October 11, 2019

Good morning everyone!

Today’s digest is full of great reviews paper, among else- from the gut microbiome to bacterial metabolic modelling. Also featured is a lovely paper regarding vaginal microbiome transplantation (with interesting translational meaning!) and a food-for-thought paper about microbiology past, present and furture (1st in the list down).

Have a great weekend and happy Jewish New year!

Food for Thought

Shift in the paradigm towards next-generation microbiology, Blaz Sterz & Luka Kronegger, FEMS Microbiology Letters

Human microbiome

** Re‐assessing microbiomes in the low‐biomass reproductive niche, Jessica L. O’Callaghan, BJOG

** Incorporating functional trade-offs into studies of the gut microbiota, Aspen T Reese, Curr. Opi. Microbiology

** Gut microbial metabolites in depression: understanding the biochemical mechanisms, Giorigia Caspani, microbial cell

** Vaginal microbiome transplantation in women with intractable bacterial vaginosis, Ahinoam Lev-Sagie, Nature Medicine

Gut microbiome diversity is associated with sleep physiology in humans, Robert P. Smith, PLOS One

Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties, P.I. Diaz, J. Dental Research

Animal microbiome

A wild microbiome improves mouse modeling of the human immune response, Sara E. Hamiltion, Lab Animal

Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability, Duy Le, Microbial Ecology

Environmental microbiome

** Implications of indoor microbial ecology and evolution on antibiotic resistance, Sarah Ben Maamar, J. Exp. science & Env. Epid.

A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability, O. Nicolitch, Scientific Reports

Preceding crop and tillage system affect winter survival of wheat and the fungal communities on young wheat roots and in soil, Hanna Friberg, FEMS Microbiology Letters

Viral microbiome

A review on viral metagenomics in extreme environments, Sonia Davila-Ramos, Frontiers in Microbiology

Methods in microbiology

Multi-faceted approaches to discovering and predicting microbial nutritional interactions, Sebastian Gude, Curr. Opi. Biotechnology

Artificial neural network-assisted Fourier transform infrared spectroscopy for differentiation of Salmonella serogroups and its application on epidemiological tracing of Salmonella Bovismorbificans outbreak isolates from fresh sprouts, Helene Obereuter, FEMS Microbioogy Letters

October 9, 2019

Today’s Digest includes plenty of human gut microbiome papers, and plant, soil, water microbiome papers. Today features a major expansion of human gut MAGs, evolution of human gut microbiome compared with apes, and how soil microbiome affects climate change and vice versa. A potentially revolutionary technology promises to finally bring microbiome dark matters into daylight, and don’t forget to check out our own Elies Bik’s excellent work on exposing scientific fraud! Enjoy.

General microbiology

Tradeoffs in hyphal traits determine mycelium architecture in saprobic fungi – Anika Lehmann et al. – Scientific Reports

Review: Nature’s recyclers: anaerobic microbial communities drive crude biomass deconstruction – Stephen P Lillington et al. – Current Opinion in Biotechnology

Review: Microbial functional diversity: From concepts to applications – Arthur Escalas e t al. – Ecology and Evolution

Antimicrobial resistance

Preprint: Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study – Ronan M Doyle et al. – bioRxiv

Human gut microbiome

** Preprint: A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome – Alexandre Almeida et al. – bioRxiv

** Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny – Katherine R. Amato et al. – Genome Biology

Press: New research furthers understanding about what shapes human gut microbiome – EurekAlert!

Review: Sodium, Hypertension, and the Gut: Does the Gut Microbiota Go Salty? – Katarina Smiljanec & Shannon L. Lennon – American Journal of Physiology-Heart and Circulatory Physiology

Tea Compounds and the Gut Microbiome: Findings from Trials and Mechanistic Studies – Timothy Bond & Emma Derbyshire – Nutrients

Fecal microbiota and metabolites are distinct in a pilot study of pediatric Crohn’s disease patients with higher levels of perceived stress – Laura M. Mackner et al. – Psychoneuroendocrinology

Review: The Gut Microbiota in Celiac Disease and probiotics – Richa Chibbar & Levinus A. Dieleman – Nutrients

Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both? – Gregg J Silverman et al. – Current Opinion in Immunology

Review: The Multiple Sclerosis Gut Microbiota: A Systematic Review – Ali Mirza et al. – Multiple Sclerosis and Related Disorders

Animal experiments

Oolong tea polyphenols ameliorate circadian rhythm of intestinal microbiome and liver clock genes in mouse model – Tongtong Guo et al. – Journal of Agricultural and Food Chemistry

Review: Caenorhabditis elegans: a model to understand host–microbe interactions – Arun Kumar et al. – Cellular and Molecular Life Sciences

Animal microbiome

Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales – Candace L. Williams et al. – Drug Discovery Today: Disease Models

Plant, root and soil microbiome

Soil Microbial Communities Involved in Reductive Dissolution of Arsenic from Arsenate-laden Minerals with Different Carbon Sources – Shigeki Yamamura et al. – Environmental Science & Technology

Volatile‐mediated antagonism of soil bacterial communities against fungi – Xiaogang Li et al. – Environmental Microbiology

Interactions between soybean, Bradyrhizobium japonicum and Soybean mosaic virus: the effects depend on the interaction sequence – Sofía Andreola et al. – Functional Plant Biology

New insights into the responses of soil microorganisms to polycyclic aromatic hydrocarbon stress by combining enzyme activity and sequencing analysis with metabolomics – Xiaona Li et al. – Environmental Pollution

Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures – Prashant Singh et al. – Scientific Reports

** Review: Soil microbiomes and climate change – Janet K. Jansson & Kirsten S. Hofmockel – Nature Reviews Microbiology

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons – Abdur Rahim Khan et al. – PLoS One

Plant-plant competition influences temporal dynamism of soil microbial enzyme activity – E. J. Schofield et al. – Soil Biology and Biochemistry

Comparison of microphototrophic communities living in different soil environments in the High Arctic – Ekaterina Pushkareva et al. – Frontiers in Ecology and Evolution

Water and extremophile microbiome

Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps – Muhammad Farhan Ul Haque et al. – Microbiome

Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site – Edoardo Puglisi et al. – Scientific Reports

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons – Abdur Rahim Khan et al. – PLoS One

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland) – Magdalena Dyda et al. – Microorganisms

Evaluating the effect of biochar on mesophilic anaerobic digestion of waste activated sludge and microbial diversity – Bo Wu et al. – Bioresource Technology

Species-specific differences in the microbiomes and organic exudates of crustose coralline algae influence bacterioplankton communities – Zachary A. Quinlan et al. – Frontiers in Microbiology

A global comparison of the bacterial communities of bilge water, boat surfaces, and external port water – Laura G. Schaerer et al. – Applied and Environmental Microbiology

Microbes in space

Simulated manned Mars exploration: effects of dietary and diurnal cycle variations on the gut microbiome of crew members in a controlled ecological life support system – Hai-Sheng Dong et al. – PeerJ

Technology

** Targeted isolation and cultivation of uncultivated bacteria by reverse genomics – Karissa L. Cross et al. – Nature Biotechnology

Bioinformatics

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases – Ole K Tørresen et al. – Nucleic Acids Research

Microbes in the news

Bill Gates thinks understanding the body’s microbiome will help solve malnutrition – Katie Palmer – Quartz

Press for yesterday’s article: Unlocking CRISPR’s Potential To Alter the Microbiome – Technology Networks

Press for yesterday’s article: New Study Finds CRISPR May Be The Secret To Improving Gut Health – Gretchen Lidicker – Mind Body Green

Drug Metabolism and Microbiome – Maryam Azizi – News Medical

The Gut-Lupus Link: How Gut Bacteria May Impact Disease Development and Activity – Lupus Foundation of America

Microbes on the market

BASF and Biomillenia Join Forces in Microbiome Research to Promote Healthy Skin – Business Wire

Non-microbiology pick

** Our own Elies Bik is featured in this Dutch report on exposing scientific fraud, and see a Google translated version here.

CRISPR-Cas9 system that kills targeted pathogenic bacteria may be microbiome friendly.

By: Puck deRoos

Please join me in welcoming our new contributor Puck deRoos. She will be writing short articles about the latest microbiome papers. I am so excited to have you on the team! – Elisabeth Bik

New research has highlighted a potential system that can specifically target pathogenic bacteria without disturbing the rest of the microbial community1.  

Currently, the ways to treat pathogenic bacterial infections are non-specific and may have unintentional longer lasting effects because they often alter the composition of the gut microbiome. The rise of multi-drug resistant bacteria has shown the limitations of general broad-spectrum antibiotics2, while phage-based therapy has been associated with  a smaller but similar rise in phage resistant bacteria3,.  Stool transplants have shown promising results in treatment of particular intestinal conditions, but are not suitable for many other diseases. In addition, they completely alter the patients gut microbiome, which may have unknown long-term effects4

 

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Cas-9 (CRISPR ASsociated protein-9) system is able to target specific microbial species, and cause cell death due to double stranded breaks in the microbial DNA. In a recent paper published in Nature Communications, researchers have developed a method to specifically target microbial pathogens using a cis-conjugative CRISPR system where all the necessary machinery is encoded within one plasmid, or bacterial DNA sequence.

The cis-conjugative plasmid system has much higher rate of conjugation, which is how bacteria transfer genetic material between different cells, than its trans-conjugative counterpart, which has the CRISPR and conjugative sequences on different plasmids. One of the reasons the cis-conjugative system is more effective is that it is able to continue to work throughout multiple conjugations, so its effect increases exponentially throughout time. In contrast,  the trans system only works once. 

The rates of conjugation were measured from host bacteria Escherichia coli to bacterial recipient Salmonella enterica. The rate for the cis system continually increased and reached a maximum of 1 X 10-2 at 24hour, while the trans system maxed out early at ~1 X 10-3 but decreased to ~1 X 10-5 at 24hours. These results showed a ~1000-fold increase in the rates of the new cis-conjugative system compared to previous trans-conjugative system. 

Macintosh HD:Users:puck:Desktop:Screen Shot 2019-10-04 at 3.51.57 PM.png

 

This new tool for targeting specific bacteria can be extremely useful within the human microbiome. Most microbial communities in our body exists as a biofilm, a community of different microorganisms that stick together on a surface. The new cis-conjugative system developed by researchers at Schulich School of Medicine and Dentistry has up to a potential 100% effective rate of conjugation with bacteria grown in a biofilm. The same cis system in a regular bacterial assay or filter based assay shows a ~500 to 1000-fold decrease in the rate of conjugation, increasing the systems usefulness in regards to the microbiome. 

In conclusion, this new method of specifically delivering a CRISPR-Cas-9 system to pathogenic bacteria without disrupting the composition of the entire microbial community is an exciting new direction for the targeted  treatment of microbial infections. 

 

1. Hamilton TA et al. Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing. Nature Communications. 10, 4544 (2019). https://doi.org/10.1038/s41467-019-12448-3

2. Theuretzbacher, U. Antibiotic innovation for future public health needs. Clin. Microbiol. Infect. 23, 713–717 (2017). 

3. Chatain-Ly, M. H. The factors affecting effectiveness of treatment in phages therapy. Front. Microbiol. 5, 51 (2014). 

4. Khanna, S. et al. Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. Microbiome 5, 55 (2017). 

 

October 7, 2019

Good Morning! Highlights of today’s digest include investigation about early childhood microbiota assembly in mother-infant participants from the Tsimane indigenous population from Amazon and with findings suggesting that socioeconomic changes may be altering interactions of highly abundant members of the microbiota in the host. Results from a gut-brain axis rat model showed possibility of novel biomarkers development for stress response based on abundance of genes in microbiomes. Finally, another study is aiming to access biologically active small molecules with antibacterial activity derived from human microbiota by sequencing of metagenomes and the use of computational and synthetic biology methods.

Pregnancy and early life
Prenatal and postnatal contributions of the maternal microbiome on offspring programming – Jasarevic and Bale – Frontiers in Neuroendocrinology

Multi-site human microbiome
*Microbiota Assembly, Structure, and Dynamics Among Tsimane Horticulturalists of the Bolivian Amazon – Sprockett et al. – bioRxiv

Human vaginal microbiome
Oncogenic Virome Benefits from the Different Vaginal Microbiome-Immune Axes – Campisciano et al. – MDPI Microorganisms

Non-optimal vaginal microbiota after azithromycin treatment for Chlamydia trachomatis infection – Tamarelle et al. – The Journal of Infectious Diseases

Human nearly-sterile sites
Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India – Gandhi et al. – MDPI Microorganisms

Human gut microbiome
Review: Synthetic ecology of the human gut microbiota – Vrancken et al. – Nature Reviews Microbiology

Review: The interaction between gut microbiome and nutrients on development of human disease through epigenetic mechanisms – Ho-Sun Lee – Genomics & Informatics

Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity – Dejean et al. – Applied and Environmental Microbiology

Pre‐and post‐serial metagenomic analysis of gut microbiota as a prognostic factor in patients undergoing haematopoietic stem cell transplantation – Kusakabe et al. – British Journal of Haematology

Animal experiments
Experimental evidence for adaptation to species-specific gut microbiota in house mice – Moeller et al. – mSphere

Low‐calcium diet in mice leads to reduced gut colonization by Enterococcus faecium – Top et al. – MicrobiologyOpen

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Arroyo et al. – PLOS ONE

Transplanting Fecal Virus-Like Particles Reduces High-Fat Diet-Induced Small Intestinal Bacterial Overgrowth in Mice – Lin et al. – Frontiers in Cellular and Infection Microbiology

*Metabolome and microbiome profiling of a stress-sensitive rat model of gut-brain axis dysfunction – Bassett et al. – Nature Scientific Reports

Animal microbiome
The composition and stability of the faecal microbiota of Merino sheep – Al Mamun et al. – Journal of Applied Microbiology

Faecal microbiota and functional capacity associated with weaning weight in meat rabbits – Fang et al. – Microbial Biotechnology

Review: Feline Virome—A Review of Novel Enteric Viruses Detected in Cats – Martino et al. – MDPI Viruses

Phylogeography and ecological niche shape the cichlid fish gut microbiota in Central American and African lakes – Baldo et al. – Frontiers in Microbiology

Plant, root and soil microbiome
Biocontrol activities of rhizobacteria associated with apple, apricot and kiwi rhizosphere against bacterial canker caused by Clavibacter michiganensis – Gautam et al. – Indian Phytopathology

Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes – Zhang et al. – mSystems

Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes – Oh et al. – Journal of Microbiology

Microbial communities in bioswale soils and their relationships to soil properties, plant species, and plant physiology – Brodsky et al. – Frontiers in Microbiology

Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation – Lee et al. – bioRxiv

Water and extremophile microbiome
Bacterial Communities of Microbial Mats of the White Sea Supralittoral and of the Littoral of the Lakes Separated from the Sea – Burganskaya et al. – Microbiology

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom – Bhatnagar et al. – bioRxiv

Bioinformatics
*A metagenomic strategy for harnessing the chemical repertoire of the human microbiome – Sugimoto et al. – Science

Techniques
Protocol: Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics – Biswapriya B. Misra – Single Cell Metabolism

An Entropy-Based Graph Construction Method for Representing and Clustering Biological Data – Ariza-Jimenez et al. – Latin American Conference on Biomedical Engineering

Microbes in the news
Artificial gut aims to expose the elusive microbiome – Anne McGovern – MIT PHYS.ORG

September 30, 2019

Monday morning digest covers exciting updates in microbiome with – meta analysis on role of probiotics in human depression , stool banking guidelines for fecal microbiota transplant, expert view on translation of gut microbiome to clinics and a historical peek into use of ceramic baby milk bottles in prehistoric times. Enjoy reading!

General microbiome

Translating the gut microbiome: ready for the clinic? – Susan V. Lynch – Nature Reviews Gatroenterology and Hepatology

Uterine immunity and microbiota: A shifting paradigm – Chiara Agostinis – Frontiers in Immunology

Human microbiome

Cigarette smoking and oral microbiota in low-income and African-American populations – Yaohua Yang – Journal of Epidemiology and Community Health

International consensus conference on stool banking for faecal microbiota transplantation in clinical practice – Giovanni Cammarota – Gut

Animal experiments

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3 – Zheng Kuang – Science

Transfusional iron overload and intravenous iron infusions modify the mouse gut microbiota similarly to dietary iron – Francesca La Carpia – Biofilms and Microbiomes

Proteome modifications of gut microbiota in mice with activity-based anorexia and starvation: Role in ATP production – Jonathan Breton – Nutrition

Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut – Ulla Hynönen – Anaerobe

Intestinal inflammation increases convulsant activity and reduces antiepileptic drug efficacy in a mouse model of epilepsy – Carmen De Caro – Scientific Reports

The fecal resistome of dairy cattle is associated with diet during nursing – Jinxin Liu – Nature Communications

Neohesperidin Prevents Colorectal Tumorigenesis by Altering the Gut Microbiota – Yanling Gong – Pharmacological Research

Changes of serum lipopolysaccharide, inflammatory factors, and cecal microbiota in obese rats with type 2 diabetes induced by Roux-en-Y gastric bypass – Jiao Wu – Nutrition

Plant, root, soil microbiome

A bioinformatics guide to plant microbiome analysis – Rares Lucaciu – Frontiers in Plant Science

Beyond pathogens: microbiota interactions with the plant immune system – Paulo José PL Teixeira – Current Opinion in Microbiology

Water microbiome

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea‐land transition – Esther Molina-Menor – Microbial Biotechnology

Probiotics

Bacillus coagulans R11 maintained intestinal villus health and decreased intestinal injury in lead-exposed mice by regulating the intestinal microbiota and influenced the function of faecal microRNAs – Si-Cheng Xing – Environmental Pollution

Effect of probiotics on depressive symptoms: A meta-analysis of human studies – Kah Kheng Goh – Psychiatry Research

Non Microbiology Picks

Milk of ruminants in ceramic baby bottles from prehistoric child graves – J. Dunne – Nature

 

September 28, 2019

Dear microbiome digest readers, on this weekend we have covered interesting review articles focusing on factors that influence the temporal development of the infant microbiome, and  the role of gut microbiota in colorectal cancer, and research articles shows the role of microbiome in managing constipation, in Atopic Dermatitis, microbiome-host interaction in Respiratory Syncytial Virus Infection, Successful fecal microbiota transplantation for the treatment of recurrent Clostridium difficile infection, sputum microbiome in asthma and COPD and various research articles from Animal microbiome/Animal experiments section including fine-scale spatial structuring of the microbial composition and diversity along the length of murine colon. Enjoy reading.

General microbiome

Impact of a Plant Sterol- and Galactooligosaccharide-Enriched Beverage on Colonic Metabolism and Gut Microbiota Composition Using an In Vitro Dynamic Model – Virginia Blanco-Morales – Journal of Agricultural and Food Chemistry

Review: Temporal development of the infant gut microbiome – Rebecca E. Moore – Open Biology

Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform – Petra Videnska – Scientific Reports

The Honeybee Gut Microbiota Is Altered after Chronic Exposure to Different Families of Insecticides and Infection by Nosema ceranaeRégis Rouzé – Microbes and Environments

Human gut microbiome

Abundance of Probiotics and Butyrate‐Production Microbiome Manages Constipation Via Short‐Chain Fatty Acids Production and Hormones Secretion – Min Zhuang – Molecular Nutrition & Food Research

Review: Gut microbiota in colorectal cancer: mechanisms of action and clinical applications – Sunny H. Wong – Nature Reviews Gastroenterology & Hepatology

Changes in the gut microbiota during and after commercial helium-oxygen saturation diving in China – Yuan Y – Occupational and Environmental Medicine

Ninety-eight years old female successfully successfully treated with fecal microbiota transplantation after recurrent Clostridium difficile infection – Bermejo Boixareu C – Medicina Clínica

Human respiratory microbiome

Sputum microbiomic clustering in asthma and COPD reveals a Haemophilus‐predominant subgroup – Sarah Diver – Allergy

Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection – Abhijeet R. Sonawane – Scientific Reports

Human skin microbiome

Cheek Microbial Communities Vary in Young Children with Atopic Dermatitis in China – Song L. – Dermatology

Animal microbiome / Animal experiments

Dietary supplementation with the extract from Eucommia ulmoides leaves changed epithelial restitution and gut microbial community and composition of weanling piglets – Peng M – PLoS One

Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale – Sarah Goertz – PLoS One

Protective activities of polysaccharides from Cipangopaludina chinensis against high-fat-diet-induced atherosclerosis via regulating gut microbiota in ApoE-deficient mice – Qingping Xiong – Food & Function

2-O-beta-D-Glucopyranosyl-L-ascorbic acid, an Ascorbic Acid Derivative Isolated from the Fruits of Lycium Barbarum L., Modulates Gut Microbiota and Palliates Colitis in Dextran Sodium Sulfate-induced Colitis in Mice – Kaiyin Huang – Journal of Agricultural and Food Chemistry

Anti‐TNF‐α therapy alters the gut microbiota in proteoglycan‐induced ankylosing spondylitis in mice – Bin Liu – MicrobiologyOpen

A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome – Alessandra Riva – Nature Communication

Antibiotic exposure disturbs the gut microbiota and its metabolic phenotype differently in rats with advanced-stage type 1 diabetes and age-matched controls – Hong Zheng – Journal of Proteome Research

Gut Microbiota and Metabolome Response of Decaisnea insignis Seed Oil on Metabolism Disorder Induced by Excess Alcohol Consumption – Xiaoxia LiuJournal of Agricultural and Food Chemistry

Microbiome news

Vaginal Microbiome and Women’s Health: More Research Needed

NAU researchers aim to find microbial link between two common respiratory diseases

September 24, 2019

Today’s digest is about diet-microbiota interactions in personalized  nutrition, interesting story on single bacterium association with fatty liver disease and how the gut microbiota adapt to red meat consumption.

General microbiome

Diet–microbiota interactions and personalized nutrition – Aleksandra A. Kolodziejczyk – Nature Reviews Microbiology

Citrobacter rodentium–host–microbiota interactions: immunity, bioenergetics and metabolism – Caroline Mullineaux-Sanders – Nature Reviews Microbiology

The interaction between the gut Microbiota and herbal medicines – Xuedong An – Biomedicine & Pharmacotherapy

Gut microbiota: what is its place in pharmacology? – Aleksandra Tarasiuk – Expert Review of Clinical Pharmacology

Human microbiome

Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae – Jing Yuan – Cell Metabolism

Association of Alterations in Intestinal Microbiota With Impaired Psychological Function in Patients With Inflammatory Bowel Diseases in Remission – Fabienne Humbel – Clinical Gastroenterology and Hepatology

Butyrate‐Producing Gut Bacteria and Viral Infections in Kidney Transplant Recipients: A Pilot Study – John R. Lee – Transplant Infectious Disease

Metabolomics and Microbial Composition Increase Insight into the Impact of Dietary Differences in Cirrhosis – I. Jane Cox – Liver International

Animal experiments

Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates – Livia S. Zaramela – Nature Microbiology

A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota – Weijun Wang – Scientific Reports

Comparative analysis of the fecal microbiota from different species of domesticated and wild suids – Florencia Correa-Fiz – Scientific Reports

Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing – Sofiya G. Shevchenko- Applied and Environmental Microbiology

Saponins from Clematis mandshurica Rupr. regulates gut microbiota and its metabolites during alleviation of collagen-induced arthritis in rats – Lin-Xiu Guo – Pharamacological Research

MHC Class II Antigen Presentation by the Intestinal Epithelium Initiates Graft-versus-Host Disease and Is Influenced by the Microbiota – Motoko Koyama – Immunity

Metformin Alters the Duodenal Microbiome and Decreases the Incidence of Pancreatic Ductal Adenocarcinoma Promoted by Diet-induced Obesity – Tien S Dong – American Journal of Physiology

Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach – Maria Guirro – PlosOne

Short-chain fatty acids and microbiota metabolites attenuate ghrelin receptor signaling – Cristina Torres-Fuentes – Faseb Journal

Effects of berberine and metformin on intestinal inflammation and gut microbiome composition in db/db mice – Wang Zhang – Biomedicine & Pharmacotherapy

Plant, root, soil microbiome

Water-soluble mercury induced by organic amendments affected microbial community assemblage in mercury-polluted paddy soil – Hualing Hu – Chemosphere

Phyllosphere colonisation by a soil Streptomyces sp. promotes plant defense responses against fungal infection – Sophie Vergnes – Molecular Plant-Microbe Interactions

Water microbiome 

Heat‐induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea – Wirulda Pootakham – Microbiology Open

Probiotics
Metabolomic profiling of oxalate-degrading probiotic Lactobacillus acidophilus and Lactobacillus gasseri – Casey A. Chamberlain – PlosOne

Probiotic Bifidobacterium bifidum G9‐1 ameliorates phytohemagglutinin‐induced diarrhea caused by intestinal dysbiosis -Yutaka Makizaki – Microbiology and Immunology