January 5, 2018

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Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology

 

 

January 4, 2017

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Implication of dysbiosis in arthritis in rats, studying soil crust biology and chemistry using metabolomics, a news article on exercise and the microbiome.

Human gut microbiome

Comprehensive analysis of polyamine transport and biosynthesis in the dominant human gut bacteria: Potential presence of novel polyamine metabolism and transport genes – Yuta Sugiyama – The International Journal of Biochemistry & Cell Biology

Animal experiments

Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis – Tejpal Gill – Arthritis & Rheumatology

Plant, root, and soil microbiome

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics – Tami L Swenson – Nature Communications

Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice – Boknam Jung – Nature Communications

Synergistic action of rhizospheric fungi with Megathyrsus maximus root speeds up hydrocarbon degradation kinetics in oil polluted soil – Michael Dare Asemoloye – Chemosphere

Pre-print: Crop diversity increases disease suppressive capacity of soil microbiomes – Ariane L Peralta – bioRxiv

Microbes in the news

Exercise Alters Our Microbiome. Is That One Reason It’s So Good for Us? – Gretchen Reynolds – The New York Times

Bifidobacterium or fiber protect against deterioration of the inner colonic mucus layer – ScienceDaily

Scientists use sound to track tiny organisms in the body – Angela Chen – The Verge

Bacteria and Cancer: Another Connection – Derek Lowe – Science Translational Medicine

January 3, 2018

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Today we have a nice event /training in social science techniques organized by NERC in Manchester, Bristol and Edinburgh (UK), few microbiology jobs, an interesting review from Arun T. Nair in “Gut Microbiome”, quite a few papers about Synechococcus in “Water and extremophile microbiome”. Check as well “Microbes on market” where you can read about Google and Microsoft investing in medicine startup DNAnexus.

Events

Social science techniques for natural scientists training funded by NERC, UK

Jobs

Microbiologist – Kent, UK

Scientist/Sr.Scientist – Strain Development, CJM Talent Solutions, San Francisco, US

Associate/Assistant Professor : Miami, Florida, FL, US

General microbiome

Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds – Clifford G. Clark – PLOS

Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing – Heather P. McLaughlin -PLOS

The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis – Anita Loeschcke -PLOS

Pregnancy and early life

Effect of innate antiviral glycoproteins in breast milk on seroconversion to rotavirus vaccine (Rotarix) in children in Lusaka, Zambia – Katayi Mwila-Kazimbaya – PLOS

Oral microbiome

Frequency and levels of candidate endodontic pathogens in acute apical abscesses as compared to asymptomatic apical periodontitis – Isabela N. Rôças – PLOS

Human vaginal microbiome

Combined oral and topical antimicrobial therapy for male partners of women with bacterial vaginosis: Acceptability, tolerability and impact on the genital microbiota of couples – A pilot study – Erica L. Plummer – PLOS

Candida albicans-derived mannoproteins activate NF-κB in reporter cells expressing TLR4, MD2 and CD14 – Traci Ness – PLOS

Replication-dependent size reduction precedes differentiation in Chlamydia trachomatis – Jennifer K. Lee – Nature Communications

Human gut microbiome

T6SS: The bacterial “fight club” in the host gut – Thibault G. Sana – PLOS Pathogens

Review: Gut Microbiota Dysfunction as Reliable Non-invasive Early Diagnostic Biomarkers in the Pathophysiology of Parkinson’s Disease: A Critical Review – Arun T Nair – Journal of Neurogastroenterology and Motility

Animal experiments

Effect of dietary xylooligosaccharides on intestinal characteristics, gut microbiota, cecal short-chain fatty acids, and plasma immune parameters of laying hens – X M Ding – Poultry Science

Influence of a diet enriched with virgin olive oil or butter on mouse gut microbiota and its correlation to physiological and biochemical parameters related to metabolic syndrome – Isabel Prieto – PLOS

Modulation of the diet and gastrointestinal microbiota normalizes systemic inflammation and β-cell chemokine expression associated with autoimmune diabetes susceptibility – Angela M. Henschel – PLOS

Dietary Lactobacillus acidophilus positively influences growth performance, gut morphology, and gut microbiology in rurally reared chickens  – C Forte – Poultry Science

Animal microbiome

Oral Disease and Microbiota in Free-Roaming Cats – Ana Whyte – Topics in Companion Animal Medicine

Review: Effect of Enterococcus Faecium Strain SF68 on Gastrointestinal Signs and Fecal Microbiome in Cats Administered Amoxicillin-Clavulanate – C. Torres-Henderson – Topics in Companion Animal Medicine

Water and extremophile microbiome

Clade and strain specific contributions of Synechococcus and Prochlorococcus to carbon export in the Sargasso Sea – Francesca De Martini – Limnology and Oceanography

Microbial proteins for organic material degradation in the deep ocean – David L. Kirchman – PNAS

Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons – Yihwan Kim – PLOS

Potential impact of global climate change on benthic deep-sea microbes – Roberto Danovaro – FEMS Microbiology Letters

Variability in the production of organic ligands, by Synechococcus PCC 7002, under different iron scenarios – Guillermo Samperio-Ramos – Journal of Oceanography

Effect of light on N2 fixation and net nitrogen release of Trichodesmium in a field study – Yangyang Lu – Biogeosciences

Microbial diversity of saline environments: searching for cytotoxic activities – Carolina Díaz-Cárdenas – AMB Express

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses – Deepak Kumaresan – BMC Microbiome

Probiotics / prebiotics

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host and Microbe

Modifying progression of aging and reducing the risk of neurodegenerative diseases by probiotics and synbiotics – Huey Shi Lye – Frontiers In Bioscience

Phages and viruses

Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves – Pantelis Katharios – PLOS

High human papillomavirus (HPV) prevalence in South African adolescents and young women encourages expanded HPV vaccination campaigns – Zizipho Z. A. Mbulawa – PLOS

Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis – Luis E. M. Villegas – PLOS

Localized Recombination Drives Diversification of Killing Spectra for Phage Derived Syringacins – David Baltrus – bioRxiv

Bioinformatics

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing – Chao Fang – Giga Science

 

Techniques

Imaging bacteria inside their host by cryo-focused ion beam milling and electron cryotomography – João M Medeiros – Current Opinion in Microbiology

Microbes in the news

Tech company’s lights being used to kill germs in ambulances

Astronauts Identify Mystery Microbes in Space for the 1st Time

Microbes on the market

Seres Therapeutics Inc (MCRB) Holdings Increased by State Street Corp

Microsoft, Google invest in precision medicine startup DNAnexus

Tina’s non-microbiology picks

Synthetic Biology in the Driving Seat of the Bioeconomy – Yensi Flores Bueso – Trends in Biotechnology

Expect exoplanet atmospheres, organs with new functions and fewer traffic jams in 2018

The best microbiome papers of 2017

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Happy New Year again!

Last week, I asked you all to vote for the best microbiome papers of 2017. And just like the previous year, we have a very clear winner. A paper that had some obvious help from the author’s Facebook friends, who all wrote in to vote 🙂

Full disclosure: I was the handling editor of this paper.

The winner is…. (drumroll)….

Second place was won by:

And in shared third/fourth place:

Other nominees were:

I wish you all the best for the new year! Hopefully, 2018 will bring even more great microbiome science papers.

January 2, 2018

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Happy New Year from the Microbiome Digest team!

General microbiome

Pre-print: Understanding How Microbiomes Influence The Systems They Inhabit: moving from a correlative to a causal research framework – E K Hall – bioRxiv

Human vaginal microbiome

A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women – Bryan A Wee – Australian and New Zealand Journal of Obstetrics and Gynaecology

Human gut microbiome

Rates of Gut Microbiome Divergence in Mammals – Alex H Nishida – Molecular Ecology

Animal microbiome

Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands) – Laura Baldo – FEMS Microbiology Ecology

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel – Microbial Ecology

Plant, root, and soil microbiome

Vertical variation of a black soil’s properties in response to freeze-thaw cycles and its links to shift of microbial community structure – Ziming Han – Science of the Total Environment

Biomass, activity and structure of rhizosphere soil microbial community under different metallophytes in a mining site – Wenhao Yang – Plant and Soil

Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin – Current Opinion in Plant Biology

Water and extremophile microbiome

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China – Jun Liu – Environmental Pollution

Pre-print: Micro-scale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N Enke – bioRxiv

Food microbiology

Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment – Narciso M Quijada – International Journal of Food Microbiology

Bioinformatics

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision – Damayanthi Herath – BMC Bioinformatics

Techniques

Serial Dilution-Based Growth Curves and Growth Curve Synchronization for High-Resolution Time Series of Bacterial Biofilm Growth – Fernando Govantes – Host-Pathogen Interactions

Microbes in the news

Fiber Is Good for You. Now Scientists May Know Why. – Carl Zimmer – The New York Times

Fast, Cheap Testing for Tuberculosis? Soon It May Be Possible – Donald G McNeil – The New York Times

How probiotics can help ward off health complications in premature babies – CTV News

Science, career, and publishing

Pre-print: Disequilibrium in Gender Ratios among Authors who Contributed Equally – Nichole A Broderick – bioRxiv

December 31, 2017

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A rich Digest to end 2017! There are several reviews on human gut microbiome and lots of papers on plant , root and soil microbiome. The airway microbiome is trending today and scientists are starting to examine rigorously the effect of herbal medicine on the gut microbiota. Happy Reading and Happy New Year!

General microbiology

Bacterial pathogens were detected from human exhaled breath using a novel protocol – Yunhao Zheng et al. – Journal of Aerosol Science

Bacteria Facilitate Enteric Virus Co-infection of Mammalian Cells and Promote Genetic Recombination – Andrea K. Erickson et al. – Cell Host & Microbe

Human airway microbiome

Review: Airway microbial metagenomics – Katarzyna Pienkowska et al. – Microbes and Infection

Respiratory syncytial virus and rhinovirus bronchiolitis are associated with distinct metabolic pathways – Christopher J Stewart et al. – Journal of Infectious Diseases

Tech Note: A breath of information: the volatilome – M. Mansurova et al. – Current Genetics

Short-term particulate matter exposure influences nasal microbiota in a population of healthy subjects – Jacopo Mariani et al. – Environmental Research

Exposure to traffic-related air pollution and the composition of the gut microbiota in overweight and obese adolescents – Tanya L. Alderete et al. – Environmental Research

Human gut microbiome

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers – Abhijit Maji et al. – Environmental Microbiology

Review: Targeting the gut barrier for the treatment of alcoholic liver disease – Zhanxiang Zhou and Wei Zhong – Liver Research

Review: Microbial Regulation of Glucose Metabolism and Insulin Resistance – Crommen S and Simon MC – Genes

Review: Gut microbiota in the pathogenesis of inflammatory bowel disease – Nishida A et al. – Clinical Journal of Gastroenterology

Review: Human Intestinal Microbiota: Interaction Between Parasites and the Host Immune Response – Oswaldo Partida-Rodríguez et al. – Archives of Medical Research

Review: Gut dysbiosis and irritable bowel syndrome: the potential role of probiotics – Nicola Principi et al. – Journal of Infection

Review: Gut Microbiota in Obesity and Metabolic Abnormalities: A Matter of Composition or Functionality? – Sofia Moran-Ramo et al. – Archives of Medical Research

In vitro: An in vitro study to assess the impact of tetracycline on the human intestinal microbiome – Ji Young Jung et al. – Anaerobe

Human gut-microbiome-brain axis

Review: Targeting gut microbiome: A novel and potential therapy for autism – Yongshou Yang et al. – Life Sciences

Metabolomics

Dark matter in host-microbiome metabolomics: Tackling the unknowns–A review – B.Y. Loulou Peisl et al. – Analytica Chimica Acta

Animal experiments

Mouse: Intestinal Ralstonia pickettii augments glucose intolerance in obesity – Shanthadevi D. Udayappan et al. – PLoS One

Pig: Structural Modulation of Gut Microbiota during Alleviation of Suckling Piglets Diarrhoea with Herbal Formula – Cui Liu et al. – Evidence-Based Complementary and Alternative Medicine

Rat: Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis – Gill T et al. – Arthritis and Rheumatology

Changes in mouse gut bacterial community in response to different types of drinking water – Marcela F. Dias et al. – Water Research

Mouse: Particle size determines the anti-inflammatory effect of wheat bran in a model of fructose over-consumption: Implication of the gut microbiota – Francesco Suriano & Audrey M. Neyrinck et al. – Journal of Functional Foods

Mouse: Mushroom polysaccharides from Ganoderma lucidum and Poria cocos reveal prebiotic functions – Imran Khan et al. – Journal of Functional Foods

Animal microbiome

Bacterial diversity of wild-caught Lutzomyia longipalpis (a vector of zoonotic visceral leishmaniasis in Brazil) under distinct physiological conditions by metagenomics analysis – Ana Clara Araújo Machado Pires et al. – Parasites & Vectors

Drosophila Perpetuates Nutritional Mutualism by Promoting the Fitness of Its Intestinal Symbiont Lactobacillus plantarum – Gilles Storelli et al. – Cell Metabolism

Analysis of the influence of living environment and age on vaginal fungal microbiome in giant pandas (Ailuropoda melanoleuca) by high throughput sequencing – Danyu Chen et al. – Microbial Pathogenesis

Plant, root and soil microbiome

Phosphate levels influence the utilisation of rice rhizodeposition carbon and the phosphate-solubilising microbial community in a paddy soil – Xi-En Long et al. – Soil Biology and Biochemistry

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms – Aspen T. Reese et al. – Ecology and Evolution

Responses of bulk and rhizosphere soil microbial communities to thermoclimatic changes in a Mediterranean ecosystem – Javier Pascual et al. – Soil Biology and Biochemistry

Remediation of arsenic in mung bean (Vigna radiata) with growth enhancement by unique arsenic-resistant bacterium Acinetobacter lwoffii – Joyati Das and Priyabrata Sarkar – Science of the Total Environment
https://www.sciencedirect.com/science/article/pii/S0048969717335830

* Opinion: Why we need a National Living Soil Repository – Daniel K. Manter et al. – PNAS

Long-term effects of nitrogen fertilization on aggregation and localization of carbon, nitrogen and microbial activities in soil – Yidong Wang et al. – Science of the Total Environment

Vineyard microbiome variations during different fertilisation practices revealed by 16s rRNA gene sequencing – Loredana Canfora et al. – Applied Soil Ecology

* Co-occurrence patterns of soybean rhizosphere microbiome at a continental scale – Baogang Zhang et al. – Soil Biology and Biochemistry

Review: Symbiotic nitrogen fixation by rhizobia — the roots of a success story – Catherine Masson-Boivin and Joel L Sachs – Current Opinion in Plant Biology

Water and extremophile microbiome

PDF: From extreme environments to human pathogens: an evolutionary journey – Donato Giovannelli and Costantino Vetriani – Biochemical Society

Comparison of Iris pseudacorus wetland systems with unplanted systems on pollutant removal and microbial community under nanosilver exposure – Juan Huang et al. – Science of the Total Environment

Impacts of design configuration and plants on the functionality of the microbial community of mesocosm-scale constructed wetlands treating ibuprofen – Liang Zhang et al. – Water Research

Microbial community evolution in partial nitritation/anammox process: From sidestream to mainstream – Yandong Yang et al. – Bioresource Technology

Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant – Luanfeng Hou et al. – Science of the Total Environment

Built environment microbiome

Microbiological air contamination in university premises and the evaluation of drug resistance of staphylococci occurring in the form of a bioaerosol – Katarzyna Wolny-Koładka et al. – Indoor and Built Environment

Phages and viruses

Virome analysis of lily plants reveals a new potyvirus – Yongqiang Li et al. – Archives of Virology

Comparative Analysis of 37 Acinetobacter Bacteriophages – Dann Turner et al. – Viruses

Antiviral systems in vector mosquitoes – Tong Liu et al. – Developmental & Comparative Immunology

Microbes in the news

Launceston associate professors studying gut microbiome in elderly Tasmanians – Carly Dolan – Examiner

Biofilm made of mulberry silk to destroy dengue virus – TNN – Times of India

Rhode Island Health Department finds E. coli bacteria, issues boil water notice – PATRICIA RESENDE & TONY GUGLIOTT – NBC 10

Op-Ed: Survival tips in the age of drug-resistant bacteria – Kevin Kavanagh – Lexington Herald Leader

* One Big Family: This Beautiful Interactive Diagram Shows How Every Organism Is Related – Fiona McMillan – Forbes

Researchers propose different approach to beat antibiotic-resistant superbugs – News Medical

 

December 30, 2017

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Enjoy your daily dose of (mostly human gut) microbiome literature!

General microbiome

Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes – Nicole Gerardo, BMC Biology

The Dark Side of IFN-γ: Its Role in Promoting Cancer Immunoevasion – Marija Mojic, International Journal of Molecular Sciences

Two-stage pretreatment of excess sludge for electricity generation in microbial fuel cell – Yi Zhang, Environmental Technology

Human respiratory microbiome

Azithromycin versus placebo for the treatment of HIV-associated chronic lung disease in children and adolescents (BREATHE trial): study protocol for a randomised controlled trial – Carmen Gonzalez-Martinez, BMC Biology

Human skin microbiome

Characterization of the facial microbiome in twins discordant for rosacea – Asifa K. Zaidi, Experimental Dermatology

Human oral microbiome

Oral health in geroscience: animal models and the aging oral cavity – Jonathan Y. An, GeroScience

Extracellular matrix Influence in Streptococcus mutans gene expression in a cariogenic biofilm – Elkin Jahir Florez Salamanca, Molecular Oral Microbiology

Human gut microbiome

The Microbiome–Gut–Behavior Axis: Crosstalk Between the Gut Microbiome and Oligodendrocytes Modulates Behavioral Responses – Achilles Ntranos, Neurotherapeutics

Antibiotics Associated Disorders and Postbiotics Induced Rescue in Gut Health – Debarati Paul, Current Pharmaceutical Design

We are not alone in our body: insights into the involvement of microbiota in the etiopathogenesis and pharmacology of mental illness –  Claudia Pisanu, Current Drug Metabolism

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003 – Francesca Bottacini, BMC Genomics

Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis – Michael A. Henson, BMC Systems Biology

Gut microbiota: Fibre restores healthy gut microbiota – Alan Morris, Nature Reviews Endocrinology

The human microbiome in evolution – Emily R. Davenport, BMC Biology

Clinical characteristics and long-term prognosis of elderly onset ulcerative colitis – Eun Mi Song, Gastroenterology and Hepatology

Environmental contributions to gastrointestinal and liver cancer in the Asia–Pacific region – Kwang-Pil Ko, Gastroenterology and Hepatology

Effect of oral tobacco use and smoking on outcomes of Crohn’s disease in India – Umang Arora, Gastroenterology and Hepatology

Irritable bowel syndrome in Asia: Pathogenesis, natural history, epidemiology, and management – Kok-Ann Gwee, Gastroenterology and Hepatology

Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial – Nina Kimer, Gastroenterology and Hepatology

The role of the microbiome and the use of probiotics in gastrointestinal disorders in adults in the Asia-Pacific region – background and recommendations of a regional consensus meeting – Uday C Ghoshal, Gastroenterology and Hepatology

Animal experiments

Inclusion of Bacillus amyloliquefaciensstrain TOA5001 in the diet of broilers suppresses the symptoms of coccidiosis by modulating intestinal microbiota – Takamitsu Tsukahara, Animal Science Journal

Characterization of the cervical bacterial community in dairy cows with metritis and during different physiological phases – Yu Wang, Theriogenology

Replacement of alfalfa hay (Medicago sativa L.) with subabul (Leucaena leucocephala) leaf meal in diets of Najdi goats: effect on digestion activity of rumen microorganisms – Tahereh Mohammadabadi, Tropical Animal Health and Production

Animal microbiome

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel, Microbial Ecology

Plant, root, and soil microbiome

Changes of microbial population and N-cycling function genes with depth in three Chinese paddy soils – Huanhuan Wang, PLOS One

Water and extremophile microbiome

Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome – Sophie S Abby, bioRxiv

Microbes in the news

Artificial intelligence identifies bacteria images quickly, accurately – Greg Slabodkin, Health Data Management

Microbes on the market

Assembly Biosciences, Inc. (ASMB) Reaches $45.08 After 7.00% Up Move; GEOX SPA (GXSBF) Shorts Raised By 18.36% – Stephen Andrade, Herald KS

December 29, 2017

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It’s a bit quiet towards the end of the year, but not without highlights. Could we fight antibiotic resistance by targeting mild infections using alternative drugs? Do we want to correct our own genes using CRISPR and what’s the future for penicillin?

Jobs

Associate Professor – Microbiology – Dental College -chennai

General microbiology

Efficient Hydrogen-Dependent Carbon Dioxide Reduction by Escherichia coli – Magali Roger et al. – Current Biology

Press: Bacteria under pressure run reaction in reverse to sequester carbon – John Timmer – Ars Technica

The Role of Type VI Secretion System Effectors in Target Cell Lysis and Subsequent Horizontal Gene Transfer – Peter David Ringel et al. – Cell Reports

Press: Predatory Bacteria Acquire Drug Resistance Directly from Rivals – Genetic Engineering & Biotechnology News

* Alternative therapeutics for self-limiting infections—An indirect approach to the antibiotic resistance challenge – Kristofer Wollein Waldetoft and Sam P. Brown – PLoS Biology

Author interview: Alternatives to Antibiotics: Why managing mild maladies matters – Beth Baker – PLoS Research News

Animal experiments

Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets – María Carla Piazzon et al. – Microbiome

Animal microbiome

Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases – Panpim Thongsripong et al. – Ecology and Evolution

Plant, root and soil microbiome

Rhizosphere-associated Alcaligenes and Bacillus strains that induce resistance against blast and sheath blight diseases, enhance plant growth and improve mineral content in rice – Kaleem U. Kakar et al. – Journal of Applied Microbiology

Microbes in the news

A week of holiday junk food could derail your gut microbiome—but there’s hope – Claire Maldarelli – Popular Science

Microbiota and Cancer – Andrea S. Blevins Prime – Cancer Therapy Advisor

Maternal Antibiotic Exposure Affects Infant Fecal Microbiota Following Vaginal Delivery – Jessica Martin – Infectious Disease Advisor

Microbe expert claims we should wash them ‘AT LEAST’ once a week at a high temperature to avoid dust mites and bacteria – Unity Blott – Daily Mail

* CORRECTING THE GENES – Santanu Chakraborty – Bangalore Mirror

Govt study finds faecal bacteria in 97 percent ‘filtered’ water jars in Dhaka – Bdnews24

* 200 million lives saved – but prognosis for penicillin is not healthy – Harry Ridgewell and Angela Long (collaborator) – Wiki Tribune

Microbes on the market

Report on sale: Human Microbiome Therapeutics Market is expected to Witness a CAGR of 14.19 % Till 2022 including Key Players: Rebiotix, Seres Therapeutics – Craig Francis – Social Articles Tracking & PR news.com

Report on sale: Microbiome Drugs Market by Production, Capacity Utilization Rate, Ex-Factory Price, Revenue, Cost, Gross and Gross Margin Analysis – Amit Pawar – Social Articles Tracking & PR news.com

 

December 28, 2017

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Not many microbiome articles today, but a good selection non the less! Dysbiosis and obesity in humans, effects of hay on suckling calfs, and MPLasso to Infer microbial association networks.

Human respiratory microbiome

The impact of persistent bacterial bronchitis on the pulmonary microbiome of children – Leah Cuthbertson – PLOS ONE

Human vaginal microbiome

The vaginal microbiome and sexually transmitted infections are interlinked: Consequences for treatment and prevention – Janneke H. H. M. van de Wijgert – PLOS Medicine

Human gut microbiome

Dysbiosis Signatures of Gut Microbiota Along the Sequence from Healthy, Young Patients to Those with Overweight and Obesity – Renyuan Gao – Obesity

The NLR Protein NLRP6 Does Not Impact Gut Microbiota Composition – Paul Lemire – Cell Reports

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Animal experiments

Effect of hay supplementation timing on rumen microbiota in suckling calves – Xueyan Lin – MicrobiologyOpen

Shaping of Intestinal Microbiota in Nlrp6- and Rag2-Deficient Mice Depends on Community Structure – Eric J.C. Gálvez – Cell Reports

Animal microbiome

Associations between Escherichia coli O157 shedding and the fecal microbiota of dairy cows – Chloe Stenkamp-Strahm – Journal of Applied Microbiology

Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals – Emma C. L. Finlayson-Trick – PLOS ONE

Plant, root, and soil microbiome

Shift of allelochemicals from Sorghum halepense in the soil and their effects on the soil’s bacterial community – Hongjuan Huang – Weed Biology and Management

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Bioinformatics

MPLasso: Inferring microbial association networks using prior microbial knowledge – Chieh Lo – PLOS Computational Biology

December 27, 2017

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Quite a few papers on the gut microbiome today, in addition to coral reef microbiomes and the sinonasal microbiome.

 

Human respiratory microbiome

The sinonasal microbiota, neural signaling, and depression in chronic rhinosinusitis – Michael Hoggard – International Forum of Allergy & Rhinology

Human skin microbiome

Clostridia in the gut and onset of atopic dermatitis via eosinophilic inflammation – Eun Lee – Annals of Allergy, Asthma & Immunology 

Human gut microbiome

In vitro human colonic fermentation of indigestible fraction isolated from lunch menus: impact on the gut metabolites and antioxidant capacity – Victor Manuel Zamora-Gasga – International Journal of Food Sciences and Nutrition

Targeting gut microbiome: A novel and potential therapy for autism – Yongshou Yang – Life Sciences

Molecular mechanistic pathway of colo-rectal carcinogenesis associated with intestinal microbiota – Paramita Mandal – Anaerobe

Gut microbiota and obesity: implications for fecal microbiota transplantation therapy – Yongbo Kang – HORMONES

Correlation between gut microbiota and personality in adults: a cross-sectional study – Han-Na Kim – Brain, Behavior, and Immunity

Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome – Adrián Camacho-Ortiz – PLOSone

Water and extremophile microbiome

Interplay between stochastic and deterministic processes in the maintenance of alternative community states in Verrucomicrobia-dominated shallow lakes – Maria E. Llames – FEMS Microbiology Ecology

Complex interactions between potentially pathogenic, opportunistic, and resident bacteria emerge during infection on a reef-building coral – Sarah A. Gignoux-Wolfsohn – FEMS Microbiology Ecology

Bacterial community composition and diversity in Kalakuli, an alpine glacial-fed lake in Muztagh Ata of the westernmost Tibetan Plateau – Keshao Liu – FEMS Microbiology Ecology