January 22, 2019

In today’s digest read about Lactobacillus mulieris sp. nov. isolated from healthy female urinary tract, diversity of Escherichia coli phages in the Danish wastewater, PLate Coverage Algorithm (PLCA) in culture-enriched metagenomics, and more. Happy reading!

General microbiome

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions – Sara L. Jackrel – mBio

Gut microbiome

Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition – Rita A. Oliveira – Nature Microbiology

Long-term impact of fecal transplantation in healthy volunteers – Oleg V. Goloshchapov – BMC Microbiology

Efficacy of faecal microbiota transplantation in Crohn’sdisease: a new target treatment?– Liyuan Xiang – Microbial Biotechnology

Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner – bioRxiv

Microreview: Causalities of war: The connection between type VI secretion system and microbiota – Luke P. Allsopp – Cellular Microbiology

Urinary microbiome

*Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group – Joana Rocha – International Journal of systematic and evolutionary microbiology

Vaginal microbiome

Vaginal Microbiota Transplantation: The Next Frontier – Kevin DeLong – The Journal of Law, Medicine, & Ethics

Respiratory microbiome

*Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota – Fiona J. Whelan – Nature Microbiology

A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-levels– Zhang Wang – bioRxiv

Eye microbiome

The closed eye harbors a unique microbiome in dry eye disease – Kent A. Willis – medRxiv

Plant/root/soil microbiome

Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants – Yan Chen – Microbiome

Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community– Jiajie Feng – Microbiome

Microbiome composition differs in hybrid and inbred maize – Maggie R. Wagner – bioRxiv

Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum – Zuluaga Mya – PlosOne

Water microbiome

Molecular Characteristics of Dissolved Organic Nitrogen and Its Interaction with Microbial Communities in a Prechlorinated Raw Water Distribution System – Hang Xu – Environmental Science and Technology

Effects of geographic location and water quality on bacterial communities in full-scale biofilters across North America – Ben Ma – FEMS Microbiology Ecology

Phages and viruses

*Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species – Nikoline S. Olsen – bioRxiv

Bioinformatics

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences – Nicole R. Narayan – BMC Genomics

Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes – Jake L. Weissman and Philip L. F. Johnson – mSystems

Review: Integrating Computational Methods to Investigate the Macroecology of Microbiomes – Rilquer Mascarenhas – Frontiers in Genetics

Assessment of single cell RNA-seq statistical methods on microbiome data – Matteo Calgaro – bioRxiv

January 17, 2020

I 100% concur with Barak about our great Microbiome Digest, and we invite YOU to join us to create useful content for our community. Today’s Digest hopefully brings you much food for thought. I would draw your attention towards two papers about insecticide and antibiotic resistance. The first is about the mechanism for malaria transmitting mosquitoes to tolerate the common pesticide, pyrethroid. The second is on a potential genetic engineering approach to replacing antibiotic resistant plasmids with artificial ones. Of course, there are many more articles and news pieces to read from. Enjoy!

Jobs and Events

MICROBIOME CONNECT SKIN USA 2020 – Global Cosmetics News

Postdoc Computational and Statistical Analysis of Microbiome Data (0.8 – 1.0 FTE) – Universiteit Utrecht

Digest this! New exhibition explores the hidden world of microbes inside — and on — you! – Ottawa Citizen

Call for papers: Cancer Evolution and Metastasis – Genome Biology

General microbiology

Setting the agenda for social science research on the human microbiome – Beth Greenhough et al. – University of Nottingham

Exploring microbial worlds – Lei Tang – Nature Methods

Community-driven Metadata Standards for Agricultural Microbiome Research – JP. Dundore-Arias et al – Phytobiomes Journal

Antimicrobial/Insecticide resistance

Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance – Kihyun Lee et al. – Microbiome

Structures of lipoprotein signal peptidase II from Staphylococcus aureus complexed with antibiotics globomycin and myxovirescin – Samir Olatunji et al. – Nature Communications

** A sensory appendage protein protects malaria vectors from pyrethroids – Victoria A. Ingham et al. – Nature

Press: Malaria-carrying mosquitoes get a leg up on insecticides – Flaminia Catteruccia – Nature

** Potentiation of curing by a broad-host-range self-transmissible vector for displacing resistance plasmids to tackle AMR – Alessandro Lazdins et al. – PLoS One

Promising antifungal activity of new oxadiazole against Candida krusei – Daniella Renata Faria et al. – PLoS One

Impact of multi-drug resistant bacteria on economic and clinical outcomes of healthcare-associated infections in adults: Systematic review and meta-analysis – Miquel Serra-Burriel et al. – PLoS One

Pregnancy and early life

The association between dietary patterns before and in early pregnancy and the risk of gestational diabetes mellitus (GDM): Data from the Malaysian SECOST cohort – Heng Yaw Yong et al. – PLoS One

Nucleic Acid-Based Screening of Maternal Serum to Detect Viruses in Women with Labor or PROM – Ankit A. Shah et al. – Reproductive Sciences

Provision of Lipid-Based Nutrient Supplements to Mothers During Pregnancy and 6 Months Postpartum and to Their Infants from 6 to 18 Months Promotes Infant Gut Microbiota Diversity at 18 Months of Age but Not Microbiota Maturation in a Rural Malawian Setting: Secondary Outcomes of a Randomized Trial – Arox W Kamng’ona et al. – The Journal of Nutrition

Human skin microbiome

Distribution of microbial communities and core microbiome in successive wound grades of diabetic foot ulcer individuals – Apoorva Jnana et al. – Applied and Environmental Microbiology

Review: The skin microbiome as a clinical biomarker in atopic eczema: Promises, navigation, and pitfalls – Matthias Reiger et al. – The Journal of Allergy and Clinical Immunology

Characterization and Analysis of the Skin Microbiota in Acne: Impact of Systemic Antibiotics – Seo-Yeon Park et al. – Journal of Clinical Medicine

Human gut microbiome

Review: Microbial Production of Bioactive Chemicals for Human Health – Xia Wu et al. – Current Opinion in Food Science

Gut microbiota compositional profile and serum metabolic phenotype in patients with primary open-angle glaucoma – Haijun Gong et al. – Experimental Eye Research

Inulin-type fructan intervention restricts the increase in gut microbiome–generated indole in patients with peritoneal dialysis: a randomized crossover study – Li Li et al. – The American Journal of Clinical Nutrition

Human reproductive microbiome

Review: The Reproductive Microbiome: An Emerging Driver of Sexual Selection, Sexual Conflict, Mating Systems, and Reproductive Isolation – Melissah Rowe et al. – Trends in Ecology & Evolution

Press: What we’re learning about the reproductive microbiome – Cell Press – Phys.org

Cancer microbiome

Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer – Ruizhong Miao – PLoS One

Animal experiments

Acute oral methylmercury exposure perturbs the gut microbiome and alters gut-brain axis related metabolites in rats – Xiaoying Lin et al. – Ecotoxicology & Environmental Safety

Perfluorooctane sulfonate alters gut microbiota-host metabolic homeostasis in mice – Limin Zhang et al. – Toxicology

Fecal transplant prevents gut dysbiosis and anxiety-like behaviour after spinal cord injury in rats – Emma K. A. Schmidt et al. – PLoS One

Impact of antibiotic-resistant bacteria in the mouse intestine on immune activation and Clostridioides difficile infection – James Keith et al. – Infection and Immunity

Animal microbiome

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea – Darien C. Capunitan et al. – Molecular Ecology

Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease – Matthew A. Scott et al. – PLoS One

Body-site specific microbiota reflect sex and age-class among wild spotted hyenas – Connie A Rojas et al. – FEMS Microbiology Ecology

Plant, root and soil microbiome

Biochar mediates microbial communities and their metabolic characteristics under continuous monoculture – Hongmiao Wu et al. – Chemosphere

Functional Metagenomic Exploration Identifies Novel Prokaryotic Copper Resistance Genes from Soil Microbiome – Chao Xing et al. – Metallomics

** A Pathogen-Responsive Gene Cluster for Highly Modified Fatty Acids in Tomato – Ju Eun Jeon et al. – Cell

Effects of soil physicochemical properties on microbial communities in different ecological niches in coastal area – Tianyun Shao et al. – Applied Soil Ecology

Soil microbial community structure and function mainly respond to indirect effects in a multifactorial climate manipulation experiment – Evi Deltedesco et al. – Soil Biology and Biochemistry

Long term effects of management practice intensification on soil microbial community structure and co-occurrence network in a non-timber plantation – Liang Xue et al. – Forest Ecology and Management

Soil microbial and macrofauna dynamics under different green manure termination methods – Carolyn B. Marshall & Derek H. Lynch – Applied Soil Ecology

Microbial abundance, composition, and function in nectar are shaped by flower visitor identity – Megan M Morris et al. – FEMS Microbiology Ecology

Ecological clusters based on responses of soil microbial phylotypes to precipitation explain ecosystem functions – Ying Wu et al. – Soil Biology and Biochemistry

Phylogenetic Analysis of Symbiotic Bacteria Associated with Two Vigna Species under Different Agro-Ecological Conditions in Venezuela – María Daniela Artigas Ramírez et al. – Microbes and Environments

Diversity and structure of bacterial community in rhizosphere of lima bean – Regina Maria Silva Sousa et al. – Applied Soil Ecology

Distinct factors drive the assembly of quinoa-associated microbiomes along elevation – Zhiquan Cai et al. – Plant and Soil

Influence of plant fraction, soil and plant species on the microbiota: a multi-kingdom comparison – Tkacz, A et al. – mBio

Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China – Pengfa Li et al. – mSystems

Water and extremophile microbiome

Impacts of antimony and arsenic co-contamination on the river sedimentary microbial community in an antimony-contaminated river – Rui Xu et al. – Science of the Total Environment

Interactions of PAH-degradation and nitrate-/sulfate-reducing assemblages in anaerobic sediment microbial community – Xunan Yang et al. – Journal Hazardous Materials

Influence of wastewater microbial community on the performance of miniaturized microbial fuel cell biosensor – Nan Xiao et al. – Bioresource Technology

Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region – Corinna Breusing et al. – PLoS One

Phages and viruses

Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion – Tanvi P. Honap et al. – PLoS One

Bioinformatics

Gclust: A Parallel Clustering Tool for Microbial Genomic Data – Ruilin Li et al. – Genomics, Proteomics & Bioinformatics

Microbes in the news

Insomnia: When I took part in a sleep study – Yella Hewings-Martin – Medical News Today

How to Keep Your Baby’s Skin Healthy When It’s Cold Outside – Joane Amay – Ebony

Prebiotics, cosmeceuticals may improve skin condition – Ingrid Torjesen – Dermatology Times

Next frontier is to identify and use good bacteria to treat specific diseases – Namita Kohli – The Week

Five next-gen depression treatments that could revolutionize the field – Alexandra Pattillo – Inverse

Coeliac disease linked to bacteria exposure – Liam Mannix – The Sydney Morning Herald

GETTING TO KNOW YOUR MICROBIOME BETTER – Kim-Anh Lê Cao – Pursuit

Common foods can help ‘landscape’ the jungle of our gut microbiome – San Diego State University – Medical Xpress

Pioneering scientists create designer prebiotics to disrupt the microbiome health space – Nikki Hancocks – NutraIngredients

Applying knowledge of the human microbiome to pig health – The Pig Site

Your microbiome reveals more about your health than your genes do – Michael Le Page – New Scientist

UH joins new national consortium to advance microbiome research – University of Hawaiʻi at Mānoa

Check out these awesomely creepy puppets of microbial creatures – Thom Dunn – BoingBoing

Microbes on the market

Bloom Science Granted Exclusive Option to License Microbiome-Based Technology for the Development of Novel Treatments for Multiple Neurological and Oncology Conditions – Bloom Science – PR Newswire

Mawi and CosmosID Collaborate to Enable More Precise Microbiome Analysis – Business Wire – Yahoo! Finance

November 23, 2019

In today’s digest read about the Darobactin (a new antibiotic that selectively kills Gram-negative pathogens by binding to the BamA protein, located in the external membrane of Gram-negative bacteria), temporal stability of the rumen microbiota, and Gardnerella species (Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis) in the vaginal microbiome. And, check out 2019 Holiday Gift Guide For Microbe Lovers. Happy weekend!

General microbiome

*A new antibiotic selectively kills Gram-negative pathogens – Yu Imai – Nature

Read the story behind the paper by Roberto Molar Candanosa, Northeastern University.

Gut microbiome

Review: The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health – Jillian L. Waters & Ruth E. Ley – BMC Biology

The gut microbiota influences how circulating immune cells in humans change from one day to the next – Jonas Schluter – bioRxiv

Vaginal microbiome

*Resolution and Cooccurrence Patterns of Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis within the Vaginal Microbiome – Janet E. Hill – Infection and Immunity

Clinical validation of the Aptima Bacterial Vaginosis and Aptima Candida/Trichomonas Vaginitis Assays: results from a prospective multi-center clinical study – Jane R. Schwebke – Journal of Clinical Microbiology

Review: Understanding and interpreting community sequencing measurements of the vaginal microbiome – HL Berman – BJOG : an International Journal of Obstetrics and Gynaecology

Endocervical microbiome

Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia – Heng Choon Cheong – PlosOne

Uterine microbiome

Does dysbiotic endometrium affect blastocyst implantation in IVF patients? – Tomoko Hashimoto & Koichi Kyono – Journal of Assisted Reproduction and Genetics

Oral microbiome

Oral microbial community composition is associated with pancreatic cancer: A case‐control study in Iran – Emily Vogtmann – Cancer Medicine

Animal microbiome

*Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements – Timothy J. Snelling – Animal Microbiome

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens – Laura Glendinning – Animal Microbiome

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status – Tucker Andrews – PlosOne

Inulin improves the egg production performance and affects the cecum microbiota of laying hens – Hongmei Shang – International Journal of Biological Macromolecules

Animal experiments

Effects of Debaryomyces hansenii treatment on intestinal mucosa microecology in mice with antibiotic-associated diarrhea – Ao Zeng – PlosOne

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium – Andre Mu – bioRxiv

Hepatitis B Virus Infection Alters Gut Microbiota Composition in Mice – Qingfeng Zhu – Front. Cell. Infect. Microbiol.

Human Gut Microbiome Transplantation in Ileitis Prone Mice: A Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients – Abigail R Basson – Inflammatory Bowel Diseases

Effects of an Escherichia coli exopolysaccharide on human and mouse gut microbiota in vitro – Baiyuan Li – International Journal of Biological Macromolecules

Ion Transport Basis of Diarrhea in a Mouse Model of Adoptive T Cell Transfer Colitis – Dulari Jayawarden – Digestive Diseases and Sciences

Water microbiome

Rewetting of three drained peatlands drives congruent compositional changes in pro- and eukaryotic microbiomes through environmental filtering – Micha Weil – bioRxiv

Phages and viruses

Herpes Simplex Virus Infection, Acyclovir and IVIG Treatment All Independently Cause Gut Dysbiosis – Chandran Ramakrishna – bioRxiv

Svetlana’s pick

Gift guide for this holiday season!
by Justine Dees

October 5, 2019

This weekend, read about how cooking food modifies the microbiome, how bacteria ‘strip off’ to evade antibiotics, and more. Check out an interesting pilot study looking at potential inclusion and exclusion criteria of donors for safe vaginal microbiota transplant. Enjoy!

Events

Bioinformatics for the Microbiome Symposium 2019, Stanford University, Monday October 28.
Some tickets are still available!

General microbiome

Mobile phones as fomites for potential pathogens in hospitals: microbiome analysis reveals hidden contaminants – Rebecca Simmonds – Journal of Hospital Infection

Review: Microbiomes as sources of emergent host phenotypes – J. B. Lynch and E. Y. Hsiao – Science

Vaginal microbiome

*Conceptual Design of a Universal Donor Screening Approach for Vaginal Microbiota Transplant – Kevin DeLong – Frontiers in Cellular and Infection Microbiology

Highly diverse anaerobe-predominant vaginal microbiota among HIV-infected pregnant women in Zambia – Joan T. Price – PlosOne

Urinary microbiome

*Possible role of L-form switching in recurrent urinary tract infection – Katarzyna M. Mickiewicz – Nature Communications

Aerococcus urinae and Globicatella sanguinis Persist in Polymicrobial Urethral Catheter Biofilms Examined in Longitudinal Profiles at the Proteomic Level – Yanbao Yu – Biochemistry Insights

Gut microbiome

*Cooking shapes the structure and function of the gut microbiome – Rachel N. Carmody – Nature Microbiology

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma – Wen Fong Ooi – Gut

Effects of Low-FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial – Selina R.Cox – Gastroenterology

Water microbiome

Trophic networks improve the performance of microbial anodes treating wastewater – Christin Koch – npj Biofilms and Microbiomes

Application of a novel molecular technique to characterise the effect of settling on microbial community composition of activated sludge – Luong N.Nguyen – Journal of Environmental Management

Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus – Ragnhildur Guðmundsdóttir – PlosOne

Animal microbiome

Looking like the locals – gut microbiome changes post-release in an endangered species – Rowena Chong – Animal microbiome

Animal experiment

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Pablo Arroyo – PlosOne

Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection – Ashley D. Smith – PlosOne

Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model – Yoshitomo Morinaga – PlosOne

Plant microbiome

Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae) – Suresh J. Gawande – PlosOne

Food

Comparison of the microbial composition of African fermented foods using amplicon sequencing – Maria Diaz – Scientific Reports

The impact of grape processing and carbonic maceration on the microbiota of early stages of winemaking – Raffaele Guzzon – Journal of Applied Microbiology

Fungi

Phyllosphere Fungal Communities of Plum and Antifungal Activity of Indigenous Phenazine-Producing Pseudomonas synxantha Against Monilinia laxa – Tamara Janakiev – Frontiers in Microbiology

Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses – Gian Maria Niccolò Benucci – PeerJ

Viruses

The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches – Federica Ungaro – United European Gastroenterology Journal

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – Obstetrics and Gynaecology

Bioinformatics

ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database – João L. Reis-Cunha – PlosOne

August 24, 2019

This weekend, read about the microbial index of skin health for children with eczema, gut microbiome of koalas, and interactions between the gut bacterial microbiome and virome of rhesus monkey. Happy reading!

General microbiome

Why we need a small data paradigm – Eric B. Hekler – BMC Medicine

Correspondence: The importance of genome sequence quality to microbial comparative genomics – Theo H. M. Smits – BMC Genomics

The applications of Big Data in molecular diagnostics – Yin Kwan Evelyn Wong – Expert Review of Molecular Diagnostics

Tiny Hidden Genes within Our Microbiome – Karin Mittelman & David Burstein – Cell

Skin microbiome

*A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children – Zheng Sun – mSystems

Gut microbiome

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight – Peng Jiang – Microbiome

Review: Gut Microbiota, Dietary Phytochemicals, and Benefits to Human Health – Ran Yin – Current Pharmacology Reports

Mild cognitive impairment has similar alterations as Alzheimer’s disease in gut microbiota – Binyin Li – Alzheimer’s & Dementia

Design of synthetic microbial consortia for gut microbiota modulation – Jorge F. Vázquez-Castellanos – Current Opinion in Pharmacology

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease – Sandra Aparecida dos Reis – Journal of Medical Microbiology

Review: Celiac disease: a comprehensive current review – Giacomo Caio – BMC Medicine

Pregnancy and early life

Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants – Kathyayini P. Gopalakrishna – Nature Medicine

Oral microbiome

Oral Microbiome and Cancer Therapy-Induced Oral Mucositis – Jean-Luc C Mougeot – JNCI Monographs

Respiratory microbiome

Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration – Annamaria Bevivino – Trends in Molecular Medicine

Water and extremophile microbiome

Effects of water recirculation rate on the microbial community and water quality in relation to the growth and survival of white shrimp (Litopenaeus vannamei) – Zhao Chen – BMC Microbiology

Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir – Ceshing Sheu – International Journal of Systematic and Evolutionary Microbiology

Bacterial Communities from Extreme Environments: Vulcano Island – Camilla Fagorzi – Diversity

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean – Susanne Kraemer – bioRxiv

Review: Metal and organic pollutants bioremediation by extremophile microorganisms – Patricia Giovanella – Journal of Hazardous Material

Animal microbiome

*Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala – Michaela D. J. Blyton – Animal microbiome

Impact of pine leaf biochar amendment on bacterial dynamics and correlation of environmental factors during pig manure composting – Jiao Li – Bioresource Technology

Animal experiment

Potential roles of gut microbiome and metabolites in modulating ALS in mice – Eran Blacher – Nature

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Inhibitory and nutrient use phenotypes among co‐existing Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil – Adil Essarioui – Environmental Microbiology

Phages and viruses

*The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites – Heng Li – Virology Journal

July 2, 2019

This Tuesday, read about the fecal microbial transplantation for cardiometabolic syndrome treatment, oral microbiome of early stage Parkinson’s disease, Finnish Health and Early Life Microbiota (HELMi) project, and more. Happy reading!

General microbiome

Review: Defining Division of Labour in Microbial Communities – Samir Giri – JMB

Review: Selective pressures during chronic infection drive microbial competition and cooperation – Jiwasmika Baishya & Catherine A. Wakeman – Biofilms and Microbiomes

Gut microbiome

*Review: Fecal Microbial Transplantation and Its Potential Application in Cardiometabolic Syndrome – Avner Leshem – Frontiers in Immunology

Review: The Microbiome and Irritable Bowel Syndrome – A Review on the Pathophysiology, Current Research and Future Therapy – Pei Pei Chong – Frontiers in Microbiology

Alterations of the bile microbiome in primary sclerosing cholangitis – Timur Liwinski – BMJ Gut Microbiota

Selective and suppressive effects of antibiotics on donor and recipient bacterial strains in gut microbiota determine transmission efficiency of blaNDM-1-bearing plasmids – Lianwei Ye – Journal of Antimicrobial Chemotherapy

Pregnancy and early life

Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve – Kattayoun Kordy – bioRxiv

Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota – Mari Hagbø – Paediatric research

*Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort – Katri Korpela – BMJ Paediatrics

Oral microbiome

*The oral microbiome of early stage Parkinson’s disease and its relationship with functional measures of motor and non-motor function – Dragos Mihaila – PlosOne

Phages and viruses

What is (not) known about the dynamics of the human gut virome in health and disease – Leen Beller Jelle Matthijnssens – Current Opinion in Virology

Water and extremophile microbiome

Characterization of indigenous bacteria from radon-rich groundwater and their tolerance to physicochemical stress – T. Nayak – International Journal of Environmental Science and Technology

Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes – Nachiket P. Marathe – Microbiome

Techniques

Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities – Shi Ming Tan – Biofilms and microbiomes

Bioinformatics

Use and abuse of correlation analyses in microbial ecology – Alex Carr – ISME Journal

Education

From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training – Annette McGrath – Plos Computational Biology

Ten quick tips for effective dimensionality reduction – Lan Huong Nguyen and Susan Holmes – Plos Computational Biology

May 29, 2019

Changes to the pig gut microbiome based on age, gut bacteria community composition in aquatic invertebrates, fungal diversity on limestone cathedral walls, chalk-talk vs PowerPoint in large microbiology lectures.

Human oral microbiome

Applications of the oral microbiome in personalized dentistry – Georgios N Belibasakis – Archives of Oral Biology

Human vaginal microbiome

Detection of Methanobrevibacter smithii in vaginal samples collected from women diagnosed with bacterial vaginosis – Ghiles Grine – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Gut Microbial Dataset of a foraging tribe from rural West Bengal – insights into unadulterated and transitional microbial abundance – Sayak Ganguli – Data in Brief

Gut microbiome of pre-adolescent children of two ethnicities residing in three distant cities – Wei Wei Thwe Khine – Scientific Reports

The eradication of Helicobacter pylori restores rather than disturbs the gastrointestinal microbiota in asymptomatic young adults – Cong He – Helicobacter

Pre-print: Cytometric fingerprints of gut microbiota predict Crohn’s disease state – Peter Rubbens – bioRxiv

Animal experiments

Rapamycin modulates tissue aging and lifespan independently of the gut microbiota in Drosophila – Joseph M Schinaman – Scientific Reports

Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition – Shanlin Ke – BMC Veterinary Research

Pre-print: Effects of Five Products on Gut Microbiota and Short-Chain Fatty Acids of Obese Rats – Simin Tan – bioRxiv

Animal microbiome

Effect of different forage-to-concentrate ratios on ruminal bacterial structure and real-time methane production in sheep – Runhang Li – PLOS ONE

Pre-print: Microbiomes from feces vs. gut in aquatic vertebrates: distinct community compositions between substrates and preservation methods – Sten Anslan – bioRxiv

Plant, root, and soil microbiome

Glycoside Hydrolase Genes Are Required for Virulence of Agrobacterium tumefaciens on Bryophyllum daigremontiana and Tomato – Stephanie L Mathews – Applied and Environmental Microbiology

Effect of water-driven changes in rice rhizosphere on Cd lability in three soils with different pH – Jinjin Wang – Journal of Environmental Sciences

Impact of AMF Claroideoglomus etunicatum on the structure of fungal communities in the tomato rhizosphere – Agnieszka Jamiołkowska – Acta Mycologica

Effect of land use and carbonates on organic matter stabilization and microbial communities in Mediterranean soils – Mireia Martí-Roura – Geoderma

Pre-print: Close-Range Interactions Favor Growth in Random-Paired Extracted Soil Bacteria – Manupriyam Dubey – bioRxiv

Water and extremophile microbiome

New microbial lineages capable of carbon fixation and nutrient cycling in deep-sea sediments of the northern South China Sea – Jiao-Mei Huang – Applied and Environmental Microbiology

Pre-print: Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep – Guojie Cui – PeerJ

Taxonomic structure and potential nitrogen metabolism of microbial assemblage in a large hypereutrophic steppe lake – Xiaodong Qu – Environmental Science and Pollution Research

Built environment

Fungal diversity and distribution across distinct biodeterioration phenomena in limestone walls of the old cathedral of Coimbra, UNESCO World Heritage Site – João Trovão – International Biodeterioration & Biodegradation

Probiotics/prebiotics

Dietary probiotics have different effects on the composition of fecal microbiota in farmed raccoon dog (Nyctereutes procyonoides) and silver fox (Vulpes vulpes fulva) – Yongjia Peng – BMC Microbiology

Microbes in the news

Microbiome therapies could be the next frontier in medicine. But how exactly do you make them? – Kate Sheridan – STAT

Possible link between infant gut microbiome and development of allergies – Bob Yirka – Medical Xpress

Science, career, and publishing

Pre-print: Rock the Chalk: A five-year comparative analysis of a large microbiology lecture course reveals improved outcomes of chalk-talk compared to PowerPoint – Christopher M Waters – bioRxiv