Category Archives: Animal microbiome

May 12, 2021

Posted on by

Good morning all! Today’s digest includes two articles discussing the role of the local tissue microbiome in cancer. In the first, Zhu et al. explore the relationship between the intratumor microbiome, immune cell infiltration, and patient survival in the context of melanoma. The second study by Wilkie et al. examines how lipopolysaccharide produced by the commensal breast microbiota impacts cancer growth.

Additionally, there is a paper by Radojević et al. in which the authors found an association between the fecal microbiota and immunogenicity of peripheral blood monocyte-derived dendritic cells in healthy donors; a study by Kim et al. showing that diet and microbiome derived amino acids impact gut enterocyte communication with the brain in Drosophila; and a paper by Tandon et al. investigating the impact of the reciprocal transplantation of water from the surface and bottom of lakes with different trophic states on microbial community composition and function.

Pregnancy and Early-Life
Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures. – Wang, S. et al., Gut Microbes.

Human Nearly-Sterile Sites
Intratumour microbiome associated with the infiltration of cytotoxic CD8+ T cells and patient survival in cutaneous melanoma. – Zhu, G. et al., European Journal of Cancer Research.

Lipopolysaccharide from the commensal microbiota of the breast enhances cancer growth: role of S100A7 and TLR4. – Wilkie, T. et al., Molecular Oncology.

Human Gut Microbiome
Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment. – Terrisse, S. et al., Cell Death & Differentiation.

Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells in vitro. – Radojević, D. et al., Gut Microbes.

Substrate‐driven differences in tryptophan catabolism by gut microbiota and Aryl hydrocarbon Receptor activation. – Huang, Z. et al., Molecular Nutrition & Food Research.

Human Oral Microbiome
The evolution and changing ecology of the African hominid oral microbiome. – Fellows Yates, J.A. et al., PNAS.

Animal Experiments
Response of the microbiome-gut-brain axis in Drosophila to amino acid deficit. – Kim, B. et al., Nature.

Coadaptation between host genome and microbiome under long-term xenobiotic-induced selection. – Wang, G-H. et al., Science Advances.

Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster. – Ankrah, N.Y.D. et al., mSystems.

Animal Microbiome
The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes. – Collins, F.W.J. et al., Gut Microbes.

Insect Microbiome
Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees. – Callegari, M. et al., npj Biofilms Microbiomes.

Seasonal Dynamics of the Honey Bee Gut Microbiota in Colonies Under Subtropical Climate. – Castelli, L. et al., Microbial Ecology.

Plant, Root, and Soil Microbiome
Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach. – Fadiji, A.E. et al., Archive of Microbiology.

Water and Extremophile Microbiome
Meta-transcriptomic profiling of functional variation of freshwater microbial communities induced by an antidepressant sertraline hydrochloride. – Cui, H. et al., Science of the Total Environment.

Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment. – Tandon, K. et al., Science of the Total Environment.

Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues. – Doering, T. et al., Microbiome.

Built Environment
The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water. – Zhang, C. et al., Frontiers in Microbiology.

Bioinformatics
A Protocol for Teaching Basic Next Generation Sequencing (NGS) Analysis Skills to Undergraduate Students Using Bash and R. – Fondi, M. & Bacci, G., Bacterial Pangenomics.

Techniques
Microdroplet-based system for culturing of environmental microorganisms using FNAP-sort. – Saito, K. et al., Scientific Reports.

May 8th, 2021

Posted on by

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a variety of interesting papers, in particular in bioinformatics! I recommend anyone interesting in metagenomic read classification to take a look at the benchmark study by Arizmendi Cardenas and collaborators. They compared read-based taxonomic classification tools on their capacity to handle ancient DNA sequences, characterized by a higher mutation rate and shorter sequences.

This digest also contains a very good review on the current state of the art network analysis methods for exploring interaction in complex microbial communities.

Finally, today’s non-microbiology pick is a piece exploring the current challenges and limitations for the annotation of microbiome dataset with high-quality metadata.

Have a great Weekend!

Human gut microbiome

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease – Aldars-Garcia et al. – Microorganisms

Animal experiments

Millet-based supplement restored gut microbial diversity of acute malnourished pigs – Li et al. – PLOS One

A mixture of quebracho and chestnut tannins drives butyrate-producing bacteria populations shift in the gut microbiota of weaned piglets – Miragoli et al. – PLOS One

Animal microbiome

Dynamic changes occur in the DNA gut virome of female cynomolgus macaques during aging – Tan et al. – Microbiology Open

Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France – Nebbak et al. – Viruses

Plant, root, and soil microbiome

Preprint: Mapping the microbial diversity and natural resistome of north Antarctica soils – Marcoleta et al. – BioRXiv

Community dynamics in rhizosphere microorganisms at different development stages of wheat growing in confined isolation environments – Ma et al. – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Book chapter: Bioprospecting Extreme Ecosystems Before They Vanish: The (Poorly Studied) Microbiology of Tropical Glaciers – Yarzabal – Extreme environment (CRC press)

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores – Pearman et al. – PLOS One

Bioinformatics

Preprint: Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study – Arizmendi Cardenas et al. – BioRXiv

Review: Network analysis methods for studying microbial communities: A mini review – Matchado et al. – Computational and sctructural Biotechnology Journal

Improving metagenomic binning results with overlapped bins using assembly graphs – Mallawaarachchi et al. – Algorithms for molecular biology

My non-microbiology picks

Preprint: Current challenges in microbiome metadata collection – Rosenfeld et al. – BioRXiv

May 05, 2021

Posted on by

Special Issue on Interplay of Gene Expression Regulation and Microbiome

Cells has a call for papers for a special issue about the ‘Interplay of Gene Expression Regulation and Microbiome‘. This Special Issue should serve as a platform to bring together recent advances in the understanding of the dynamic interplay between gene regulation and host-microbiome interaction.

Human oral microbiome

Anna Karenina and the subgingival microbiome associated with periodontitis – Altabtaei et al. – Microbiome

Human gut microbiome

[REVIEW]The Association Between Intestinal Bacteria and Allergic Diseases—Cause or Consequence? – Han et al. – Front. Cell. Infect. Microbiol.

[Review]Exploring the Modulatory Effects of Gut Microbiota in Anti-Cancer Therapy – Li, Deng & Chen – Front. Oncol.

[REVIEW]The interplay between Helicobacter pylori and gastrointestinal microbiota – Chen et al. Gut Microbes

Do Antibiotics Cause Obesity Through Long-term Alterations in the Gut Microbiome? A Review of Current Evidence – Vallianou et al. – Metabploism

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

Gut microbiota contributes to the development of hypertension in a genetic mouse model of systemic lupus erythematosus – de la Visitación et al. – British Journal of Pharmacology

Infant gut microbiota modulation by human milk disaccharides in humanized microbiome mice – Rubio-Del-Campo – Gut Microbes

Animal microbiome (for animals in the wild)

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing – Apostolopoulos et al. PLOS One

Bioinformatics

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 – Beghini et al. – eLife

Techniques

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements – Tourlousse et al. – Microbiome

May 4, 2021

Posted on by

In today’s post – host-microbe marker for inflammatory bowel disease, evolution of soil bacterium along the climate gradient, how C. difficile exploits host metabolite under inflammatory conditions induced by its own toxins and differential response of commensals to alter C. difficle virulence.

Job Posting

Microbiome Scientific Researcher, Computational (Cancer Immunology) – Genentech South San Francisco, California

General Microbiome

Endothelium–gut communication: IGF‐1Rs crosstalk with microbiota – Zhen Bouman Chen – EMBO reports

Recent advances in marine algae oligosaccharides: structure, analysis, and potential prebiotic activities – Xu-Ting Xie – Critical Reviews in Food Science and Nutrition

Human Microbiome

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men – Jun Li – Gut

Gut Dysbiosis Associated with Antibiotics and Disease Severity and Its Relation to Mortality in Critically Ill Patients – Masahiro Ojima – Digestive Diseases and Sciences

Effects of Totum-63 on glucose homeostasis and post-prandial glycemia: a translational study – Vivien Chavanelle – American Journal of Physiology Endocrinology and Metabolism

Impact of a fermented soy beverage supplemented with acerola by-product on the gut microbiota from lean and obese subjects using an in vitro model of the human colon – Antonio Diogo Silva Vieira – Environmental biotechnology

Decoding the matrix: multiomics reveals host-microbe biomarker for inflammatory bowel disease – Monica Viladomiu – The Journal of Clinical Investigation

Animal Microbiome

C. difficile exploits a host metabolite produced during toxin-mediated disease – Kali M. Pruss – Nature

In vivo commensal control of Clostridioides difficile virulence – Brintha P. Girinathan – BioRxiv

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing – Neoklis Apostolopoulos – PlosOne

Plant, root and soil microbiome

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient – Alexander B. Chase – PNAS

Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation – Spencer Diamond – BioRxiv

Water microbiome

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem – Ya-Jou Chen – ISME Journal

Techniques

Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S – Yi‐Chun Yeh – Environmental Microbiology

Bacteria

Completion of the gut microbial epi-bile acid pathway – Heidi L. Doden – Gut Microbes

Possible effects of Porphyromonas gingivalis on the blood-brain barrier in Alzheimer’s disease – Ingar Olsen – Expert Review of Anti-infective Therapy

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii – Tao Luo – Nature Communications

May 3, 2021

Posted on by

Water microbiome

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea – Płaza et al. – PLoS ONE

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru – Romero et al. – PLoS ONE

Distribution and diversity of eukaryotic microalgae in Kuwait waters assessed using 18S rRNA gene sequencing – Kumar et al. – PLoS ONE

Plant microbiome

Toward understanding microbiota homeostasis in the plant kingdom – Paasch & He – PLoS Pathogens

Animal microbiome

Seasonal dynamics of diet–gut microbiota interaction in adaptation of yaks to life at high altitude – Guo et al. – npj Biofilms and Microbiomes

Low biomass microbiome

Experimental parameters defining ultra-low biomass bioaerosol analysis – Luhung et al. – npj Biofilms and Microbiomes

Human gut microbiome

A rich meconium metabolome in human infants is associated with early-life gut microbiota composition and reduced allergic sensitization – Petersen et al. – Cell Reports Medicine

April 28, 2021

Posted on by

General microbiome

Microbiota regulate innate immune signaling and protective immunity against cancer – Xing et al. – Cell Host & Microbe

Pregnancy and early life

[PREPRINT]Diet Potentially Drives the Differentiation of Eating Behaviours via Alterations to the Gut Microbiome in Infants – Yan et al. – bioRxiv

[REVIEW]Impact of Maternal Nutritional Supplementation during Pregnancy and Lactation on the Infant Gut or Breastmilk Microbiota: A Systematic Review – Zaidi, Moore & Okala – Nutrients

Infant Gut Microbiome Is Enriched with Bifidobacteria longumssp. infantisin Old Order Mennoniteswith Traditional Farming Lifestyle – Seppo et al. – Allergy

Human skin microbiome

Can antibiotic‐induced changes in the composition of the hair follicle microbiome regulate human hair growth? – Lousada et al. – Experimental Dermatology

Human gut microbiome

Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome – Hu et al. – Theranostics

Alteration of gut microbial profile in patients with diabetic nephropathy – Du et al. – Endocrine

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

Sargassum fusiforme fucoidan modifies gut microbiota and intestinal metabolites during alleviation of hyperglycemia in type 2 diabetic mice – Wu et al. – Food & Function

Bidirectional interaction of nobiletin and gut microbiota in mice fed with a high-fat diet – Zhang et al. – Food & Function

Reshaping of the gastrointestinal microbiome alters atherosclerotic plaque inflammation resolution in mice – Garshick et al. – Scientif Reports

Animal microbiome (for animals in the wild)

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits – Zheng et al. – PLOS One

Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone – Antwis et al. – Journal of Animal Ecology

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

[PREPRINT]A Scenic River in Rural Ohio Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy et al. – bioRxiv

[PREPRINT]Diversity of free-living prokaryotes on terrestrial and marine Antarctic habitats – Bendia et al. – bioRxiv

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics – Cabello-Yeves – Environmental Microbiome

Techniques

Obtaining deeper insights into microbiome diversity using a simple method to block host and non‐targets in amplicon sequencing – Mayer et al. – Molecular Ecology Resources

April 24th, 2021

Posted on by

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a wide range of topics to explore! I particularly recommend taking the time to read at the fascinating review listed below exploring horizontal gene transfer in environmental microbial communities. They describe how advances in the computational analysis of metagenomic data has allowed us to dive deeper in understanding these processes in microbiomes.

Among the list of very interesting research papers in this digest, you’ll find a fascinating study exploring the symbiotic microbial communities associated with deeper corals. Although extensive litterature has been published on coral microbiomes from shallow waters, this papers is the first to examine microbial communities associated with the deep photosymbiotic corals, living at more than 150 m of depth!

Today’s non-microbiology pick is a really interesting paper from Faldelmola and collaborators reporting on the development by the Pan-African H3Africa Bioinformatics Network of two data portals for African genomic medicine and African microbiomes datasets. The paper explore how they lead a very successful 6-days hackathon allowing to efficiently develop these two important scientific ressources, but also how they build a collaborative community of African researchers and experts.

Have a great Weekend!

General microbiome

Review: Examining horizontal gene transfer in microbial communities – Brito – Nature reviews microbiology

Preprint: Evidence for a billion-years arms race between viruses, virophages and eukaryotes – Barreat and Katzourakis – BioRxiV

Unifying community detection across scales from genomes to landscapes – Hudon et al. – Oikos

Human gut microbiome

Preprint: Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Watson et al. – BioRxiV

Animal experiments

Diversity and characteristics of raw milk microbiota from Korean dairy farms using metagenomic and culturomic analysis – Ryu et al. – Food control

Animal microbiome

Preprint: Reclassification of seven honey bee symbiont strains as Bombella apis – Smith et al. – BioRxiV

Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth) – Rouzé et al. – ISME Journal

Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes – Thongsripong et al. – Scientific reports

Water and extremophile microbiome

Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents – McAllister et al. – ISME Journal

Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones – Sun et al. – ISME Journal

Morphological complexity affects the diversity of marine microbiomes – Lemay et al. – ISME Journal

Preprint: Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic – Ferreira et al. – BioRxiV

Bioinformatics

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC – Parrello et al. – Plos One

A roadmap for metagenomic enzyme discovery – Robinson et al. – Natural Product Reports

Techniques

Preprint: Synergistic effect of short- and long-read sequencing on functional meta-omics – Galata et al. – BioRxiV

My non-microbiology picks

H3ABioNet genomic medicine and microbiome data portals hackathon proceedings – Fadlelmola et al. – Database

April 23, 2021

Posted on by

Good morning from New Jersey! Lots of papers to share today, particularly regarding animal microbiota and new bioinformatics tools.

General microbiome

Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer, Alice Tzeng et al., Genome Medicine

Pregnancy and early life

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition, Xuanji Li et al., Cell Host & Microbe

Multi-site human microbiome

Review: Microbiome-immune interactions in tuberculosis, Giorgia Mori et al., PLOS Pathogens

Human gut microbiome

Dynamic Changes in Microbiome Composition Following Mare’s Milk Intake for Prevention of Collateral Antibiotic Effect, Almagul Kushugulova et al., Frontiers in Cellular and Infection Microbiology

Review: The aging gut microbiome and its impact on host immunity, Bosco and Noti, Genes & Immunity

Animal experiments

Ingestion of Bifidobacterium longum changes miRNA levels in the brains of mice, DeVries and Horstman et al., PLOS ONE

Heat-inactivated Lactobacillus plantarum nF1 promotes intestinal health in Loperamide-induced constipation rats, Seon-Ah Park et al., PLOS ONE

The pregnane X receptor drives sexually dimorphic hepatic changes in lipid and xenobiotic metabolism in response to gut microbiota in mice, Sharon Ann Barretto et al., Microbiome

One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome, Arnon Gal et al., PLOS ONE

Animal microbiome

Diversity and functional landscapes in the microbiota of animals in the wild, Levin, Raab, Pinto, and Rothschild et al., Science

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history, Tyler J. Carrier et al., PNAS

Diet and gut microbiome enterotype are associated at the population level in African buffalo, Claire E. Couch et al., Nature Communications

Coral microbiome changes over the day–night cycle, Alicia M. Caughman et al., Coral Reefs

An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota, Mao and Chuang et al., PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Preprint: Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops, Adina Howe et al., bioRxiv

Influence of Plant Host and Organ, Management Strategy, and Spore Traits on Microbiome Composition, Kristi Gdanetz et al., Phytobiomes Journal

Built environment

Categorisation of culturable bioaerosols in a fruit juice manufacturing facility, Shirleen M. Theisinger et al., PLOS ONE

Bioinformatics

Preprint: Deconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination, Senay Yitbarek et al., bioRxiv

Preprint: Extended taxonomic profiling of diverse environments with mOTUs 2.6, Hans-Joachim Ruscheweyh et al., bioRxiv

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome, Donovan H. Parks et al., Frontiers in Microbiology

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC, Bruce Parrello et al., PLOS ONE

April 21, 2021

Posted on by

General microbiome

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection – Mu et al. – Microbiome

Pregnancy and early life

A Microbiota-Directed Food Intervention for Undernourished Children – Chen et al. – The New England Journal of Medicine

Bacterial-fungal interactions in the neonatal gut influence asthma outcomes later in life – Boutin et al. – eLife

Human vaginal microbiome

[REVIEW]The effect of different contraceptive methods on the vaginal microbiome – Bastianelli et al. – Expert Review of Clinical Pharmacology

Human gut microbiome and virome

The Gut Microbiome in Progressive Multiple Sclerosis – Cox et al. – Annals of Neurology

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity – Zuo et al. – Microbiome

[REVIEW]The Gut Microbiome: a New Frontier in Musculoskeletal Research – Li et al. – Current Osteoporosis Reports

[REVIEW]Inflammation‐driven brain and gut barrier dysfunction in stress and mood disorders – Doney et al. – European Journal of Neuroscience

The gut microbiota is associated with clinical response to statin treatment in patients with coronary artery disease – Wang et al. – Atherosclerosis

[REVIEW]Dietary restrictions modulate the gut microbiota: Implications for health and disease – Schmidt and Lorentz – Nutrition Research

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

Altering the microbiome inhibits tumorigenesis in a mouse model of oviductal high-grade serous carcinoma – Chen et al. – Cancer Research

Screening of probiotic candidates in a simulated piglet small intestine in vitro model – Hansen et al. – FEMS Microbiology Letters

Animal microbiome (for animals in the wild)

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history – Carrier et al. – PNAS

[PREPRINT]Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding and that E. coli from these dogs are shared with humans and cause opportunistic infections – Mounsey et al. – bioRxiv

Diversity structure of the microbial communities in the guts of four neotropical termite species – Vikram et al. – PeerJ

Alteration of gut microbiota with a broad‐spectrum antibiotic does not impair maternal care in the European earwig – van Meyel et al. – Journal of Evolutionary Biology

Food microbiology

The effects of vegetable pickling conditions on the dynamics of microbiota and metabolites – Sawada et al. – PeerJ

Techniques

[PREPRINT]Development of Microbiome Biomarkers for IgA: a Joint Modeling Approach – Sengupta et al. – bioRxiv

April 14, 2021

Posted on by

General microbiome

[REVIEW]The microbiome and human cancer – Sepich-Poore et al. – Science

[PERSPECTIVE]A framework for microbiome science in public health – Wilkinson et al. – Nature Medicine

A framework for microbiome science in public health –

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Shaw et al. – Science Advances

Human gut microbiome

[REVIEW]Immune System, Microbiota, and Microbial Metabolites: The Unresolved Triad in Colorectal Cancer Microenvironment – Hanus et al. – Front. Immunol.

[REVIEW]Microbiome and colorectal cancer: A review of the past, present, and future – Johns & Petrelli – Surgical Oncology

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

Microbiota-derived short chain fatty acids modulate microglia and promote Aβ plaque deposition – Colombo et al. – eLife

Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns – Juanola et al.

Animal microbiome (for animals in the wild)

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis – Dittmer & Brucker – Microbiome

Plant, root, and soil microbiome

Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation – Li et al. – Microbiome

Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils – Bao et al. – Microbiome

Rhizosphere community selection reveals bacteria associated with reduced root disease – Yin et al. – Microbiome

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps) – Perez-Mon – Microbioal Genomics

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

[PREPRINT]The Polar Night Shift: Annual Dynamics and Drivers of Microbial Community Structure in the Arctic Ocean – Wietz et al. – bioRxiv

Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities – Fortunato et al. – Environmental Microbiology

Plasmids

[PREPRINT]Plasmid fitness costs are caused by specific genetic conflicts – Hall et al. – bioRxiv

Bioinformatics

[PREPRINT]Comprehensive benchmarking of tools to identify phages in metagenomic shotgun sequencing data – Ho, Millard & van Schaik – bioRxiv