December 6, 2019

Today’s post is about metabolic networks of the human gut microbiota with host, how aging affects microbial world in humans, microbiome in honey bee and lifestyle dependent gut microbiota gradients in diverse Indian population. Have a nice weekend!

General microbiome

Review: Metabolic networks of the human gut microbiota – Susannah Selber-Hnatiw – Microbiology

Review: Cannabinoids and the Microbiota‐Gut‐Brain‐Axis: Emerging Effects of Cannabidiol and Potential Applications to Alcohol Use Disorders – Hollis C. Karoly – Alcoholism Clinical and Experimental Research

Review: The Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging – Oscar Salvador Barrera-Vázquez – Journal of Gerontology

Review: Nanotechnology intervention of the microbiome for cancer therapy – Wantong Song – Nature Nanotechnology

Commentary: Gut microbiome influences exercise response – Claire Greenhill – Nature Reviews Endocrinology

Human microbiome

Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma – Victor Tetz – Scientific Reports

Lifestyle induced microbial gradients: An Indian perspective – Rashmi Singh – Frontiers in Microbiology

Microbiota, type 2 diabetes and non-alcoholic fatty liver disease: protocol of an observational study – Benedetta M. Motta – Journal of Translational Medicine

Antibiotic exposure and the risk of colorectal adenoma and carcinoma: systematic review and meta‐analysis of observational studies – Leigh N. Sanyaolu – Colorectal Disease

Higher frequency of vertebrate‐infecting viruses in the gut of infants born to mothers with type 1 diabetes – Ki Wook Kim – Pediatric Diabetes

Animal experiments

Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics – Jie Han – Scientific Reports

Division of labor in honey bee gut microbiota for plant polysaccharide digestion – Hao Zheng – PNAS

The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera) – Michelle A. Taylor – PlosOne

Seven-day Green Tea Supplementation Revamps Gut Microbiome and Caecum/Skin Metabolome in Mice from Stress – Eun Sung Jung – Scientific Reports

Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonization travel – Raies A. Mir – PlosOne

Characterization of the cecal microbiome composition of Wenchang chickens before and after fattening – Zhen Tan – PlosOne

SOD1 deficiency alters gastrointestinal microbiota and metabolites in mice – Haruka Sagi – Experimental Gerontology

Plant, soil, root microbiome

Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere – Michael D. Jochum – PlosOne

Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing – Preshita S. Gadkari – FEMS Microbiology Ecology

Techniques

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces – Richard W. Hagan – American Journal of Physical Anthropology

Microbes in the news

How Microbiomes Affect Fear – Quanta Magazine

Rainforest Dwellers and Urbanites Have Consistently Different Microbiomes – Scientific American

Human Microbiome Modulators Market is Furbishing worldwide with Bayer, BioGaia, Chr. Hansen Holding, DowDuPont – News Description

December 2, 2019

Good Morning! Highlights of today’s digest include investigation of microbial communities from ground water sources to develop bioremediation strategies for removal of contaminating micropollutants for production of drinking water, another study with whole-virome analysis identifies changes in the human gut virome in inflammatory bowl diseases with a hope to develop biomarkers and therapeutics. Also, take a look at cool techniques such as Photo-PCR with gold nanorods and irradiation that shortens time for cell lysis and termocycling allowing rapid detection of bacteria as a point-of-care diagnostic tool. Enjoy!

Human skin microbiome
Review: Revealing the secret life of skin With the microbiome you never walk alone – Sfriso et al. – International Journal of Cosmetic Science

Human urinary tract microbiome
ANTIBIOTIC EXPOSURE IN LONG-TERM CARE FACILITIES IS ASSOCIATED WITH URINARY MICROBIOME PERTURBATIONS – Schell et al. – Innovation in Aging

Human gut microbiome
In silico Identification of Riboswitches in the Human Gut Microbiome for
Therapeutic Applications
– Kumari and Som – Journal of RNA and Genomics

Animal microbiome
Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish – Parata et al. – FEMS Microbial Ecology

Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys – Weber et al. – Environmental Microbiology

Geographically isolated Colorado potato beetle mediating distinct defense responses in potato is associated with the alteration of gut microbiota – Wang et al. – Journal of Pest Science

Plant, root and soil microbiome
Dynamics of bacterial community in litter and soil along a chronosequence of Robinia pseudoacacia plantations – Xu et al. – Science of The Total Environment

Influence of invasion by Sosnowsky’s hogweed on nematode communities and microbial activity in forest and grassland ecosystems – Cerevkova et al. – Global Ecology and Conservation

Water and extremophile microbiome
*Exploring groundwater microbial communities for natural attenuation potential of micropollutants – Aldas-Vargas et al. – bioRxiv

Shifts in dimethylated sulfur concentrations and microbiome composition in the red-tide causing dinoflagellate Alexandrium minutum during a simulated marine heatwave – Deschaseaux et al. – Biogeosciences

Artificial light at night erases positive interactions across trophic levels – Maggi et al. – Functional Ecology

Review: Linking metagenomics to aquatic microbial ecology and biogeochemical cycles – Grossart et al. – Limnology and Oceanography

Anaerobic microbial communities can influence algal growth and nutrient removal from anaerobic digestate – Bankston and Higgins – Bioresource Technology

Analysis of microbial communities involved in organic matter and nitrogen removal in a full-scale moving bed biofilm reactor located near the Polar Arctic Circle – Rodriguez-Sanchez et al. – International Biodeterioration & Biodegradation

Enhanced volatile fatty acid production and microbial population analysis in anaerobic treatment of high strength wastewater – Lim et al. – Journal of Water Process Engineering

Rainfall Influences on Microbial Community Dynamics in an Urban Watershed – Banka et al. – Journal of Student-Scientists’ Research

Management of water bodies in show caves – A microbial approach – Moldovan et al. – Tourism Management

Built-environment
Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms – Fu et al. – bioRxiv

Food microbiology
Integrated Meta-omics Approaches To Understand the Microbiome of Spontaneous Fermentation of Traditional Chinese Pu-erh Tea – Zhao et al. – mSystems

Phages and viruses
*Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease – Clooney et al. – Cell Host & Microbe

Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study – Lindfors et al. – BMJ Gut

Bioinformatics
Detecting contamination in viromes using ViromeQC – Zolfo et al. – Nature Biotechnology

Review: Metagenomics: Is it a powerful tool to obtain lipases for application in biocatalysis? – Almeida et al. – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

Techniques
In-depth serum virome analysis in patients with acute liver failure with indeterminate etiology – Ren et al. – Archives of Virology

Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using VirusFISH – Castillo et al. – bioRxiv

High-efficiency multi-site genomic editing (HEMSE) of Pseudomonas putida through thermoinducible ssDNA recombineering – Aparicio et al. – bioRxiv

A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses – Geisen et al. – bioRxiv

MiniReview: Next-Generation Sequencing Coupled With in situ Hybridization: A Novel Diagnostic Platform to Investigate Swine Emerging Pathogens and New Variants of Endemic Viruses – Resende et al. – Frontiers in Veterinary Science

*Gold Nanorod-based Photo-PCR System for One-Step, Rapid Detection of Bacteria – Kim et al. – Nanotheranostics

Science career
Using a Systems Change Framework to Evaluate Academic Equity & Climate Efforts in a Graduate Program – Wallace and York – bioRxiv

November 30, 2019

Have a nice weekend! In this Digest, we have a set of reviews about the gut-brain axis, covering associations between microbiota and neurological diseases, as well as a set of reviews about the connection between the microbiome and the immune system. We have also a paper about the microbiome from people living in high-altitude environments, and of course, several papers more. 

 

Human and General Microbiome

Gut microbiota composition in Himalayan and Andean populations and its relationship with diet, lifestyle and adaptation to the high-altitude environment – Andrea Quagliariello – Journal of Anthropological Sciences

Microbiological evidences for gastric cardiac microflora dysbiosis inducing the progression of inflammation – Ruijing Yan – Journal of Gastroenterology and Hepatology

Review: Targeting the gut microbiota for the treatment of irritable bowel syndrome – Charles C. Herndon – The Kaohsiung Journal of Medical Sciences

Review: The Gut Microbiome and Treatment-Resistance in Schizophrenia – Mary V. Seeman – Psychiatric Quarterly

Review: The Role of the Gut Microbiota in the Pathogenesis of Parkinson’s Disease – Dongming Yang – Frontiers in Neurology

Editorial: Interactions of the microbiota with the mucosal immune system – Calum C. Bain – Immunology

Review: Understanding immune-microbiota interactions in the intestine – Philip P. Ahern – Immunology

Review: The interaction of intestinal microbiota and innate lymphoid cells in health and disease throughout life – Stephanie C. Ganal‐Vonarburg – Immunology

Review: Immunological mechanisms underpinning faecal microbiota transplantation for the treatment of inflammatory bowel disease – M. N. Quraishi – Clinical and Experimental Immunology

Review: Population Genetics in the Human Microbiome – Nandita R. Garud – Trends in Genetics

Review: Gut Microbiota And The Use Of Probiotics In Constipation In Children And Adolescents: Systematic Review – Daiane Oliveira Vale San Gomes – Revista Paulista de Pediatria

Review: The gut microbiota modulates both browning of white adipose tissue and the activity of brown adipose tissue – José María Moreno-Navarrete – Reviews in Endocrine and Metabolic Disorders

Decoding Microbiome Research for Clinical Psychiatry – Jane A. Foster – The Canadian Journal of Psychiatry

Lactobacillus iners Is Associated with Vaginal Dysbiosis in Healthy Pregnant Women: A Preliminary Study – Nengneng Zheng – BioMed Research International

Human Endometrial Microbiota at Term of Normal Pregnancies – Claudia Leoni – Genes (MDPI)

Helicobacter pylori Infection Aggravates Dysbiosis of Gut Microbiome in Children With Gastritis – Lu Yang – Frontiers in Cellular and Infection Microbiology

The Effect of Gut Microbiome Composition on Human Immune Responses: An Exploration of Interference by Helminth Infections – Ivonne Martin – Frontiers in Genetics

Metagenome-wide association study of the alterations in the intestinal microbiome composition of ankylosing spondylitis patients and the effect of traditional and herbal treatment – RunYue Huang – Journal of Medical Microbiology 

Gut Microbiota and Cardiometabolic Risk Factors in Hemodialysis Patients: A Pilot Study – Annabel Biruete – Topics in Clinical Nutrition

Habitual animal fat consumption in shaping gut microbiota and microbial metabolites – Yi Wan – Food and Function

 

Animal Microbiome and Animal Experiments

Division of labor in honey bee gut microbiota for plant polysaccharide digestion – Hao Zheng – PNAS

Exploring interactions between xenobiotics, microbiota, and neurotoxicity in zebrafish – Luísa B. Bertotto – NeuroToxicology

The Skin Microbiota of Eleutherodactylus Frogs: Effects of Host Ecology, Phylogeny, and Local Environment – Liza Garcia-Recinos – Frontiers in Microbiology

The intestinal microbiota of lake anchovy varies according to sex, body size, and local habitat in Taihu Lake, China – Min Jiang – Microbiology Open

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition – Nicholas M. Fountain‐Jones – Journal of Animal Ecology

Immunodeficiency Promotes Adaptive Alterations of Host Gut Microbiome: An Observational Metagenomic Study in Mice – Shuyu Zheng – Frontiers in Microbiology

Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics – Jie Han – Scientific Reports

Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome – Rafael J. Vivero – Scientific Reports

Ochratoxin A induces liver inflammation: involvement of intestinal microbiota – Wence Wang – Microbiome

Toxicity, Pharmacokinetics, and Gut Microbiome of Oral Administration of Sesterterpene MHO7 Derived from a Marine Fungus – Wei Tian – Marine Drugs

 

Bioinformatics

AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data –  M. Shaffer – BMC Bioinformatics

Managing batch effects in microbiome data – Yiwen Wang – Briefings in Bioinformatics

Review: Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities – Duo Jiang – Frontiers in Genetics

 

Methods

Exploring the chemical space of the human microbiome – Lei Tang – Nature Methods

 

Other

Microbiome Response to Hot Water Treatment and Potential Synergy With Biological Control on Stored Apples – Birgit Wassermann – Frontiers in Microbiology 

Year in Review: Big data and tiny proteins: shining a light on the dark corners of the gut microbiome – Suzanne Devkota – Nature Reviews Gastroenterology & Hepatology 

 

November 17, 2019

Good Morning! Highlights of today’s digest include a promising probiotic effect of Lactobaccillus helveticus on acute liver failure as shown in an animal model study. Findings from another study about soil sterilization and how it leads to healthier soil microbiome and plant growth by modulating promotion of plant and beneficial microbes associations. Finally, check out an investigation aiming to generate a standardized approach for microbiome profiling by evaluating a series of hypervariable regions of 16S gene and estimating community richness across diverse sample types. Many review articles are also posted. Enjoy!

Pregnancy and early life

Acquisition and Development of the Extremely Preterm Infant Microbiota Across Multiple Anatomical Sites – Young et al. – J of Pediatric Gastroebterology and Nutrition

Multi-site human microbiome

Review: Urobiome: In Sickness and in Health – Wojciuk et al. – Microorganisms

Review: The Skin and Gut Microbiome and Its Role in Common Dermatologic Conditions – Ellis et al. – Microorganisms

Human oral microbiome

Analysis of the human oral microbiome from modern and historical samples with SPARSE and EToKi – Achtman and Zhou – bioRxiv

Human vaginal microbiome

HIV infection is associated with preterm delivery independent of vaginal microbiota in pregnant African women – Gudza-Mugabe et al. – The Journal of Infectious Diseases

Human gut microbiome

Review: Microbial Phenolic Metabolites: Which Molecules Actually Have an Effect on Human Health? – Marhuenda-Munoz et al. – Nutrients

Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification – Paepe et al. – ISME

Bifidogenic and butyrogenic effects of young barely leaf extract in an in vitro human colonic microbiota model – Sasaki et al. – AMB Express

Animal experiments

Dietary energy and protein levels influenced the growth performance, ruminal morphology and fermentation and microbial diversity of lambs – Cui et al. – Scientific Reports

*Lactobacillus helveticus R0052 alleviates liver injury by modulating gut microbiome and metabolome in d-galactosamine-treated rats – Wang et al. – Applied Microbiology and Biotechnology

Plant, root and soil microbiome

Evaluation of the ecological restoration of a coal mine dump by exploring the characteristics of microbial communities – Chen et al. – Applied Soil Ecology

*Soil sterilization leads to re-colonization of a healthier rhizosphere microbiome – Li et al. – Rhizosphere

Water and extremophile microbiome

Microbial composition and variability of natural marine planktonic and biofouling communities from the Bay of Bengal – Angelova et al. – Frontiers in Microbiology

Changes to the microbial communities within groundwater in response to a large crustal earthquake in Kumamoto, southern Japan – Morimura et al. – Journal of Hydrology

Increasing oxygen defciency changes rare and moderately abundant bacterial communities in coastal soft sediments – Sinkko et al. – Scientific Reports Nature Research

Probiotics / peribiotics

Review: Recent systems biology approaches for probiotics use in health aspects: a review – Yadave and Shukla – 3 Biotech

Bioinformatics

A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome – Darcy et al. – bioRxiv

Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study – Bai et al. – JMIR Medical Informatics

Techniques

*Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework – Wasimuddin et al. – bioRxiv

Rapid, selective and single cell electrical detection of antibiotic resistant bacteria – Kumar et al. – bioRxiv

Droplet Digital PCR Technology for Detection of Ilyonectria liriodendri from Grapevine Environmental Samples – Martinez Diz et al. – APS Publications

November 16, 2019

In today’s digest read about the Million Microbiome of Humans Project, problems in studies of the gut microbiome in Parkinson’s disease, and how bats’ gut bacteria are more closely tied to where bats live. Happy weekend!

Gut microbiome

*Review: Increasing Comparability and Utility of Gut Microbiome Studies in Parkinson’s Disease: A Systematic Review – Jeffrey M. Boertien – Journal of Parkinson’s Disease

Microbiome‐immune‐metabolic axis in the epidemic of childhood obesity: Evidence and opportunities – Halle J. Kincaid – Obesity Reviews

Vaginal microbiome

Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy – Andrew Oliver – bioRxiv

Respiratory microbiome

Review: The microbiome of the upper respiratory tract in health and disease – Christina Kumpitsch – BMC Biology

Animal experiments

Lactobacillus helveticus R0052 alleviates liver injury by modulating gut microbiome and metabolome in d-galactosamine-treated rats – Qiangqiang Wang – Applied Microbiology and Biotechnology

Comparison of the fecal, cecal, and mucus microbiome in male and female mice after TNBS-induced colitis – Ariangela J. Kozik – PlosOne

Cranberry extracts promote growth of Bacteroidaceae and decrease abundance of Enterobacteriaceae in a human gut simulator model – Kathleen O’Connor – PlosOne

Animal microbiome

*Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome – Holly L. Lutz – mSystems

High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China – Hongling Wei – BMC Genomics

Probiotics

Production of multiple bacteriocins, including the novel bacteriocin gassericin M, by Lactobacillus gasseri LM19, a strain isolated from human milk – Enriqueta Garcia-Gutierrez – bioRxiv

Infected chronic ischemic wound topically treated with a multi-strain probiotic formulation: a novel tailored treatment strategy – Salvatore Venosi – Journal of Translational Medicine

Genomic and epidemiological evidence of bacterial transmission from probiotic capsule to blood in ICU patients – Idan Yelin – Nature Medicine

Water microbiome

Species-level microbiome composition of activated sludge – introducing the MiDAS 3 ecosystem-specific reference database and taxonomy – Marta Nierychlo – bioRxiv

Comparative microbial diversity across temperature gradients in hot springs from Yellowstone and Iceland – Peter T Podar – bioRxiv

Niche partitioning of microbial communities in riverine floodplains – Marc Peipoch – Scientific Reports

Biodegradability of wastewater determines microbial assembly mechanisms in full-scale wastewater treatment plants – Bing Zhang – Water Research

Techniques

Microfluidic cultivation and analysis tools for interaction studies of microbial co-cultures – Alina Burmeister and Alexander Grünberger – Current Opinion in Biotechnology

Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae – Leon Peto – PlosOne

Microbiome in News

*Million Microbiome of Humans Project – PRNewswire
Scientists from China, Sweden, Denmark, France, Latvia and other countries will cooperate in microbial metagenomic research, aiming to analyze one million microbial samples and build the world’s largest database of human microbiome.

Childhood Asthma and the Airway Microbiome.

Increased risk of childhood asthma development associated with specific infant airway microbiota 1

By: Puck deRoos

According to the CDC the prevalence of childhood asthma has dramatically increased within the past decade, rising to become the top reason for missed school days and affecting over 6 million children in the United States alone2

Researchers at the University of Copenhagen have found an association between an infant’s airway microbiota at one month old and the development of childhood asthma by age six. 

Previously, another factor associated with an increased risk of developing childhood asthma was delivery via cesarean section3, while living with farm animals, an older sibling, or attending day care decreased the risk of developing childhood asthma 4,5

In this new study, scientists have specifically found a correlation between the presence of Veillonella (importance 28.1%), Prevotella (23.7%), and Gemella (importance 16.3%) bacteria in the airway at age one month with an increased risk of asthma development before age six. Furthermore, they analyzed the topical airway immune profile from the mucosal lining and discovered an independent correlation between the previously mentioned bacteria and the development of childhood asthma. 

At age one month, researchers found that children who developed asthma had a higher diversity of microbes, but also have an increased ratio of high-risk bacteria Vallonella and Prevotella. They found no association between specific taxa of microbes and asthma development by 6 years at ages 1 week or 3 months old. 

A larger proportion of high-risk bacteria in a critical period of airway immune development poses a major threat to normal development. The children who developed asthma early in life showed a reduction in tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β), which are secreted by the bodies immune cells to fight inflammation and infections. They convergently showed an increase in Chemokine (C-C motif) ligand 2 (CCL2) and CCL17 levels in the topical immune profile. 

The airway microbiota samples were taken during the first three months of life from 700 children monitored for the development of asthma using 16S ribosomal RNA gene amplicon sequencing from the population based Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC 2010). The use of this cohort strengthened the results of the study because all children were sampled during infancy before the development of any symptoms, and were uniformly monitored for the development of any asthmatic symptoms through childhood. 

The findings of this study suggest that the development of childhood asthma may be connected to the interactions between early-life airway microbiota and the developing immune system. Because different areas of the human body have different microbial compositions which are considered healthy, determining specific microbes increasing the risk for childhood asthma may provide tools to prevent the disease’s spread.

  1. Thorsen, J., Rasmussen, M.A., Waage, J. et al. Infant airway microbiota and topical immune perturbations in the origins of childhood asthma. Nat Commun 10, 5001 (2019) doi:10.1038/s41467-019-12989-7
  2. The Centers for Disease Control and Prevention (CDC, 2019).
  3. Thavagnanam, S., Fleming, J., Bromley, A., Shields, M. D. & Cardwell, C. R. A meta-analysis of the association between Caesarean section and childhood asthma. Clin. Exp. Allergy38, 629–633 (2008).
  4. Illi, S. et al. Protection from childhood asthma and allergy in Alpine farm environments—the GABRIEL advanced studies. J. Allergy Clin. Immunol. 129, 1470–1477.e6 (2012).
  5. Ball, T. M. et al. Siblings, day-care attendance, and the risk of asthma and wheezing during childhood. N. Engl. J. Med.343, 538–543 (2000).

November 11, 2019

Monday’s morning digest is all about interesting updates in microbiome field – real time sampling of international travelers to study antibiotic resistant bacteria, new techniques on using rectal swabs instead of fecal samples to study infant microbiota, 16srRNA gene sequencing for strain level identification and if neutraceutical consumption helps in multiple sclerosis! Finally some interesting review articles on microbial ecology in wine making and a Movember month featured article on association of gut microbiome with men’s sexual health. Enjoy reading!

General microbiome

From the vineyard to the winery: how microbial ecology drives regional distinctiveness of wine – Di Liu – Frontiers in Microbiology

The Gut Microbiome and Men’s Sexual Health – Mohamad M. Osman – Current Sexual Heath Reports

Antibacterial Soaps and Other Cleaners May Actually Be Aiding in the Development of Super Bacteria – Shimon Shatzmiller – Pharmacology, Toxicology and Pharmaceutics

Dietary lipids, gut microbiota and lipid metabolism – Marc Schoeler – Reviews in Endocrine and Metabolic Disorders

Human microbiome

Functional characterisation of gut microbiota and metabolism in Type 2 diabetes indicates that Clostridiales and Enterococcus could play a key role in the disease – Marina Mora-Ortiz – BioRxiv

Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions – A. Kantele – BioRxiv

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome – Zhuye Jie – BioRxiv

Antimicrobial resistance gene prevalence in a population of patients with advanced dementia is related to specific pathobionts – Aislinn D. Rowan-Nash – BioRxiv

Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018 – Mónica Arteaga – BioRxiv

Molecular Reconstruction of the Diet in Human Stool Samples – Frank Maixner – mSystems

Infant microbiome

Impacts of Delivery Mode on Very Low Birth Weight Infants’ Oral Microbiome – Hongping Li – Pediatrics and Neonatology

Biomarker Research in ADHD: the Impact of Nutrition (BRAIN) – study protocol of an open-label trial to investigate the mechanisms underlying the effects of a few-foods diet on ADHD symptoms in children – Tim Stobernack – BMJ Open

Immunometabolic approaches to prevent, detect, and treat neonatal sepsis – Maria Giulia Conti – Pediatric Research

Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing – Marta Reyman – Scientific Reports

Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course – R. E. Ventura – Scientific Reports

Animal experiments

Vasoactive intestinal peptide deficiency is associated with altered gut microbiota communities in male and female C57BL/6 mice – Manpreet Bains – Frontiers in Microbiology

Metabolic analysis of regionally distinct gut microbial communities using an in vitro platform – Jenni Firrman – Agricultural and Environmental Chemistry

Effect of Diet on the Enteric Microbiome of the Wood-Eating Catfish Panaque nigrolineatus – Harold J. Schreier – Frontiers in Microbiology

A high-fat/high-protein, Atkins-type diet exacerbates Clostridioides (Clostridium) difficile infection in mice, whereas a high-carbohydrate diet protects – Chrisabelle C. Mefferd – BioRxiv

Plant, soil, root microbiome

Effects of repeated applications of urea with DMPP on ammonia oxidizers, denitrifiers, and non-targeted microbial communities of an agricultural soil in Queensland, Australia – Aineah Obed Luchibia – Applied Soil Ecology

Covariation of diet and gut microbiome in African megafauna – Tyler R. Kartzinel – PNAS

Fungal communities resist recovery in sand mine restoration – Miranda Hart – Frontiers in Forest and Global Change

Microbial community structure and ecology in sediments of a pristine mangrove forest – C.O.Santana – BioRxiv

Bridging the gap between single-strain and community-level plant-microbe chemical interactions – Bridget O’Banion – Molecular Plant-Microbe Interactions

A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome – Johan HJ Leveau – Current Opinion in Microbiology

Water microbiome

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems Amy E. Zimmerman – Nature Reviews Microbiology

Down to the bone: the role of overlooked endolithic microbiomes in reef coral health – Mathieu Pernice – ISME Journal

Differential responses of stream water and bed sediment microbial communities to watershed degradation – Hehuan Liao – Environment International

B12 production by marine microbial communities and Dinoroseobacter shibae continuous cultures under different growth and respiration rates – Josue Villegas-Mendoza – Aquatic Microbial Ecology

Quantifying the contribution of microbial immigration in engineered water systems – Ran Mei – Microbiome

Microbial community rearrangements in power-to-biomethane reactors employing mesophilic biogas digestate – Norbert Ács – Frontiers in Energy Research

Techniques

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis – Jethro S. Johnson – Nature Communications

AMR – An R Package for Working with Antimicrobial Resistance Data – Matthijs S. Berends – BioRxiv

Probiotics Prebiotics

The effect of emerging nutraceutical interventions for clinical and biological outcomes in multiple sclerosis: A systematic review – Wolfgang Marx – Multiple Sclerosis and Related Disorders

Resveratrol treatment improves the altered metabolism and related dysbiosis of gut programed by prenatal high-fat diet and postnatal high-fat diet exposure – Yi-Chuan Huang – The Journal of Nutritional Biochemistry

The effects of inulin on gut microbial composition: a systematic review of evidence from human studies – Quentin Le Bastard – European Journal of Clinical Microbiology & Infectious Diseases