Category Archives: Water microbiome

February 1, 2020

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Today’s Digest brings you an Outlook collection on human gut microbiome by Nature, a Hi-C investigation of the evolution of the gut microbiota, and be careful with the dust, there’s transferrable antimicrobial genes within!

Events

Reshaping the Microbiome through Nutrition – Nature Conference – San Diego, CA

General microbiology

Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling – Richard P. Sequeira et al. – Nature Microbiology

** The gut microbiome – Nature Outlook

Antimicrobial resistance

The negative cofactor 2 complex is a key regulator of drug resistance in Aspergillus fumigatus – Takanori Furukawa et al. – Nature Communications

Plasmid-mediated metronidazole resistance in Clostridioides difficile – Ilse M. Boekhoud et al. – Nature Communications

A Common Practice of Widespread Antimicrobial Use in Horse Production Promotes Multi-Drug Resistance – S. Álvarez–Narváez et al. – Scientific Reports

Surveys of knowledge and awareness of antibiotic use and antimicrobial resistance in general population: A systematic review – PLoS One

Antimicrobial resistance patterns and molecular resistance markers of Campylobacter jejuni isolates from human diarrheal cases – Mohamed Elhadidy et al. – PLoS One

Review: Antibiotic resistance: turning evolutionary principles into clinical reality – Dan I Andersson et al. – FEMS Microbiology Reviews

Antibiotic resistome associated with microbial communities in an integrated wastewater reclamation system – Kaifeng Yu et al. – Water Research

Human gut microbiome

** Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation – Eitan Yaffe & David A. Relman – Nature Microbiology

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease – Nadine Fornelos et al. – Nature Microbiology

Human cancer microbiome

The Influence of Lung Microbiota on Lung Carcinogenesis, Immunity, and Immunotherapy – Ariel G. Ramírez-Labrada et al. – Trends in Cancer

Built environment microbiome

** Mobilizable antibiotic resistance genes are present in dust microbial communities – Sarah Ben Maamar et al. – PLoS Pathogens

Indoor and outdoor airborne bacterial and fungal air quality in kindergartens: seasonal distribution, genera, levels, and factors influencing their concentration – Farhad Mirkhond Chegini et al. – Building and Environment

Metabolomics

Targeted metabolomics of pellicle and saliva in children with different caries activity – Annika Schulz et al. – Scientific Reports

Animal experiments

Review: The role of the microbiota in sedentary life style disorders and ageing: Lessons from the animal kingdom – P.W. O’Toole & P.G. Shiels – Journal of Internal Medicine

Animal microbiome

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes – Nina Montoya-Ciriaco et al. – Microbiome

Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets – Francesca Romana Massacci et al. – Animal Microbiome

Plant, root and soil microbiome

Effects of soil chemical properties and fractions of Pb, Cd, and Zn on bacterial and fungal communities – Xiaomei Pan et al. – Science of the Total Environment

Resilience of the microbial communities of semiarid agricultural soils during natural climatic variability events – Lumarie Pérez-Guzmán et al. – Applied Soil Ecology

Effects of microbial inoculants on the fermentation characteristics and microbial communities of sweet sorghum bagasse silage – Miaoyin Dong et al. – Scientific Reports

Water and extremophile microbiome

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing – Genevieve L. Fernandes et al. – Frontiers in Microbiology

Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure – Xiaolong Wang et al. – Environmental Science & Technology

Methane yield enhancement of mesophilic and thermophilic anaerobic co-digestion of algal biomass and food waste using algal biochar: Semi-continuous operation and microbial community analysis – Le Zhang et al. – Bioresource Technology

Characterization and co-occurrence of microbial community in epiphytic biofilms and surface sediments of wetlands with submersed macrophytes – Yuansi Liu et al. – Science of the Total Environment

Phages and viruses

** Giant virus diversity and host interactions through global metagenomics – Frederik Schulz et al. – Nature

Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China – Bingqian Qu et al. – PLoS One

Outbreak of Pneumonia of Unknown Etiology in Wuhan China: the Mystery and the Miracle – Hongzhou Lu et al. – Journal of Medical Virology

Bioinformatics

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing – Andrei Prodan et al. – PLoS One

Microbes in the news

Walnuts May Benefit Gut Bacteria and Improve Heart Health – Karina Lichtenstein – Medicine Net

How to create living art with microbes – Eugenia Angulo – BBVA OpenMind

January 22, 2020

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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 8, 2020

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Today’s digest features a retrospective mini-review of mothur, study on gut microbiomes of over 900 vertebrate species [Spoiler alert: birds and bats share similarities in their microbiome], findings of fifteen-thousand-year-old viruses in glacier ice, and more. Happy reading!

Gut microbiome

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform – Christian Munck – Nature Communications

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

Gut dysbiosis induces the development of pre-eclampsia through bacterial translocation– Xia Chen – Gut

Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals – Aftab Ahmad – PlosOne

Alterations of human lung and gut microbiome in non-small cell lung carcinomas and distant metastasis – Hui Lu – bioRxiv

The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for human complex diseases – Fengzhe Xu – bioRxiv

Oral microbiome

Acquisition of Oral Microbiota is Driven by Environment, Not Host Genetics – Chiranjit Mukherjee – bioRxiv

Animal microbiome

*Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats– Se Jin Song – mBio

Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities – Nikola Palevich – Applied and Environmental Microbiology

Inside out: microbiota dynamics during host-plant adaptation of whiteflies – Diego Santos-Garcia – The ISME Journal

Blood Loss Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Gut Microbiome of Rabbits – Junjie Yang – Current Microbiology

Probiotics

In Vitro Probiotic Potential of Hemophilin-producing Strains of Haemophilus haemolyticus – Brianna Atto – bioRxiv

Quantifying and engineering mucus adhesion of probiotics – Zachary J. S. Mays – bioRxiv

Plant/root/soil microbiome

Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in super arid environments – Ashraf Al-Ashhab – bioRxiv

Secreted metabolite-mediated interactions between rhizosphere bacteria and Trichoderma biocontrol agents – Ningxiao Li – PlosOne

Water microbiome

Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses – Daehyun Daniel Kim – bioRxiv

Viruses

*Glacier ice archives fifteen-thousand-year-old viruses – Zhi-Ping Zhong – bioRxiv

Meeting report: Viruses in the Built Environment (VIBE) meeting report – Aaron J. Prussin – Microbiome

Bioinformatics

*Minireview: Reintroducing mothur: 10 Years Later – Patrick D. Schloss – Applied and Environmental Microbiology

FunGeCo : A web based tool for estimation of Functional potential of bacterial genomes and microbiomes using Gene Context information – Swadha Anand – Bioinformatics

December 27, 2019

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Today’s Digest brings you a report linking gut microbiota and metabolites, a study on dishwasher rubber as a bacterial reservoir, a news piece for your guide to probiotics, and many more. If we don’t see you again in 2019, Happy New Year! May 2020 bring much success and happiness!

General microbiology

Preprint: The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes – Maria A. Sierra et al. – bioRxiv

A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships – Suyeon Kim et al. – BMC Genomics

Antimicrobial resistance

Preprint: Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment – Morteza Roodgar et al. – bioRxiv

Human oral microbiome

Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities – Sayaka Katagiri et al. – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Microbiome in Chronic Obstructive Pulmonary Disease: Role of Natural Products Against Microbial Pathogens – Alessia Santoro et al. – Current Medicinal Chemistry

Human gut microbiome

Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi – Siddhika Pareek et al. – npj Biofilms and Microbiomes

Review: The influence of dietary patterns on gut microbiome and its consequences for nonalcoholic fatty liver disease – Qing-Song Zhang et al. – Trends in Food Science and Technology

** Relationship between gut microbiota and circulating metabolites in population-based cohorts – Dina Vojinovic et al. – Nature Communications

Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination – Jacob A. Cram et al. – PLoS One

Preprint: The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for human complex diseases – Fengzhe Xu & Yuanqing Fu et al. – bioRxiv

Effect of Helicobacter pylori on gastrointestinal microbiota: a population-based study in Linqu, a high-risk area of gastric cancer – Yang Guo et al. – Gut

Human gut-microbiome-brain axis

The relationship between the gut microbiome and mild cognitive impairment in patients without dementia: a cross-sectional study conducted in Japan – Naoki Saji et al. – Scientific Reports

Synergistic effects of APOE and sex on the gut microbiome of young EFAD transgenic mice – Juan Maldonado Weng et al. – Molecular Neurodegeneration

Metabolomics

Tech Note: Boost that metabolomic confidence – Vivien Marx – Nature Methods

The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics

Animal experiments

Allergic inflammation alters the lung microbiome and hinders synergistic co-infection with H1N1 influenza virus and Streptococcus pneumoniae in C57BL/6 mice – Kim S. LeMessurier et al. – Scientific Reports

Jatrorrhizine Balances the Gut Microbiota and Reverses Learning and Memory Deficits in APP/PS1 transgenic mice – Sheng Wang et al. – Scientific Reports

The impact of gut microbiota manipulation with antibiotics on colon tumorigenesis in a murine model – Jae Gon Lee et al. – PLoS One

Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the porcine neonatal gut – Hongbin Liu et al. – BMC Biology

Built environment microbiome

** The dishwasher rubber seal acts as a reservoir of bacteria in the home environment – Jerneja Zupančič et al. – BMC Microbiology

Plant, root and soil microbiome

Development of microbial communities in organochlorine pesticide contaminated soil: A post-reclamation perspective – Helga E.Balázs et al. – Applied Soil Ecology

Towards simple tools to assess functional effects of contaminants on natural microbial and invertebrate sediment communities – Stéphane Pesce et al. – Environmental Science and Pollution Research

Core rhizosphere microbiomes of dryland wheat are influenced by location and land-use history – Daniel C Schlatter et al. – Applied and Environmental Microbiology

Water and extremophile microbiome

Single molecule sequencing reveals response of manganese-oxidizing microbiome to different biofilter media in drinking water systems – Xin Zhao et al. – Water Research

Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics – Jose M. Haro-Moreno et al. – Frontiers in Microbiology

Phages and viruses

News & Views: Phages build anti-defence barriers – Eugene V. Koonin & Mart Krupovic – Nature Microbiology

Microbes in the news

The Best Thing That Happened This Week: Dogs Rule Because They Drool – Sandy Hingston – Philadelphia Magazine

** A guide to the best probiotics – Louisa Richards/Katherine Marengo – Medical News Today

Having a Dog as a Child Is Tied to a Lower Risk of Schizophrenia as an Adult – Nicholas Bakalar – New York Times

Expanding virophage diversity – DOE/Joint Genome Institute

Microbes on the market

Carbiotix to partner with Italian university on neuroinflammation project – Nathan Gray – Nutraingredients

Human Microbiome Market is Expected to Touch US$ 1888.9 Mn by 2026 – Sheila Shipman – News Cast Report

The next frontier – Aaron Massecar – Today’s Veterinary Business

December 23, 2019

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In today’s digest read about the subway microbiome (from surface and air samples collected at 16 subway stations in Oslo, Norway), role of Staphylococcus epidermidis in healthy maturation of the nasal microbiome, effect of storage and time on urinary microbiome, and more. Happy Holidays!

General microbiome

The emergence of microbiome centres – Jennifer B. H. Martiny – Nature Microbiology

Subway microbiome

*The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities– Jostein Gohli – Microbiome

Gut microbiome

Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut– Pichet Praveschotinunt – Nature Communications

Urinary microbiome

*The urinary microbiota composition remains stable over time and under various storage conditions – Caspar Bundgaard-Nielsen – bioRxiv

Vaginal microbiome

Review: Genetic Heterogeneity and Taxonomic Diversity among Gardnerella Species – Joana Castro – Trends in Microbiology

Nasal microbiome

*Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production – Qian Liu – Cell Host & Microbes

Animal microbiome

Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China – Chunlai Wang – mSystems

Animal experiments

Altered microbiota composition reflects enhanced communication in 15q11-13 CNV mice– Dian Eurike Septyaningtrias – Neuroscience Research

Plant/root/soil microbiome

Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities – S. Emilia Hannula – mBio

Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland– Jie Yang – Scientific Reports

Water microbiome

Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge– Chenbing Ai – Microorganisms

Viruses

Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves – Victor Golyaev – Scientific Reports

Bioinformatics

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise – Valentina Peona – bioRxiv

Transcriptome assembly from long-read RNA-seq alignments with StringTie2– Sam Kovaka – Genome Biology

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework – Guo Liang Gan – BMC Bioinformatics

The Generalized Matrix Decomposition Biplot and Its Application to Microbiome Data – Yue Wang – mSystems

December 20, 2019

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This may be our last edition of the Microbiome Digest before the holidays kick in. A rich and dynamic Digest brings you all things microbiome (apologies for the tight formatting). An encouraging report on how we can reduce antimicrobial resistance organically, an amazing recovery of a human genome and an oral microbiome from chewed birch pitch thousands of years ago, and a network analysis reveals four levels of hierarchical trophic interactions in the human gut microbiome. Enjoy Reading and Happy Holidays!
Events
BMC Medicine’s upcoming collection, New Frontiers in Diagnosis, Treatment and Management of Neuromuscular Disorders, is soliciting submissions.
Current Issue of The ISME Journal
The 9th Gut Microbiota for Health World Summit – March 7 and 8 2020 in Madrid, Spain
General microbiology
High-order interactions distort the functional landscape of microbial consortia – Sanchez-Gorostiaga & Bajić et al. – PLoS Biology
Antimicrobial resistance
Human skin microbiome
Human oral microbiome
** A 5700 year-old human genome and oral microbiome from chewed birch pitch – Theis Z. T. Jensen et al. – Nature Communications
Press: Ancient “Chewing Gum” Reveals a 5,700-Year-Old Microbiome – Jim Daley – Scientific American
Human respiratory microbiome
Press: Child asthma flare-ups coincide with microbiome changes – JULIA EVANGELOU STRAIT-WUSTL – Futurity
Human gut microbiome
Human vaginal microbiome
Human gut-microbiota-brain axis
Review: Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain – Kan Gao et al. – Advances in Nutrition
Cancer microbiome
Metabolomics
The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics
Animal experiments
Animal microbiome
Plant, root and soil microbiome
Root microbiomes as indicators of seagrass health – Belinda C Martin et al. – FEMS Microbiology Ecology
Water and extremophile microbiome
Phages and viruses
Technology
Manipulating rod-shaped bacteria with optical tweezers – Zheng Zhang et al. – Scientific Reports
Bioinformatics
** Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang et al. – PLoS Computational Biology
Microbes in the news
The microbiome is fundamental to both health and disease – Fabian Brockotter – Poultry World
Low FODMAP Diet Helps IDB Patients – Kenny Walter – MDMAG
Oral Health: Caring for the Other Microbiome – Julia Peterman – Whole Foods Magazine
Non-microbiology pick

 

November 23, 2019

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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

November 20, 2019

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Today’s Digest brings you a comprehensive on microbial recovery after antibiotics, a series of studies in Blood on microbial changes after bone marrow transplant, how global ecological factors can drive soil microbiota evolution, and much more. Enjoy!

General microbiology

Preprint: Horizontal gene transfer drives the evolution of dependencies in bacteria – Akshit Goyal – bioRxiv

Antimicrobial resistance

Cross Journal Series: Health Policy and the Management of Antimicrobial Resistance in LMICs – BMC

** Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs – Katharine Michelle Ng et al. – Cell Host & Microbe

Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer – Ryan V Trexler & Terrence H Bell – FEMS Microbiology Letters

Natural products discovery and potential for new antibiotics – Olga Genilloud – Current Opinion in Microbiology

Engineering enzymatic assembly lines to produce new antibiotics – Kenan AJ Bozhüyük et al. – Current Opinion in Microbiology

Human gut microbiome

Antibiotic Exposures and Dietary Intakes Are Associated with Changes in Microbiota Compositions in Allogeneic Hematopoietic Stem Cell Transplant Patients – Chi L. Nguyen et al. – Blood

Impact of Antibiotics on Gut Microbiota Diversity and the Results of a Prospective Dietary Assessment in Patients with Multiple Myeloma Undergoing Autologous Hematopoietic Stem Cell Transplantation – Christopher D’Angelo et al. – Blood

** Impact of Gut Mycobiota Composition on Outcomes after Allogeneic Hematopoietic Cell Transplantation – Florent Malard et al. – Blood

Functional microbiome deficits associated with ageing: Chronological age threshold – Susana Ruiz‐Ruiz et al. – Aging Cell

Human gut-microbiome-brain axis

Review: Gut Microbiota: A Perspective for Psychiatrists – Rea K. et al. – Neuropsychobiology

Metabolomics

Review: Metabolomics biotechnology, applications, and future trends: a systematic review – Qiang Yang et al. – RSC Adv

Animal experiments

Hematopoietic Npc1 mutation shifts gut microbiota composition in Ldlr−/− mice on a high-fat, high-cholesterol diet – Tom Houben et al. – Scientific Reports

Animal microbiome

Cross-kingdom analysis of nymphal-stage Ixodes scapularis microbial communities in relation to Borrelia burgdorferi infection and load – William J Landesman et al. – FEMS Microbiology Ecology

Abdominal microbial communities in ants depend on colony membership rather than caste and are linked to colony productivity – Francisca H. I. D. Segers et al. – Ecology and Evolution

Plant, root and soil microbiome

The invasive potential of a hybrid species: insights from soil chemical properties and soil microbial communities – Feng Sun et al. – Journal of Plant Ecology

** The role of multiple global change factors in driving soil functions and microbial biodiversity – Matthias C. Rillig et al. – Science

Influence of sulfur fertilization on CuO nanoparticles migration and transformation in soil pore water from the rice (Oryza sativa L.) rhizosphere – Lijuan Sun et al. – Environmental Pollution

Water and extremophile microbiome

Effect of temperature on opportunistic pathogen gene markers and microbial communities in long-term stored roof-harvested rainwater – Xiaodong Zhang et al. – Environmental Research

Metabolic profiling of cold adaptation of a deep-sea psychrotolerant Microbacterium sediminis to prolonged low temperature under high hydrostatic pressure – Jin-Mei Xia et al. – Applied Microbiology and Biotechnology

Groundwater cable bacteria conserve energy by sulfur disproportionation – Hubert Müller et al. – The ISME Journal

Bioinformatics

Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks – Attayeb Mohsen et al. – BMC Bioinformatics

Microbes in the news

New Etiology of Rheumatoid Arthritis Identified in the Gut Microbiome – Frieda Wiley – Rheumatology Network

Gut microbiome diversity associates with sleep quality in healthy adults – Allison Clark – Gut Microbiota For Health

Metagenomics Unlocks Unknowns of Diarrheal Disease Cases in Children – John Toon – GA Tech

Clues for predicting premature birth risk may be found in mother’s immune system, microbiome – Amanda Keener – Genetic Literacy Project

Study offers a bird’s eye view of a bird’s smell – Kaylie Connors – Great Lakes Echo

Microbes on the market

Lancôme brings microbiome hub to Hong Kong with DFS – Elena Dimama – DFNI

November 11, 2019

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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

November 8, 2019

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Today’s week-end digest is about new bioinformatic tools (MGnify, PIME, MDiNE) for microbiota analysis, how chemical and built environment of home affects human microbiota and  guidelines for the gut microbiome studies in hypertension.

General microbiome

Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners – Sara C. Di Rienzi – Advances in Nutrition

Bacteriophages in gastroenterology—from biology to clinical applications – João Sabino – Alimentary Pharmacology and Therapeutics

Boosting natural history research via metagenomic clean-up of crowdsourced feces – Amrita Srivathsan – Plos Biology

Human microbiome

Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis – Stuart Astbury – Gut Microbes

Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension – Francine Z. Marques – Hypertension

The association between dietary fibre deficiency and high-income lifestyle-associated diseases: Burkitt’s hypothesis revisited – Stephen J. O’Keefe – The Lancet Gastroenterology and Hepatology

Animal experiments

Bacterial Swarming as a Protective Response to Intestinal Stress – Weijie Chen – BioRxiv

Flaxseed oil supplementation improves intestinal function and immunity, associated with altered intestinal microbiome and fatty acid profile in pigs with intrauterine growth retardation – Lianqiang Che – Food and Function

Gamma-aminobutyric acid-producing lactobacilli positively affect metabolism and depressive-like behaviour in a mouse model of metabolic syndrome – E. Patterson – Scientific Reports

Plant, root and soil microbiome

Short term effects of different green manure amendments on the composition of main microbial groups and microbial activity of a submerged rice cropping system – Muhammad Israr Khan – Applied Soil Ecology

Cost-effective in-situ remediation technologies for complete mineralization of dyes contaminated soils – Vipul R. Patel – Chemosphere

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea – Lijun Bao – Microorganisms

Tracing the evolutionary routes of plant–microbiota interactions – Carmen Escudero-Martinez – Current Opinion in Microbiology

Water microbiome

Diet shapes cold‐water corals bacterial communities – Pierre E. Galand – Environmental Microbiology

Built Environment

Home chemical and microbial transitions across urbanization – Laura-Isobel McCall – Nature Microbiology

Techniques

Learning representations of microbe–metabolite interactions – James T. Morton – Nature Methods

MGnify: the microbiome analysis resource in 2020 – Alex L. Mitchell – Nucleic Acids Research

PIME: A package for discovery of novel differences among microbial communities – Luiz Fernando W. Roesch – Molecular Ecology Resources

MDiNE: A model to estimate differential co-occurrence networks in microbiome studies – Kevin McGregor – Bioinformatics

Probiotics

Fermentation of plant-based milk alternatives for improved flavour and nutritional value – Muzi Tangyu – Applied Microbiology and Biotechnology

Modulations of Probiotics on Gut Microbiota in a 5‐Fluorouracil‐Induced Mouse Model of Mucositis – Chun Yan Yeung – Journal of Gastroenterology and Hepatology

The effect of an additive containing three Lactobacillus species on the fermentation pattern and microbiological status of silage – Maja Fijałkowska – Journal of the Science of Food and Agriculture

Microbes in the news

Gut Microbiome Puts the Brakes on Iron Absorption – Michigan Medicine

The Link Between Sleep and Your Gut Microbiome – Health central

Microbiome in China: Cosmetic trend will ‘heat up’ by the end of 2020, says expert – Cosmetics Design-Asia

Enterome Enters Research Collaboration With Major Cancer Center Focused on New Microbiome-derived Immunotherapies – Yahoo Finance

Non Microbiology Picks

Is running associated with a lower risk of all-cause, cardiovascular and cancer mortality, and is the more the better? A systematic review and meta-analysis – Zeljko Pedisic – British Journal of Sports Medicine