biofilm formation by Aspergillus – Pranab Mukherjee – Journal of Investigative Dermatology

Microbiome-free fatty acid cross-talk in the human pilosebaceous gland – S. Singh – Journal of Investigative Dermatology

Changes of lesional and non-lesional skin microbiome in the treatment course of atopic dermatitis – J. Na – Journal of Investigative Dermatology

Human gut microbiome

Clinical, functional, behavioural and epigenomic biomarkers of obesity – Claudio L. Lafortuna – Frontiers in Bioscience

‘Collinsella phocaeensis’ sp. nov., ‘Clostridium merdae’ sp. nov., ‘Sutterella massiliensis’ sp. nov., ‘Sutturella timonensis’ sp. nov., ‘Enorma phocaeensis’ sp. nov., ‘Mailhella massiliensis’ gen. nov., sp. nov., ‘Mordavella massiliensis’ gen. nov., sp. nov. and ‘Massiliprevotella massiliensis’ gen. nov., sp. nov., 9 new species isolated from fresh stool samples of healthy French patients – S. Ndongo – New Microbes and New Infections

Editorial: Understanding Crohn’s Disease: Immunity, Genes and Microbes – Amelia Sarmento – Frontiers in Immunology

Human Derived Gut Microbiota Modulates Colonic Secretion in Mice by Regulating 5-HT3 Receptor Expression via Acetate Production – Yogesh Bhattarai – American Journal of Physiology: Gastrointestinal and Liver Physiology

Gastroparesis and lipid metabolism-associated dysbiosis in Wistar Kyoto rats – Julie E Dalziel – American Journal of Physiology: Gastrointestinal and Liver Physiology

How do they stick together? Bacterial adhesins implicated in the binding of bacteria to the human gastrointestinal mucins – Bélinda Ringot-Destrez – Biochemical Society Transactions

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort – Elin Org – BioMed Central Genome Biology

Gut microbiota plays a role in the development of alopecia areata – Lekha Nair – Journal of Investigative Dermatology

Dysbiosis of gut microbiota by ampicillin exacerbates vitiligo – S. Akhtar – Journal of Investigative Dermatology

More frequent hemodialysis does not effectively clear protein-bound azotemic solutes derived from gut microbiome metabolism – Andrew Davenport – Kidney International

Gut microbiota and Hepatitis B virus-Induced Chronic Liver Disease: implications for faecal microbiota transplantation therapy – Yongbo Kang – Journal of Hospital Infection

The effect of probiotics as a treatment for constipation in elderly people: a systematic review – Maria Isabel Martínez-Martínez – Archives of Gerontology and Geriatrics

Colonic microbiota encroachment correlates with dysglycemia in humans – Benoit Chassaing – Cellular and Molecular Gastroenterology and Hepatology

Animal microbiome

Liver microbiome of Peromyscus leucopus, a key reservoir host species for emerging infectious diseases in North America – Adrien André – Infection, Genetics and Evolution

Plant, root, and soil microbiome

Conversion of rainforest into agroforestry and monoculture plantation in China: Consequences for soil phosphorus forms and microbial community – Jinchuang Wang – Science of the Total Environment

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

Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere – Jordan Vacheron – Genome Anouncements

Wars between microbes on roots and fruits – Ben Lugtenberg – F1000Research

Food microbiology

Metagenomic assessment of the microbial diversity in ground pork products from markets in the North Central Region of South Korea – Ok-Kyung Koo – Journal
Journal of Environmental Science and Health

Growth of selected probiotic bacterial strains with fructans from Nendran banana and garlic – Ravichandran Shalini – LWT: Food Science and Technology


Suitability of various DNA extraction methods for a traditional Chinese paocai system
Nan Zhao – Bioengineered

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies – William W. Greenwald – BioMed Central Genomics

Microbes in the news

IISc makes two potent molecules to fight TB – Ravindranath Prasad – The Hindu

Essential California: Inside UC Irvine hospital’s bacteria outbreak among infants – Benjamin Oreskes and Shelby Grad – Los Angeles Times

April 2, 2017

An article on the transfer of Rickettsia via ticks and news articles on various pathogens in the news!

Events and jobs

Bioengineering researcher – Shell Oil Company

Animal microbiome

Catalase is a determinant of the colonization and transovarial transmission of Rickettsia parkeri in the Gulf Coast tick Amblyomma maculatum – Khemraj Budachetri – Insect Molecular Biology

Microbes in the News

Bacteria could be cause of dolphin stranding deaths on Cape – Mary Ann Bragg – Cape Cod Times

Bacteria found in drinking water flushed – Marianne Napoles – Champion Newspapers

NICU at Maryland hospital to reopen after investigation of Pseudomonas bacteria – Arelis R. Hernández – Albuquerque Journal

February 4, 2017

Today: articles on the nutrient niches that exist in the gut, how bifidobacterium might be functioning as a probiotic, and probiotic treatment in Bactrocera cucurbitae (melon fly), and astronaut’s gut bacteria in flight.

General microbiome

Effect of fermentation temperature on hydrogen production from xylose and the succession of hydrogen-producing microflora – Chunsheng Qiu – Journal of Chemical Technology and Biotechnology

Dental and periodontal health, and microbiological and salivary conditions in patients with or without diabetes undergoing haemodialysis – Gerhard Schmalz – International Dental Journal

Human gut microbiome

Microbial nutrient niches in the gut – Fátima C. Pereira – Environmental Microbiology

MicroRNAs at the epicenter of intestinal homeostasis – Antoaneta Belcheva – BioEssays

Oscillospira and related bacteria – From metagenomic species to metabolic features – Uri Gophna – Environmental Microbiology

Association between small-intestinal bacterial overgrowth and deep vein thrombosis in patients with spinal cord injuries – X. Cheng – Journal of Thrombosis and Haemostasis

Prioritization of polysaccharide utilization and control of regulator activation in Bacteroides thetaiotaomicron – Nathan D. Schwalm III – Molecular Microbiology

Animal experiments

Malondialdehyde epitopes are sterile mediators of hepatic inflammation in hypercholesterolemic mice – Clara Jana-Lui Busch – Hepatology

Time- and strain-specific downregulation of intestinal EPAS1 via miR-148a by Bifidobacterium bifidum – Amel Taibi – Molecular Nutrition and Food Research

Animal microbiome

Enhanced fitness of a Bactrocera cucurbitae genetic sexing strain based on the addition of gut-isolated probiotics (Enterobacter spec.) to the larval diet – Mingyan Yao – Entomologia Experimentalis et Applicata

Water and extremophile microbiome

Chemotype diversity in Planktothrix rubescens (cyanobacteria) populations is correlated to lake depth – Danka Haruštiaková – Environmental Microbiology Reports

Genomic and physiological analyses of ‘Reinekea forsetii’ reveal a versatile opportunistic lifestyle during spring algae blooms – Burak Avcı – Environmental Microbiology


DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes – Lemian Liu – Molecular Ecology Resources

Microbes in the news

Change in astronaut’s gut bacteria attributed to spaceflight

Oral dose of phage cocktail prevents infection and cholera-like symptoms in animal model

UNH researchers ID bacteria contaminating seafood

Tap Water Free of Diarrhea-Causing Bacteria: Pittsburgh Mayor

Science in the News series kicks off with ‘Big Bacteria, Big Pharma, Big Problems’

Salicylic acid promotes nasal mucosa colonization by Staphylococcus aureus

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

New Market Analysis: The global clinical microbiology market is projected to reach USD 5.77 Billion by 2021

Bacteria Hysteria

SHOCKING: You won’t BELIEVE how many GERMS are on your hands