January 24, 2020

Have a nice weekend! Today in this Digest, we have several papers about different interventions, microbes, and compounds with positive properties. And, of course, more papers. Enjoy.

 

Human and General Microbiome

Review: The microbiota and the hypothalamus-pituitary-adrenocortical (HPA) axis, implications for anxiety and stress disorders – Linoy Mia Frankiensztajn – Current Opinion in Neurobiology

Review: The Role of Meat Protein in Generation of Oxidative Stress and Pathophysiology of Metabolic Syndromes – Muhammad Ijaz Ahmad – Food Science of Animal Resources

Identifying determinants of bacterial fitness in a model of human gut microbial succession – Lihui Feng – PNAS

Reduced environmental bacterial load during early development and gut colonisation has detrimental health consequences in Japanese quail. – Ngare Wilkinson  – Heliyon

Review: Immunological Role of the Maternal Uterine Microbiome in Pregnancy: Pregnancies Pathologies and Alterated Microbiota – Jonah Bardos – Frontiers in Immunology

Association between the faecal short-chain fatty acid propionate and infant sleep – Anne-Louise M. Heath – European Journal of Clinical Nutrition

Prenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial – Mathis H. Hjelmsø – Nature Communications 

Physical fitness in community-dwelling older adults is linked to dietary intake, gut microbiota, and metabolomic signatures – Josué L. Castro‐Mejía – Aging Cell

Temporal Gut Microbial Changes Predict Recurrent Clostridiodes Difficile Infection in Patients With and Without Ulcerative Colitis – Allen A Lee – Inflammatory Bowel Diseases

Impacts of the Plateau Environment on the Gut Microbiota and Blood Clinical Indexes in Han and Tibetan Individuals – Zhilong Jia – mSystems

Intestinal microbes influence development of thymic lymphocytes in early life – Maria Ennamorati – PNAS

The cervicovaginal mucus barrier to HIV-1 is diminished in bacterial vaginosis – Thuy Hoang – PLoS Pathogens

Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families – Jian Yang – Beneficial Microbes

Characteristic gut microbiota and predicted metabolic functions in women with PCOS – Ling Zhou – Endocrine Connections 

Obese adolescents with PCOS have altered biodiversity and relative abundance in gastrointestinal microbiota – Beza Jobira – The Journal of Clinical Endocrinology & Metabolism

Association between blood omega-3 polyunsaturated fatty acids and the gut microbiota among breast cancer survivors – A. Horigome – Beneficial Microbes

Editorial: Processed food affects the gut microbiota: The revolution has started – Michael A Kamm – Journal of Gastroenterology and Hepatology

Commentary: mSphere of Influence: the Mycobiota in Human Health and Disease – Soo Chan Lee – mSphere

 

Animal Microbiota and Animal Model experiments

Letter: TCF-1 deficiency influences the composition of intestinal microbiota and enhances susceptibility to colonic inflammation – Guotao Yu – Protein & Cell 

Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota – Rieka Chijiiwa – Microbiome

Antidepressant treatment with fluoxetine during pregnancy and lactation modulates the gut microbiome and metabolome in a rat model relevant to depression – Anouschka S Ramsteijn – Gut Microbes

 

Beneficial Microbes and Compounds

Review: Fecal microbiota transplantation in disease therapy – Hanna Antushevich – Clinica Chimica Acta

Review: Microbiota and alcohol use disorder: are psychobiotics a novel therapeutic strategy? – Alicia Rodriguez-Gonzalez – Current Pharmaceutical Design

Mining possible associations of faecal A. muciniphila colonisation patterns with host adiposity and cardiometabolic markers in an adult population – E.K. Mitsou – Beneficial Microbes

Probiotics maintain intestinal secretory immunoglobulin A levels in healthy formula-fed infants: a randomised, double-blind, placebo-controlled study – L. Xiao – Beneficial Microbes

Effect of rice bran fermented with Saccharomyces cerevisiae and Lactobacillus plantarum on gut microbiome of mice fed high-sucrose diet – J. Shibayama – Beneficial Microbes

Inulin with different degrees of polymerization protects against diet-induced endotoxemia and inflammation in association with gut microbiota regulation in mice – Li-Li Li – Scientific Reports

Understanding the Scope of Do-It-Yourself Fecal Microbiota Transplant – Chiazotam Ekekezie – The American Journal of Gastroenterology

Milk Fermented by Lactobacillus paracasei NCC 2461 (ST11) Modulates the Immune Response and Microbiota to Exert its Protective Effects Against Salmonella typhimurium Infection in Mice – Leonardo Borges Acurcio – Probiotics and Antimicrobial Proteins 

Recovery of Lactobacillus casei strain Shirota (LcS) from faeces of healthy Singapore adults after intake of fermented milk – W.W.T. Khine – Beneficial Microbes

Seabuckthorn (Hippophaë rhamnoides) Freeze-Dried Powder Protects against High-Fat Diet-Induced Obesity, Lipid Metabolism Disorders by Modulating the Gut Microbiota of Mice – Caixia Guo – Nutrients

Chitooligosaccharides Modulate Glucose-Lipid Metabolism by Suppressing SMYD3 Pathways and Regulating Gut Microflora – Qiutong Wang – Marine Drugs

Lactobacillus and Pediococcus ameliorate progression of non-alcoholic fatty liver disease through modulation of the gut microbiome – Na Young Lee – Gut Microbes

Review: Antimicrobials for food and feed; a bacteriocin perspective – Paula M O’Connor – Current Opinion in Biotechnology

 

Bioinformatics

Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks – Henry Xing – Bioinformatics

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota – Christian Diener – mSystems

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 20, 2020

Have a nice monday! Today, in this Digest we have a good amount of papers about different beneficial interventions based on the microbiome such as probiotics, synbiotics and others. We have also papers about the microbiome in brain disorders, new evidence about microbiota changes in IBS, the impact of early antibiotic use on infant microbiota and the relation between mycobiome and childhood caries. Enjoy!

Human and General Microbiome

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

Systematic Review: Gut microbial changes of patients with psychotic and affective disorders: A systematic review – Nina Vindegaard – Schizophrenia Research

Review: The progress of gut microbiome research related to brain disorders – Sibo Zhu – Journal of Neuroinflammation

Review: Unraveling How Candida albicans Forms Sexual Biofilms – Austin M. Perry – Journal of Fungi

In Brief: Host-microbiome interactions lost during flight – Ashley York – Nature Reviews Microbiology

Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome – Johanna Sundin – Scientific Reports

Antibiotics in early life associate with specific gut microbiota signatures in a prospective longitudinal infant cohort – Katri Korpela – Pediatric Research 

Activated Drp1-mediated mitochondrial ROS influence the gut microbiome and intestinal barrier after hemorrhagic shock – Chenyang Duan – Aging

Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages – Aurélie Mathieu – Nature Communications

Impact of commonly used drugs on the composition and metabolic function of the gut microbiota – Arnau Vich Vila – Nature Communications

Site-specific profiling of the dental mycobiome reveals strong taxonomic shifts during progression of early childhood caries – Lauren M. O’Connell – Applied and Environmental Microbiology

Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles – Pande Putu Erawijantari – Gut (BMJ)

Dysbiosis Signatures of Fecal Microbiota in South African Infants with Respiratory, Gastrointestinal, and Other Diseases – Srinivasan Krishnamoorthy – The Journal of Pediatrics

Cervicovaginal Microbiome and Urine Metabolome Paired Analysis Reveals Niche Partitioning of the Microbiota in Patients with Human Papilloma Virus Infections – Nataliya Chorna – Metabolites (MDPI)

Animal Microbiomes and Animal Model Experiments

The mitochondrial negative regulator MCJ modulates the interplay between microbiota and the host during ulcerative colitis – Miguel Angel Pascual-Itoiz – Scientific Reports

Effects of peptidoglycan on the development of steatohepatitis – Meiling Jin – Biochimica et Biophysica Acta (BBA) – Molecular and Cell Biology of Lipids

Phylosymbiosis across deeply diverging lineages in omnivorous cockroaches – Kara A. Tinker – Applied and Environmental Microbiology

Metagenomic shotgun analyses reveal complex patterns of intra- and interspecific variation in the intestinal microbiomes of codfishes – Even Sannes Riiser – Applied and Environmental Microbiology

Beneficial Microbes and Compounds

Review: Effects of probiotics on type II diabetes mellitus: a meta-analysis – Yun-Wen Tao – Journal of Translational Medicine

Opinion: Improving Risk-Benefit in Faecal Transplantation through Microbiome Screening – Lito E. Papanicolas – Trends in Microbiology

Akkermansia muciniphila Prevents Fatty Liver, Decreases Serum Triglycerides, and Maintains Gut Homeostasis – Sejeong Kim – Applied and Environmental Microbiology

Lactobacillus Protects Against S. Typhimurium-Induced Intestinal Inflammation by Determining the Fate of Epithelial Proliferation and Differentiation – Xiaoxi Lu – Molecular Nutrition & Food Research

Probiotics Prevent Dysbiosis and the Raise in Blood Pressure in Genetic Hypertension: Role of Short-chain Fatty Acids – Iñaki Robles‐Vera – Molecular Nutrition & Food Research

Tuna Bone Powder Alleviates Glucocorticoid-Induced Osteoporosis Via Coregulation of the NF-κB and Wnt/β-Catenin Signaling Pathways and Modulation of Gut Microbiota Composition and Metabolism – Chenyang Lu – Molecular Nutrition & Food Research

A 2-strain mixture of Lactobacillus acidophilus in the treatment of irritable bowel syndrome: A placebo-controlled randomized clinical trial – Stéphane Sadrin – Digestive and Liver Disease

Lactobacillus reuteri DSM 17938 and Magnesium Oxide in Children with Functional Chronic Constipation: A Double-Blind and Randomized Clinical Trial – Megumi Kubota – Nutrients

Chemical Profile, Antioxidative, and Gut Microbiota Modulatory Properties of Ganpu Tea: A Derivative of Pu-erh Tea – Yuying Zheng – Nutrients

Effects of Synbiotic Supplement on Human Gut Microbiota, Body Composition and Weight Loss in Obesity – Igor N. Sergeev – Nutrients

Antidiabetic Effect of Casein Glycomacropeptide Hydrolysates on High-Fat Diet and STZ-Induced Diabetic Mice via Regulating Insulin Signaling in Skeletal Muscle and Modulating Gut Microbiota – Qichen Yuan – Nutrients

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

January 16, 2020

Good morning/night everyone!

What I love about writing for MD is the huge diversity of topics we’re meeting along the process of making the daily digest. Even though I’m mostly working on plant and root microbiome, it’s amazing to see how diverse is the world of microbiome and how much more there is to accomplish. Check out today’s digest- and don’t forget the News section as well! it is highly interesting!

General Microbiology

Detection of phylogenetic core groups in diverse microbial ecosystems, Marcos Parras Molto, bioRxiv

Isolation of an archaeon at the prokaryote–eukaryote interface, Hiroyuki Imachi, Nature

Ferrosomes are iron storage organelles formed by broadly conserved gene clusters in bacteria and archaea, Carly R. Grant , bioRxiv

Human microbiome

Distribution of microbial communities and core microbiome in successive wound grades of diabetic foot ulcer individuals, Apoorva Jnana, AEM

Animal microbiome

Parasites modulate the gut-microbiome in insects: A proof-of-concept study, Brian Fredensborg, PlosONE

The effect of diet on the gastrointestinal microbiome of juvenile rehabilitating green turtles (Chelonia mydas), Jennifer Bloodgood ,PlosONE

Rotten-skin disease significantly changed giant spiny frog(Paa spinosa) gut microbiota, Tuoyu He, bioRxiv

Bacterial Biogeography of the Colon in Dogs With Chronic Inflammatory Enteropathy, Paula Giaretta, Veterniary Pathology

Plant and environmental microbiome

Biostimulants applied to maize seeds modulate the enzymatic activity and metaproteome of the rhizosphere, Monica Mattarozzi, Applied Soil Ecology

Biological inhibition of soil nitrification by forest tree species affects Nitrobacter populations, Amandine Laffite, Environmental Microbiology

Extremophile microalgae: An overview, Veronica Malavasi , Journal of Phycology

Methods in microbiome

**Taxonomic classification method for metagenomics based on
core protein families with Core-Kaiju
, Anna Tovo, bioRxiv

**Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance, Xianding Deng , Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling, Ching Jian, PlosONE

The effect of storage conditions on microbial communities in stool, Kristien Nel Van Zyl, PlosONE

Beyond mass spectrometry, the next step in proteomics, Winston and Gregory Timp, Science Advances

Microbiome in the news

Illumina Announces New Sequencing System, Partnership with Roche and Software Suite to Accelerate Adoption of Genomics

Integrating microbiomes into clinical trials – the importance of time

Bayer and Azitra partnership looks to develop skin microbiome products for eczema

**Please read! our mental health is the MOST important thing in our life! Researchers facing ‘shocking’ levels of stress, survey reveals

January 11, 2020

Science doesn’t rest! Today’s Digest brings you several seminal papers and many news pieces. Highlights include a mouse study probing the mechanism behind maternally provisioned immunity for infants, a major effect to characterize mouse gut microbiota, a study on the diversity of the uncultured viruses of bacteria and archaea, and last but not least, a DIY method to deplete ribosomal RNA from your total RNA!

General microbiology

Preprint: Detection of phylogenetic core groups in diverse microbial ecosystems – Marcos Parras-Moltó & Daniel Aguirre de Cárcer – bioRxiv

Antimicrobial resistance

Preprint: Investigating the impact of combination phage and antibiotic therapy: a modeling study – Selenne Banuelos et al. – bioRxiv

Human liver microbiome

Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease – Silvia Sookoian et al. – Gut

Cancer microbiome

Review: Roles of microbiota in response to cancer immunotherapy – Kentaro Inamura – Seminars in Cancer Biology

Animal experiments

Butyrate attenuated fat gain through gut microbiota modulation in db/db mice following dapagliflozin treatment – Tae Jung Oh et al. – Scientific Reports

Microvesicles from Lactobacillus reuteri (DSM-17938) completely reproduce modulation of gut motility by bacteria in mice – Christine L. West et al. – PLoS One

** Mouse: Microbiota-targeted maternal antibodies protect neonates from enteric infection – Wen Zheng et al. – Nature

Press: Maternal Microbiome Protects Newborns from Deadly Diarrheal Infections – Genengnews

Animal microbiome

** The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria – Chang Liu et al. – Nature Communications

Energy conservation involving 2 respiratory circuits – Marie Charlotte Schoelmerich et al. – PNAS

Press: New metabolic pathway discovered in rumen microbiome – EurekAlert

Plant, root and soil microbiome

Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes – Samuel Bickel & Dani Or – Nature Communications

Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics – Cheng Gao et al. – Nature Communications

Phages and viruses

** Charting the diversity of uncultured viruses of Archaea and Bacteria – F. H. Coutinho, R. A. Edwards & F. Rodríguez-Valera – BMC Biology

Technology

** Preprint: A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies – Peter H. Culviner et al. – bioRxiv

Microbes in the news

Gut Microbiomes Are Linked To Diet And Evolution—Except In Flying Animals – Linh Anh Cat – Forbes

7 Effects of Greasy Food on Your Body – Elise Mandl – Healthline

Gut microbes may improve stroke recovery – University of Kentucky – EurekAlert

Surprising Ways A Virus Can Be A Man’s Best Friend – Mishal Shaheen et al. – The Health Mania

Twin Studies Examine Cohabiting Affect on Gut Microbiome – Technology Networks

Microbes on the market

Shoreline Biome expands presence in Asia to include Japan – Yahoo! Finance

Synthetic Biologics Receives FDA Guidance at Type C Meeting for SYN-004 (ribaxamase) Phase 1b/2a Clinical Trial in Allogeneic HCT Recipients – Synthetic Biologics – PR Newswire

Johnson & Johnson To Collaborate With Microbiome Biotech On Childhood Allergies – Taylor Carmichael – The Motley Fool

Kaleido Bio teams up with J&J to identify microbiome metabolic candidates – Douglas W. House – Seeking Alpha

Finch Therapeutics Completes Enrollment in Potentially Pivotal Trial of CP101, an Investigational Oral Full-Spectrum Microbiota® Therapy for the Prevention of Recurrent C. difficile Infection – The Tullahoma News

January 10, 2020

In today’s weekend post- maternal antibodies targeting microbiota protect mice from neonatal infection, exercise improves gestational diabetes in rodent models, bacterial signature in NAFLD and TMAO as negative predictor of human embryo quality. Happy reading and a nice weekend!

General microbiome

Adolescence and aging: impact of adolescence inflammatory stress and microbiota alterations on brain development, aging and neurodegeneration – Nour Yahfoufi – The Journal of Geronotology

Preclinical and clinical relevance of probiotics and synbiotics in colorectal carcinogenesis: a systematic review – Bruna C.S. Cruz – Nutrition Reviews

Gut microbiota: a new piece in understanding hepatocarcinogenesis – An Zhou – Cancer Letters

Gut Microbiota, Diet, and Chronic Diseases: The Role Played by Oxidative Stress – Elisardo C. Vasquez – Oxidative Medicine and Cellular Longevity

New insights on the colonization of the human gut by health-promoting bacteria – Sinead T. Morrin – Applied Microbiology and Biotechnology

Human microbiome

Salivary microbiota and inflammation‐related proteins in patients with psoriasis – Daniel Belstrøm – Oral Diseases

Oral butyrate does not affect innate immunity and islet autoimmunity in individuals with longstanding type 1 diabetes: a randomised controlled trial – Pieter F. de Groot – Diabetologia

Fusobacterium nucleatum in the colorectum, and its association with cancer risk and survival: a systematic review and meta-analysis – Christian Gethings-Behncke – Cancer Epidemiology Biomarkers and Prevention

Potential impact of removing metronidazole from treatment armamentarium of mild acute Clostridioides difficile infection – Shani Zilberman-Itskovich – Future Medicine

Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease Silvia Sookoian – Gut

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels – Mohammad Tauqeer Alam – Gut Pathogens

Early life microbiota

Antibiotic Resistance Genes in the Gut Microbiota of Children with Autistic Spectrum Disorder as Possible Predictors of the Disease – Alexey S. Kovtun – Microbial Drug Resistance

Trimethylamine-N-oxide is present in human follicular fluid and is a negative predictor of embryo quality – R.A.Nagy – Human Reproduction

Animal experiments

Microbiota-targeted maternal antibodies protect neonates from enteric infection – Wen Zheng – Nature

Characterization of metabolic and inflammatory profiles of transition dairy cows fed an energy-restricted diet – Giulia Esposito – Journal of Animal Science

Microbiota dependent production of butyrate is required for the bone anabolic activity of PTH – Jau-Yi Li – Journal of Clinical Investigation

Betaine addition as a potent ruminal fermentation modulator under hyperthermal and hyperosmotic conditions in vitro – Mubarik Mahmood – Journal of the Science of Food and Agriculture

Investigating temporal microbial dynamics in the rumen of beef calves raised on two farms during early life – Eóin O’Hara – FEMS Microbial Ecology

Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization – Matthew K. Schnizlein – mSphere

Post‐natal co‐development of the microbiota and gut barrier function follows different paths in the small and large intestine in piglets – Alexis Pierre Arnaud – Faseb Journal

Phellinus linteus polysaccharide extract improves insulin resistance by regulating gut microbiota composition – Yangyang Liu – Faseb Journal

Exercise improves metabolic function and alters the microbiome in rats with gestational diabetes – Dayana Mahizir – Faseb Journal

Microbial reconstitution reverses early female puberty induced by maternal high-fat diet during lactation – Mengjie Wang – Endocrinology

Fecal microbiota as a noninvasive biomarker to predict the tissue iron accumulation in intestine epithelial cells and liver – Bingdong Liu – Faseb Journal

Techniques

Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles – Yali Liang – mSphere