August 10th, 2020

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God morgon!

Good morning from Sweden. Today’s digest is a light one but carries a preprint with some very important findings. The study has suggested that the nCoV can potentially hijack the immune system completely by infecting the lymphocytes. This might lead to impaired antibody and T-cell response, something that could have a serious implication on the success of the much-awaited vaccine. (Unfortunately, for some unknown reasons, the PDF of the preprint is inaccessible to me! Let me know down in the comments if you are able to download it.)

A new paper in BMC microbiome shows a correlation between the indoor dust microbiota and the microbiota of infant airways. A classic example of how our environment impacts our health.  There is another interesting preprint where the authors show that a fungus alters its virulence when it is challenged by predatory amoebae. Perhaps the amoeba challenge selects for the warrior mutants which then carry on their warring ways!

Elsewhere in the digest is a preprint where Plasmodium knowlesi was used as a model to successfully determine new vaccine targets against more dangerous Plasmodium vivax, a paper detailing the effect of polar light cycles on the Antarctic lake microbiome, and identification of haloarchael species in Korean gut microbiota.

COVID-19

Preprint: Infection of human lymphomononuclear cells by SARS-CoV-2 – Marjorie C Pontelli, et al.

General Microbiology

Preprint: Amoeba predation of Cryptococcus neoformans results in pleiotropic changes to traits associated with virulence – Man Shun Fu, et al.

Preprint: Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates – Duncan N Ndegwa, et al.

General microbiome

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community – Pratibha Panwar, et al. – Microbiome

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota – Shashank Gupta, et al. – Microbiome

Archaea/Gut microbiota

The human gut archaeome: identification of diverse haloarchaea in Korean subjects – Joon Yong Kim, et al. – Microbiome

Techniques

Preprint: Successful introduction of the Colour Test into inexperienced settings – Kadri Klaos

Zoom Seminar

How a healthy gut microbe affects your whole body? – Karen Ranzi, Holistic Health Coach, Award-Winning Author, Motivational Speaker, Natural Foods Chef, Speech and Feeding Therapist (phew!)

August 9, 2020

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Good morning and a wonderful Sunday!
While you are eating your Sunday eggs and sipping your coffee, enjoy the small collection of microbiome et al. papers- exactly the right size for a Sunday morning.
Visit the microbial community living at Antarctic volcanoes with the preprint from Benda et al. or read the findings by Gibb et al. that indicate that human-managed ecosystems favor the presence of reservoirs of zoonotic diseases- very interesting in the light of the current pandemic. Enjoy!

Human gut microbiome

Essential oils and microbiota: Implications for diet and weight control – Nurhan Unusan – Trends in Food Science & Technology

Animal microbiome

The Gut Microbiota of Pheasant Lineages Reflects Their Host Genetic Variation – Jinmei Ding et al – Frontiers in Genetics

Water and extremophile microbiome

*Preprint: Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica – Amanda G Benda – BioRxiv

Review: New Microbial Biodiversity in Marine Sediments – Brett J Baker et al. – Annual Review of Marine Science

Bioinformatics

Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities – Lukas Beule et al – PeerJ

Techniques

Ten simple rules for reading a scientific paper – Maureen A. Carey et al – PLOS Computational Biology

Judith’s non-microbiology picks

*Zoonotic host diversity increases in human-dominated ecosystems – Rory Gibb et al – Nature

August 8, 2020

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Have a nice weekend, everyone! Today, in this Digest we have articles about the use of microbiome as markers of successful FMT for graft-versus-host disease treatment, as well as a set of papers about probiotics and different aspects of health, including an RCT in hypertensive women. In addition, other papers showing associations between microbiota and exposure to androgens in neonates, and a paper about the influence of the microablative fractional radiofrequency technique on microbiota of treated postmenopausal women.

Microbiome Research

Bacteroides fragilis is a potential marker of effective microbiota transplantation in acute graft-versus-host disease treatment – Oleg V. Goloshchapov – Cellular Therapy and Transplantation

Impact of microablative fractional radiofrequency on the vaginal health, microbiota, and cellularity of postmenopausal women – Ayane Cristine Sarmento – Clinics (Sao Paulo)

Gut Microbiota and Liver Interaction through Immune System Cross-Talk: A Comprehensive Review at the Time of the SARS-CoV-2 Pandemic – Emidio Scarpellini – Journal of Clinical Medicine

Neonatal exposure to androgens dynamically alters gut microbiota architecture – Alexia Barroso – Journal of Endocrinology

Environmental Microbiome

Physicochemical Parameters Affecting the Distribution and Diversity of the Water Column Microbial Community in the High-Altitude Andean Lake System of La Brava and La Punta – Reynaldo Núñez Salazar – Microorganisms

Preprint: Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica – Amanda G Bendia – BioRxiv

Animal Models

Metagenomic insights into the effects of nanobubble water on the composition of gut microbiota in mice – Zitao Guo – Food and Function

Beneficial Microbes, Compounds, and Interventions

Effects of probiotic therapy on cardio-metabolic parameters and autonomic modulation in hypertensive women: a randomized, triple-blind, placebo-controlled trial – Larissa de Fátima Romão da Silva – Foods

Dietary Components, Microbial Metabolites and Human Health: Reading between the Lines – Yao Guo – Foods

Microbiota on Biotics: Probiotics, Prebiotics, and Synbiotics to Optimize Growth and Metabolism – Price T. Edwards – Gastrointestinal And Liver Physiology

The Effectiveness of Multi-Session FMT Treatment in Active Ulcerative Colitis Patients: A Pilot Study – Dorota Mańkowska-Wierzbicka – Biomedicines

Neurological and cognitive significance of probiotics: a holy grail deciding individual personality – Muhammad Afzal – Future Medicine

Bioinformatics and Genomics

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community – Maria A. Sierra  – Genes

Preprint: Genome-based targeted sequencing as a reproducible microbial community profiling assay – Jacquelynn Benjamino – BioRxiv

August 6, 2020

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Good morning from Minnesota! A broad selection of papers to share with you today: Immune responses in lung transplant patients, an examination of how hurricanes can alter the soil microbiome, and a cool preprint on host–microbe interactions in stickleback, plus 10 more—

Human respiratory microbiome

(Preprint) Nasal commensal, Staphylococcus epidermidis shapes the mucosal environment to prevent influenza virus invasion through Serpine1 induction, Ara Jo et al., bioRxiv

Cystic Fibrosis Lung Transplant Recipients Have Suppressed Airway Interferon Responses during Pseudomonas Infection, Daniel T. Dugger et al., Cell Reports Medicine

Human gut microbiome

The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients, Qianqian Zeng et al., Scientific Reports

Home, Sweet Home: How Mucus Accommodates our Microbiota, Benjamin X Wang et al., The FEBS Journal

Animal experiments

Preprint: Immune gene expression covaries with gut microbiome composition in stickleback, Lauren E Fuess et al., bioRxiv

Transient neonatal antibiotic exposure increases susceptibility to late-onset sepsis driven by microbiota-dependent suppression of type 3 innate lymphoid cells, Xinying Niu et al., Scientific Reports

Animal microbiome

Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire, Robert Pieper et al., The ISME Journal

Plant, root, and soil microbiome

Major changes in grapevine wood microbiota are associated with the onset of esca, a devastating trunk disease, Emilie Bruez et al., Environmental Microbiology

Increase in abundance and decrease in richness of soil microbes following Hurricane Otto in three primary forest types in the Northern Zone of Costa Rica, William D. Eaton et al., PLOS ONE

Water and extremophile microbiome

Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data, Alise J Ponsero et al., Nucleic Acids Research

Microbial communities can predict the ecological condition of headwater streams, Robert H. Hilderbrand et al., PLOS ONE

Bioinformatics

(Preprint) Snipe: Highly sensitive pathogen detection from metagenomic sequencing data, Lihong Huang et al., bioRxiv

Techniques

Impact of time and temperature on gut microbiota and SCFA composition in stool samples, Janet L. Cunningham et al., PLOS ONE

August 5, 2020

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Today’s Microbiome Digest showcases a study of a microbiota derived metabolite that promotes HDAC3 in the gut indicating an epigenetic senror of the microbiota, as well as several interesting papers from Cell Host & Microbe, Nature Microbiology and mSystems.

Covid-19

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic – Boni et al. Nature Microbiology

Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients – Wang et al. Cell Host & Microbe

General microbiome

The human gut archaeome: identification of diverse haloarchaea in Korean subjects – Kim et al. BMC Microbiome. 

Microbiota-derived metabolite promotes HDAC3 activity in the gut – Wu et al. Nature

Antibiotics

Distinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosis – Bellerose et al. mSystems

Novel Antimicrobials from Uncultured Bacteria Acting against Mycobacterium tuberculosis – Quigley et al. mBio

 

Water and extremophile microbiome

Microbial Metabolic Redundancy Is a Key Mechanism in a Sulfur-Rich Glacial Ecosystem – Trivedi et al. mSystems

Bioinformatics

Precise Species Identification for Enterobacter: a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. Nov. – Wu et a. mSystems

Phages and viruses

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome – Wolf et al. Nature Microbiology

August 4, 2020

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Greetings Everyone. Today’s Microbiome Digest comprises of a wide variety of topics covering soil microbiota, tumor to water to extremophile microbiome. The digest has some reviews, books, as well as interesting articles on how synthetic microbial communities facilitate sustainable growth and the role of microbial communities in balancing the environment. A terrific news article covering the isolation of microbes buried beneath the sea floor for more than 100 million years. Today’s digest can be summarized by a quote by Julie Morley.

“Every being devotes and dedicates itself to some innate purpose. Single cells, microbes, plants, insects, animals – every being makes it own unique contribution” – Julie J. Morley

General microbiome

*Shifts in the microbiota associated with male mosquitoes (Aedes aegypti) exposed to an obligate gut fungal symbiont (Zancudomyces culisetae) – Jonas Frankel-Bricker – Scientific Reports

Microbiome-derived metabolites reproduce the mitochondrial dysfunction and decreased insulin sensitivity observed in type 2 diabetes – Ormsby et al – bioRxiv

*Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth – Zuñiga et al – Nature Communications

Multi-site human microbiome

Microbiome harbored within tumors: a new chance to revisit our understanding of cancer pathogenesis and treatment – Zhao et al – Signal Transduction and Targeted Therapy

Human skin microbiome
Paradigms and Perspectives: The skin microbiome as a clinical biomarker in atopic eczema: Promises, navigation, and pitfalls – Reiger et al – The journal of Allergy and Clinical Immunology

Human gut microbiome
Review: Gut microbiota and atherosclerosis: role of B cell for atherosclerosis focusing on the gut-immune-B2 cell axis – Chen et al – Journal of Molecular Medicine

Gut microbiome a promising target for management of respiratory diseases – Trivedi et al – Biochemical Journal

*A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota – Aakko et al – Scientific Reports

Effects of antibiotic treatment on gut microbiota and how to overcome its negative impacts on human health – Ribeiro et al – ACS Infect. Dis

Animal experiments
Dynamics of uterine microbiota in postpartum dairy cows with clinical or subclinical endometritis – Pascottini et al – Scientific Reports

Plant, root, and soil microbiome
Book chapter: The Extended Microbiota: How Microbes Shape Plant-Insect Interactions – Mayoral-Peña et al – Evolutionary Ecology of Plant-Herbivore Interaction

Response of Soil Microbial Community to C:N:P Stoichiometry along a Caragana korshinskii Restoration Gradient on the Loess Plateau, China – Zhang et al – forests

Review: The endosphere microbial communities, a great promise in agriculture – Adeleke et al – International Microbiology

Water and extremophile microbiome
Influence of microorganisms on initial soil formation along a glacier forefield on King George Island, maritime Antarctica – Krauze et al – Biogeosciences

Review: Microbial communities of soda lakes and pans in the Carpathian Basin: a review – Tamás Felföldi – Biologia Futura

Fungal Community in Antarctic Soil Along the Retreating Collins Glacier (Fildes Peninsula, King George Island) – dos Santos et al – microorganims

Culture Independent Diversity of Bacterial Communities Indigenous to Lower Altitude at Laohugou Glacial Environment – Ali et al – Geomicrobiology Journal

Review: Methanosarcina acetivorans: A Model for Mechanistic Understanding of Aceticlastic and Reverse Methanogenesis – James G. Ferry – Front.Microbiol

The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation – Chung et al – Front.Microbiol

Food microbiology
FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation – Vaccalluzzo et al – Food Microbiology


Bioinformatics
Book: A Bioinformatics Primer for the Analysis of Illumina MiSeq Data of Litter-Associated Fungi and Bacteria – Seena et al – Methods to Study Litter Decomposition

Techniques
Review: Method development for cross-study microbiome data mining: challenges and opportunities – Su et al – Computational and Structural Biotechnology Journal

Microbes in the news
*Scientists pull living microbes, possibly 100 million years old, from beneath the sea – Elizabeth Pennnisi – Science

August 3, 2020

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Greetings from Colorado.
Today the Microbiome Digest brings you a variety of the latest microbiome related publications including brain, gut, fecal and oral microbiome, plant-microbial interactions and soil biodiversity. Enjoy!.

Covid-19

Rapid Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by Tungsten Trioxide-Based (WO3) Photocatalysis – Ghezzi et al. – bioRxiv

Human Microbiome: brain, gut, fecal and oral

This is the brain on probiotics – Annalisa M. VanHook – Science

Assessment of inter-laboratory variation in the characterization and analysis of the mucosal microbiota in Crohn’s disease and ulcerative colitis – Szamosi et al. -Frontiers in Microbiology

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Huus et al. – Microbiome

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity – Utter et al. – bioRxiv

Plant, root and soil microbiome

Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogen – Liu et al. – bioRxiv

A Bacterial Effector Protein Hijacks Plant Metabolism to Support Pathogen Nutrition – Xian et al. – Cell Host & Microbe

Development and application of low-cost and eco-sustainable bio- stimulant containing a new plant growth-promoting strain Kosakonia pseudosacchari TL13 – Romano et al. – Frontiers in Microbiology

Environmental microbiology

Blind spots in global soil biodiversity and ecosystem function research – Guerra et al. – Nature Communications

Microbiome Diversity and Community-Level Change Points within Manure-based small Biogas Plants – Theuerl et al. – Microorganisms

August 1, 2020

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Pregnancy and early life
Maternal diet during pregnancy and intestinal markers are associated with early gut microbiota – Selma-Royo et al. – European Journal of Nutrition

Human vaginal microbiome
Changes in the vaginal microbiota across a gradient of urbanization – Vargas-Robles et al. – Scientific Reports

Human gut microbiome
Usefulness of Machine Learning-Based GutMicrobiome Analysis for Identifying Patients with Irritable Bowels Syndrome – Fukui et al. – Journal of Clinical Medicine

Preprint – A pilot study of the effect of deployment on the gut microbiome and traveler’s diarrhea susceptibility – Stamps et al.

Gastric Microbiota in a Low–Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions – Ndegwa et al. – Clinical and Translational Gastroenterology

Sexual dimorphism of gut microbiota at different pubertal status – Yuan et al. – Microbial Cell Factories

Animal experiments
Preprint – Intestinal inflammation and altered gut microbiota associated with inflammatory bowel disease renders mice susceptible to Clostridioides difficile colonization and infection – Close et al.

Different effects of constitutive and induced microbiota modulation on microglia in a mouse model of Alzheimer’s disease – Mezo et al. – Acta Neuropathologica Communications

Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome – Biagi et al. – Microorganisms


Animal microbiome
Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast – Vendl et al. – Scientific Reports

Modeling host-microbiome interactions for the prediction of meat quality and carcass composition traits in swine – Khanal et al. – Genetics Selection Evolution


Plant, root, and soil microbiome
Water management and phenology influence the root-associated rice field microbiota – Chialva et al. – FEMS Microbiology Ecology

Water and extremophile microbiome
Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years – Morono et al. – Nature Communications

July 31, 2020

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Today’s digest features studies on hospital-associated bacterial communities on window components, the effect of urbanization on the vaginal microbiota of Amerindians, nitrate as a potential prebiotic for oral health, and the latest news in bioinformatics. Happy reading!

General microbiome

Microbial species interactions determine community diversity in fluctuating environments – Shota Shibasaki – bioRxiv

Review: The host-associated archaeome – Guillaume Borrel – Nature Reviews Microbiology

Oral microbiome

*Nitrate as a potential prebiotic for the oral microbiome – Bob T. Rosier – Scientific Reports

Skin microbiome

Deep skin dysbiosis in vitiligo patients: link with mitochondrial and immune changes – Hanene Bzioueche – medRxiv

Gut microbiome

Review: The microbiome: An emerging key player in aging and longevity– Minhoo Kim and Bérénice A. Benayoun – Translational Medicine of Aging

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Kelsey E. Huus – Microbiome

Vaginal microbiome

*Changes in the vaginal microbiota across a gradient of urbanization – Daniela Vargas-Robles – Scientific Reports

Comparison between a novel molecular tool and conventional methods for diagnostic classification of bacterial vaginosis: is integration of the two approaches necessary for a better evaluation? – Margherita Scapaticci – New Microbiologica

Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence – Norhan Alhajjar – bioRxiv

Association between Vaginal Bacterial Microbiota and Vaginal Yeast Colonization – McKenna C Eastment – The Journal of Infectious Diseases

Urinary microbiome

Review: The microbiome in urological diseases – Kwang Woo Lee – Investigive and Clinical Urology

Review: FimH and Anti-Adhesive Therapeutics: A Disarming Strategy Against Uropathogens – Meysam Sarshar – Antibiotics

Characterization of urinary microbiome in patients with bladder cancer: Results from a single-institution, feasibility study – Juan Chipollini – Urologic Oncology: Seminars and Original Investigations

Animal microbiome

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage – Jolinda Pollock – Scientific Reports

Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers – Juan J. Quereda – Frontiers in Veterinary Science

Animal experiment

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Eliran Kadosh – Nature

An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut – Gustavo Caballero-Flores – Cell Host & Microbe

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin – Damien J. Cabral – mSystems

Water and extremophile microbiome

Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer – Jessica Hinojosa – Water Research

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities – Tyler J. Arbour – Frontiers in Microbiology

Food microbiome

Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring – Luca Belleggia – Food Microbiology

Built environment

*Viable bacterial communities on hospital window components in patient rooms – Patrick F. Horve – PeerJ

Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation – Ganesh Babu Malli Mohan – mSystems

Phages and viruses

Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone – Anastasia Tsiola – Viruses

Bioinformatics

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets – Yi Yue – BMC Bioinformatics

Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach – Christian Milani – mSystems

Automated prediction and annotation of small proteins in microbial genomes– Matthew G Durrant and Ami S Bhatt – bioRxiv

Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data – Abigail L. Lind – bioRxiv

MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline – Carlos A. Ruiz-Perez – bioRxiv

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra – Caroline Weis – Bioinformatics

NetCoMi: Network Construction and Comparison for Microbiome Data in R – Stefanie Peschel – bioRxiv

Review: Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses – Ana Elena Pérez-Cobas – Microbial Genomics

Podcast

Machine learning for drug development with Marinka Zitnik – Jacob Schreiber – The Bioinformatics Chat

July 30, 2020

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Hello from Lübeck! This week started slowly but our todays post covers quite a range of topics with a couple of reviews about our understanding of the gut microbiome related to digestive diseases. Of particular note is a publication by Kadosh et al. (Nature 2020) linking the gut microbiome and p53 in mice. This highlights the role of the microenvironment on cancer in general.

● Human vaginal microbiome

Changes in the vaginal microbiota following antibiotic treatment for Mycoplasma genitalium, Chlamydia trachomatis and bacterial vaginosis – Ahrens et al. – Plos One

● Human gut microbiome

[REVIEW] Gut Microbiome Modulates Response to Cancer Immunotherapy – Khan et al. – Digestive Diseases and Sciences

[REVIEW] Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration – Ruan et al. – Digestive Diseases and Sciences

[REVIEW] Microbiome and Its Role in Irritable Bowel Syndrome – Pimentel and Lembo – Digestive Diseases and Sciences

[REVIEW] Diet and Gut Microbes Act Coordinately to Enhance Programmed Cell Death and Reduce Colorectal Cancer Risk – Chapkin et al. – Digestive Diseases and Sciences

Diversity of Gut Microbiota and Bifidobacterial Community of Chinese Subjects of Different Ages and from Different Regions – Yang et al. – Microorganisms

[PREPRINT] Gut Microbiota Changes in Nonalcoholic Fatty Liver Disease and Concomitant Cardiovascular Diseases – Kurinna – bioarxiv

Lactobacillus plantarum-Mediated Regulation of Dietary Aluminum Induces Changes in the Human Gut Microbiota: an In Vitro Colonic Fermentation Study – Yu et al. – Probiotics and Antimicrobial Proteins

Troublesome friends within us: the role of gut microbiota on rheumatoid arthritis etiopathogenesis and its clinical and therapeutic relevance – Reyes-Castillo et al. – Clinical and Experimental Medicine

Duodenal Microbiota in Stunted Undernourished Children with Enteropathy – Chen et al. – The New Englang Journal of Medicine

Small molecules, big effects: microbial metabolites in intestinal immunity – Glotfelty, Wong and Levy – AJP Gastrointestinal and Liver Physiology

● Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Kadosh et al. – Nature

Impact of PepT1 deletion on microbiota composition and colitis requires multiple generations – Viennois et al. – npj Biofilms and Microbiomes

● Plant, root, and soil microbiome

[REVIEW] Recent advances in the role of plant metabolites in shaping the root microbiome – Jacoby et al. – F1000

● Food microbiology

Selection of cereal-sourced lactic acid bacteria as candidate starters for the baking industry – Milanovic et al. – Plos One

The sources and transmission routes of microbial populations throughout a meat processing facility – Zwirzitz et al. – npj Biofilms and Microbiomes

● Phages and viruses

[PREPRINT] Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis – Yan – bioarxiv

● Bioinformatics

[REVIEW] Tools for Analysis of the Microbiome – Galloway-Pena and Hanson – Digestive Diseases and Sciences

● Techniques

Microbial community dissimilarity for source tracking with application in forensic studies – Carter et al. – Plos One

● Microbes in the news

Pilot study examines facial microbiome diversity – Petrou – Dermatology Times

The 2020 Way To Treat Your Skin Is All About Bacteria, Bugs And Microbiomes – Driver – ELLE