March 27, 2020

We begin with a few updates about the recent research news about COVID 19 and how as a scientist you might be able to help. As a result of the global lock down, many conferences and seminars have moved online. You will find some of the microbiome-related online events in today’s post. Please also have a look at a special issue of the Philosophical Transactions of the Royal Society for conceptual challenges in microbial community ecology.

COVID-19
Coronavirus vaccines: five key questions as trials begin – Nature News


How blood from coronavirus survivors might save lives – Nature News

COVID-19 Pandemic: Scientist volunteer form

An initiative to redirect scientific resources towards the fight against COVID-19

Virtual Events
Virtual Conference: 6th Annual Translational Microbiome Conference

Guts & Bugs: A virtual GI seminar series by Edelblum Lab

Let’s go viral: online microbiology seminars in partnership with International Society of Microbial Ecology
Schedule can be found via Twitter #MicroSeminar @MicroSeminar

General microbiome
SPECIAL ISSUE: Phillosophical Transactions of the Royal Society B : Conceptual challenges in microbial community ecology

Human respiratory microbiome
Review: Respiratory microbiome and epithelial interactions shape immunity in the lungs – Invernizzi et al. – Immunology

Human oral microbiome
Polymicrobial periodontal disease triggers a wide radius of effect and unique virome – Gao et al. – npj Biofilms and Microbiomes

Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers – Sato et al. – npj Biofilms and Microbiomes

Spatial Ecology of the Human Tongue Dorsum Microbiome – Wilbert et al. – Cell Reports

Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile – Chatzigiannidou et al. – npj Biofilms and Microbiomes

Dysbiotic oral microbiota and infected salivary glands in Sjögren’s syndrome – Alam et al. – PLOS ONE

Animal experiments
Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth – Consuegra et al. – PLOS Biology

Bacterially produced metabolites protect C. elegans neurons from degeneration – Urrutia et al. – PLOS Biology

Dynamic interactions within the host-associated microbiota cause tumor formation in the basal metazoan Hydra – Rathje et al. – PLOS Pathogens

Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice – Jangid et al. – PLOS ONE

Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production – Osbelt et al. – PLOS Pathogens

Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme – Langner et al. – PLOS ONE

Animal microbiome
Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity – Edenborough et al. – PLOS ONE

Plant, root, and soil microbiome
Towards Nutrition-Sensitive Agriculture: An evaluation of biocontrol effects, nutritional value, and ecological impact of bacterial inoculants – Passera et al. – Science of The Total Environment

Book Chapter: Rhizobacteria Versus Chelating Agents: Tool for Phytoremediation – Kaur et al. – Microbial Technology for Health and Environment

Book Chapter: Applications of Microorganisms in Agriculture – Doley et al. – Microbial Technology for Health and Environment

Plant Invasion Has Limited Impact on Soil Microbial alpha Diversity: A Meta-Analysis – Custer & van Diepen – Diversity

Water microbiome
Carbonate facies‐specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT – Ingalls et al. – Geobiology

The microbiome of modern microbialites in Bacalar Lagoon, Mexico – Yanez-Montalvo et al. – PLOS ONE

Food microbiology
Variations in Fungal Community and Diversity in Doushen With Different Flavors – Luo et at. – Frontiers in Microbiology

Bioinformatics
MetaBridge: An Integrative Multi‐Omics Tool for Metabolite‐Enzyme Mapping – Blimkie et al. – Current Protocols in Bioinformatics

Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA – McClenaghan et al. – PLOS ONE

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph – Gautreau et al. – PLOS Computational Biology

The Community Simulator: A Python package for microbial ecology – Marsland et al. – PLOS ONE

Techniques
Genome-based species-specific primers for rapid identification of six species of Lactobacillus acidophilusgroup using multiplex PCR – You & Kim – PLOS ONE

Pathogens and microbiome
Commensal Neisseria cinerea impairs Neisseria meningitidis microcolony development and reduces pathogen colonisation of epithelial cells – Custodio et al. – PLOS Pathogens

Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation – Wiles et al. – PLOS Biology

March 24, 2020

Today’s Digest features a study to use engineered Acinetobacter to boost host immunity against bacterial pneumonia, and a review on the relationship between plant-microbe symbiosis and agriculture.The coronavirus is probably on the mind of all of us. Listen to Dr. Blaser talk about it. Stay well and keep reading.

Job

Research Tech II – CHOP Microbiome Center

COVID-19

Editorial: Coronavirus: three things all governments and their science advisers must do now – Nature

World View: Don’t rush to deploy COVID-19 vaccines and drugs without sufficient safety guarantees – Shibo Jiang – Nature

Q&A: The novel coronavirus outbreak causing COVID-19 – Dale Fisher & David Heymann – BMC Medicine

** Dr. Martin Blaser answers coronavirus questions from Twitter (full video available) – mlive.com

General microbiology

Regulation of fungal decomposition at single-cell level – Michiel Op De Beeck et al. – The ISME Journal

Antimicrobial resistance

** Broad-spectrum suppression of bacterial pneumonia by aminoglycoside-propagated Acinetobacter baumannii – M. Indriati Hood-Pishchany et al. – PLoS Pathogens

Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions – Kelly Gravuer et al. – PNAS

Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities – Maria-Elisabeth Böhm et al. – Microbiome

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection – Lingdi Zhang et al. – Microbiome

Human gut microbiome

The role of gut microbiota in bone homeostasis – Jyotirmaya Behera et al. – Bone

Animal experiments

Docosahexaenoate-enriched fish oil and medium chain triglycerides shape the feline plasma lipidome and synergistically decrease circulating gut microbiome-derived putrefactive postbiotics – Matthew I. Jackson & Dennis E. Jewell – PLoS One

Animal microbiome

The rodent vaginal microbiome across the estrous cycle and the effect of genital nerve electrical stimulation – Micah Levy et al. – PLoS One

The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering – Hongfang Wang et al. – BMC Microbiology

Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision? – Tian-Zhong Jing et al. – Microbiome

Predictive ability of host genetics and rumen microbiome for subclinical ketosis – Grum Gebreyesus et al. – Journal of Dairy Science

Plant, root and soil microbiome

** Review: Agriculture and the Disruption of Plant–Microbial Symbiosis – Stephanie S. Porter & Joel L. Sachs – Trends in Ecology & Evolution

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil – Steven J. Blazewicz et al. – The ISME Journal

Reusing oil and gas produced water for agricultural irrigation: Effects on soil health and the soil microbiome – Hannah Miller et al. – Science of the Total Environment

Network analysis reveals the strengthening of microbial interaction in biological soil crust development in the Mu Us Sandy Land, northwestern China – Hong Zhou et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Performance and functional microbial communities of denitrification process of a novel MFC-granular sludge coupling system – Qiujin Deng et al. – Bioresource Technology

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake – Yang Liu et al. – Scientific Reports

Associations between redox-sensitive trace metals and microbial communities in a Proterozoic ocean analogue – Kathryn I. Rico et al. – Geobiology

Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater – Paul G McAteer et al. – Bioresource Technology

Bioinformatics

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search – Xiaoquan Su et al. – mSystems

Microbes in the news

How the mi­cro­biome is in­volved in the de­vel­op­ment of can­cer – Christian Urban – MedicalXpress

How a Fiber-Rich Plant-Based Diet Keeps Your Gut Microbiome Happy and Healthy – Chelsea Debret – One Green Planet

Gerhart: Keeping well during a pandemic – Timothy Gerhart – Your Valley

Study shows positive effect of cover crops on soil microbiome – AgriNews

Microbiome search engine can increase efficiency in disease detection and diagnosis – Chinese Academy of Sciences – EurekAlert

7 Ways A Gastroenterologist Supports His Microbiome & Overall Health – Marvin Singh – mbg Health

Infliximab Helps Gut Microbiome in Children with Crohn’s, Study Finds – Ana Pena – IBD News Today

Microbes on the market

DuPont, APC Microbiome Ireland link up for babies – Melody M. Bomgardner – C&EN

March 23, 2020

In today’s digest, review on biliary tract microbiome, effect of disinfection on water microbiome, resveratrol on adipose tissue browning via gut microbiome modelling and influence of livestock farm environment on human gut microbiota and antibiotic resistome.

Hope all readers are staying safe at home!

General microbiome

Intestinal microbiota and its association with colon cancer and red/processed meat consumption – Nadine Abu‐Ghazaleh – Journal of Gastroenterology and Hepatology

Is it time to consider gut microbiome readouts for precision diagnosis and treatment of alcoholic liver disease? – Gail A.M. Cresci – Hepatology

Biliary tract microbiota: a new kid on the block of liver diseases? – Nicoletti A – European Review for Medical and Pharmacological Sciences

Human microbiome

Characteristics of the urinary microbiome in kidney stone patients with hypertension – Fengping Liu – Journal of Translational Medicine

Pregnancy associates with alterations to the host and microbial proteome in vaginal mucosa – Christina Farr Zuend – American Journal of Reproductive Immunology

Prebiotics inhibit proteolysis by gut bacteria in a host diet-dependent manner: a three stage continuous in vitro gut model experiment – Xuedan Wang – Applied and Environmental Microbiology

Animal experiments

Resveratrol enhances brown adipose tissue activity and white adipose tissue browning in part by regulating bile acid metabolism via gut microbiota remodeling – Suocheng Hui – International Journal of Obesity

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms – Jian Sun – Nature Communications

Effects of the dietary fibre inulin and Trichuris suis products on inflammatory responses in lipopolysaccharide-stimulated macrophages – Laura J. Myhill – Molecular Immunology

Deoxycholic Acid-Induced Gut Dysbiosis Disrupts Bile Acid Enterohepatic Circulation and Promotes Intestinal Inflammation – Mengque Xu – Digestive Diseases and Sciences

Commensal Bacteria Impact a Protozoan’s Integration into Murine Gut Microbiota in a Dietary Nutrient-dependent Manner – Applied and Environmental Microbiology

Plant, root and soil microbiome

Rhizosphere fungal communities of wild and cultivated soybeans grown in three different soil suspensions – Chunling Chang – Applied Soil Ecology

Straw decreased N2O emissions from flooded paddy soils via altering denitrifying bacterial community compositions and soil organic carbon fractions – Ning Wang – FEMS Microbial Ecology

Water microbiome

Microbial communities from subglacial water of naled ice bodies in the forefield of Werenskioldbreen, Svalbard – Sławomir Sułowicz – Science of the Total Environment

Disinfection exhibits systematic impacts on the drinking water microbiome – Zihan Dai – Microbiome

Microbial diversity in deep subsurface hot brines of the North West Poland: from a community structure to isolate characteristics – Agnieszka Kalwasińska – Applied and Environmental Microbiology

Non microbiology picks

Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs – Sangeun Jeon – BioRxiv

Comparative Pathogenesis Of COVID-19, MERS And SARS In A Non-Human Primate Model – Barry Rockx – BioRxiv

March 20, 2020

Good morning! I hope this post finds you well. There are lots of new microbiome papers to share, including work on the disruption of E. coli biofilms, inconsistent diets used in Drosophila microbiome studies, and the effects of pollution on soil microbial communities.

General microbiome

Biosynthesis of silver nanoparticles by Fusarium scirpi and its potential as antimicrobial agent against uropathogenic Escherichia coli biofilms, Candelario Rodríguez-Serrano et al., PLOS ONE


Human gut microbiome

Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy, Aadra P. Bhatt et al., PNAS

Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans (preprint), Tomasz Wilmanski et al., bioRxiv

Propionic Acid Shapes the Multiple Sclerosis Disease Course by an Immunomodulatory Mechanism, Alexander Duscha et al., Cell

Adjusting for age improves identification of gut microbiome alterations in multiple diseases, Tarini S Ghosh et al., eLife

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms, Jian Sun et al., Nature Communications

Review – Altering Routine Intensive Care Unit Practices to Support Commensalism, Hamilton and Behal, Nutrition in Clinical Practice

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota, Ashley E. Kates et al., Frontiers in Cellular and Infection Microbiology

Meta-analysis – Assessing the efficacy and safety of fecal microbiota transplantation and probiotic VSL#3 for active ulcerative colitis: A systematic review and meta-analysis, Xiaofei Dang et al., PLOS ONE


Other human microbiome

Subgingival Host-Microbial Interactions in Hyperglycemic Individuals, P.S. Kumar et al., Journal of Dental Research

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers, Gabriele Andrea Lugli et al., FEMS Microbiology Ecology


Animal experiments

Effects of intestinal flora on the pharmacokinetics and pharmacodynamics of aspirin in high-altitude hypoxia, Sun and Zhang et al., PLOS ONE

Meta-analysis of diets used in Drosophila microbiome research and introduction of the Drosophila Dietary Composition Calculator (DDCC) (preprint), Broderick and Lesperance, bioRxiv

The Carnivorous Digestive System and Bamboo Diet of Giant Pandas May Shape Their Low Gut Bacterial Diversity, Wei Gui et al., Conservation Physiology


Animal microbiome

Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome, Coleman and Whitfield-Cargile et al., PLOS ONE

Dietary substitution of soybean oil with coconut oil in the absence of dietary antibiotics supports growth performance and immune function in nursery and grower pigs, Andrea G. Braundmeier-Fleming et al., Journal of Animal Science and Biotechnology

Isoflavone supplementation, via red clover hay, alters the rumen microbial community and promotes weight gain of steers grazing mixed grass pastures, Brittany E. Harlow et al., PLOS ONE

Domesticated equine species and their derived hybrids differ in their fecal microbiota, J.E. Edwards et al., Animal Microbiome

Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken, Khin K.Z. Mon et al., Scientific Reports


Plant, root, and soil microbiome

Acute effects of PAH contamination on microbial community of different forest soils, Enrica Picariello et al., Environmental Pollution

Context-dependent Dynamics Lead to the Assembly of Functionally Distinct Microbial Communities, Leonora S Bittleston et al., Nature Communications

Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: a tale of two oases, Eden Zhang et al., Microbiome

Perspective – Toward Comprehensive Plant Microbiome Research, Kari Saikkonen et al., Frontiers in Ecology and Evolution


Water and extremophile microbiome

Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans, Samuel A. Vohsen et al., Microbiome


Food microbiology

Lactic Acid Bacteria Isolated From Korean Kimchi Activate the Vitamin D Receptor–autophagy Signaling Pathways, Rong Lu et al., Inflammatory Bowel Diseases

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome, Bryn C. Taylor et al., mSystems

Differential Microbial Composition of Monovarietal and Blended Extra Virgin Olive Oils Determines Oil Quality During Storage, Zullo and Ciafardini, Microorganisms


Phages and viruses

Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota, Germán Bonilla-Rosso et al., PNAS


Bioinformatics

FORENSIC: an Online Platform for Fecal Source Identification, Adélaïde Roguet et al., mSystems

Review – Accurate and complete genomes from metagenomes, Lin-Xing Chen et al., Genome Research

Powmic: An R Package for Power Assessment in Microbiome Case-Control Studies, Li Chen, Bioinformatics


Techniques

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs, Leyuan Li et al., Microbiome


Non-microbiology picks

Marketplace shrimp mislabeling in North Carolina, Morgan L. Korzik et al., PLOS ONE

March 16, 2020

To all the work-from-home researchers (like me!), today’s digest covers microbiome in memory recognition, enteric neuropathy and neurodevelopmental disorder in rodent models. Gut microbiome in cardiovascular disease, a dual mechanism antibiotic and shifts in human gut microbiome and metabolome following gastric bypass. An important preprint that Covid-19 could not induce reinfection in infected rhesus macaques and that Ibuprofen may aggravate Covid-19 infection.

General microbiome

Gut microbiota and cardiovascular disease: opportunities and challenges – Negin Kazemian – Microbiome

Human microbiome
Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response – Jose U. Scher – Nature Reviews Rheumatology

Long-term metal exposure changes gut microbiota of residents surrounding a mining and smelting area – Mengmeng Shao – Scientific Reports

Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery – Zehra Esra Ilhan – NPJ biofilms and microbiomes

Animal experiments

Habitat and seasonality shape the structure of tench (Tinca tinca L.) gut microbiome – Tomasz Dulski – Scientific Reports

Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome – Zhijian Huang – Microbiome

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis – Jun Miyoshi – BioRxiv

Gut microbiota manipulation during the prepubertal period shapes behavioral abnormalities in a mouse neurodevelopmental disorder model – Justin M. Saunders – Scientific Reports

Minocycline-induced microbiome alterations predict cafeteria diet-induced spatial recognition memory impairments in rats – Sarah-Jane Leigh – Translational Psychiatry

A purified membrane protein from Akkermansia muciniphila or the pasteurised bacterium blunts colitis associated tumourigenesis by modulation of CD8+ T cells in mice – Lijuan Wang – Gut

PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice – Jingli Li – Science of The Total Environment

High‐fat diet–induced alterations to gut microbiota and gut‐derived lipoteichoic acid contributes to the development of enteric neuropathy – Yvonne Nyavor – Neurogastroenterology and Motility

Plant, root and soil microbiome

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil – L. V. Alteio – mSystems

Impact of plants on the diversity and activity of methylotrophs in soil – Michael C. Macey – Microbiome

Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds – Samantha C. Waterworth – BioRxiv

Techniques

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures – Nathan D. Olson – Microbiome

Antibiotic resistance

A dual-mechanism antibiotic targets Gram-negative bacteria and avoids drug resistance – James K. Martin – BioRxiv

Non microbiology picks

Reinfection could not occur in SARS-CoV-2 infected rhesus macaques – Linlin Bao – BioRxiv

Anti-inflammatories may aggravate Covid-19, France advises – The Guardian

March 14, 2020

Events

NYSCC Microbiome Program Postponed – Happi

General microbiome

Weakest link dynamics predict apparent antibiotic interactions in a model cross-feeding community – EM Adamowicz – bioRxiv

Simultaneous copper removal and electricity production and microbial community in microbial fuel cells with different cathode catalysts – Y Wu – Bioresource Technology

Multi-site human microbiome

Disrupted tongue microbiota and detection of nonindigenous bacteria on the day of allogeneic hematopoietic stem cell transplantation – S Oku – PLoS Pathogens

Human vaginal microbiome

Changes in key vaginal bacteria among postpartum African women initiating intramuscular depot-medroxyprogesterone acetate – BM Whitney – PLoS One

Human gut microbiome

Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach – S Pan – Microorganisms

A Story of Liver and Gut Microbes: How Does the Intestinal Flora Affect Liver Disease? A Review of the Literature – M Giuffrè – American Journal of Physiology

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – EW Yu – PLoS Medicine

Animal experiments 

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis – J Miyoshi – bioRxiv

Low mutational load and high mutation rate variation in gut commensal bacteria – RS Ramiro – PLoS Biology

Response to mechanical loading in rat Achilles tendon healing is influenced by the microbiome – F Dietrich-Zagonel – PLoS One

Plant, root, and soil microbiome

Testing the two-step model of plant root microbiome acquisition under multiple plant species and soil sources – HR Barajas – bioRxiv

A survey of invasive plants on grassland soil microbial communities and ecosystem services – JK Bell – Scientific Data

Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest – H Yao – FEMS Microbiology Ecology

Water and extremophile microbiome 

Metagenomic Insights into Microbial Metabolisms of a Sulfur-Influenced Glacial Ecosystem – CB Trivedi – bioRxiv

Diel, daily, and spatial variation of coral reef seawater microbial communities – L Weber – PLoS One

Food microbiology

Shotgun Metagenomic Analysis Reveals New Insights on Bacterial Community Profiles in Tempeh – A Yulandi – bioRxiv

Phages and viruses

Identification of viruses belonging to the family Partitiviridae from plant transcriptomes – Y Jo – bioRxiv

The Restrictome of Flaviviruses – L Berthoux – Virologica Sinica

Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus – E Fahsbender – PLoS One

Techniques

Intestinal Organoids: A Tool for Modelling Diet–Microbiome–Host Interactions – J Rubert – Trends in Endocrinology and Metabolism

Microbes in the news

Microbiome studies may require correction for PPI use – MD edge

As You Age, So Does Your Microbiome – Technology Networks

DuPont Nutrition & Biosciences and APC Microbiome Ireland on infant gut health project – Nutra Ingredients

The Role of Zinc: It’s More Important than You Think –  UMass Lowell

Microbiome Therapeutics Market to Make Great Impact in near Future by 2026 – Nyse News Times

Mapping Bacterial Neighborhoods in Gut – Mirage News

Non-microbe picks

Sorry, we’re open: Golden Open Access and inequality in the natural sciences – RJ Gray – bioRxiv

Quantifying and contextualizing the impact of bioRxiv preprints through automated social media audience segmentation – J Carlson – bioRxiv

Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature – CFD Carneiro – bioRxiv

Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics – P Smyth – bioRxiv

March 10, 2020

Today’s digest features a study on the fecal microbiota transplantation and obesity, a comprehensive overview of the diversity and abundance of antibiotic resistance genes in migratory birds, and more. Happy reading!

Gut microbiome

*Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – Elaine W. Yu – PlosMedicine

Diet influences the functions of the human intestinal microbiome – Maria De Angelis — Scientific Reports

Bacillus coagulans SANK 70258 suppresses Enterobacteriaceae in the microbiota of ulcerative colitis in vitro and enhances butyrogenesis in healthy microbiota – Kengo Sasaki – Applied Microbiology and Biotechnology

Mini review: Gut epithelial metabolism as a key driver of intestinal dysbiosis associated with noncommunicable diseases – Catherine D. Shelton and Mariana X. Byndloss – Infection and Immunity

Etiologic features of diarrheagenic microbes in stool specimens from patients with acute diarrhea in Thailand – Kazuhisa Okad – Scientific reports

Raman‐activated sorting of antibiotic‐resistant bacteria in human gut microbiota – Yi Wang – Environmental Microbiology

Animal microbiome

*Metagenomic analysis reveals the microbiome and resistome in migratory birds – Jian Cao – Microbiome

Lack of evidence for microbiota in the placental and fetal tissues of rhesus macaques – Kevin R. Theis – bioRxiv

Animal experiment

Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms – David VanInsberghe – Nature Microbiology

Plant/root/soil microbiome

Long-Term Phytoremediation of Coastal Saline Soil Reveals Plant Species-Specific Patterns of Microbial Community Recruitment – Xiaogai Wang – mSystems

Impact of Soil Microbial Amendments on Tomato Rhizosphere Microbiome and Plant Growth in Field Soil – Andrea Nuzzo – Microbial Ecology

Bioinformatics

DeepMAsED: Evaluating the quality of metagenomic assemblies– Olga Mineeva – Bioinformatics

A method for achieving complete microbial genomes and better quality bins from metagenomics data – Lauren M. Lui – bioRxiv

Estimating relative biomasses of organisms in microbiota using “phylopeptidomics” – Olivier Pible – Microbiome