August 24, 2019

This weekend, read about the microbial index of skin health for children with eczema, gut microbiome of koalas, and interactions between the gut bacterial microbiome and virome of rhesus monkey. Happy reading!

General microbiome

Why we need a small data paradigm – Eric B. Hekler – BMC Medicine

Correspondence: The importance of genome sequence quality to microbial comparative genomics – Theo H. M. Smits – BMC Genomics

The applications of Big Data in molecular diagnostics – Yin Kwan Evelyn Wong – Expert Review of Molecular Diagnostics

Tiny Hidden Genes within Our Microbiome – Karin Mittelman & David Burstein – Cell

Skin microbiome

*A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children – Zheng Sun – mSystems

Gut microbiome

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight – Peng Jiang – Microbiome

Review: Gut Microbiota, Dietary Phytochemicals, and Benefits to Human Health – Ran Yin – Current Pharmacology Reports

Mild cognitive impairment has similar alterations as Alzheimer’s disease in gut microbiota – Binyin Li – Alzheimer’s & Dementia

Design of synthetic microbial consortia for gut microbiota modulation – Jorge F. Vázquez-Castellanos – Current Opinion in Pharmacology

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease – Sandra Aparecida dos Reis – Journal of Medical Microbiology

Review: Celiac disease: a comprehensive current review – Giacomo Caio – BMC Medicine

Pregnancy and early life

Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants – Kathyayini P. Gopalakrishna – Nature Medicine

Oral microbiome

Oral Microbiome and Cancer Therapy-Induced Oral Mucositis – Jean-Luc C Mougeot – JNCI Monographs

Respiratory microbiome

Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration – Annamaria Bevivino – Trends in Molecular Medicine

Water and extremophile microbiome

Effects of water recirculation rate on the microbial community and water quality in relation to the growth and survival of white shrimp (Litopenaeus vannamei) – Zhao Chen – BMC Microbiology

Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir – Ceshing Sheu – International Journal of Systematic and Evolutionary Microbiology

Bacterial Communities from Extreme Environments: Vulcano Island – Camilla Fagorzi – Diversity

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean – Susanne Kraemer – bioRxiv

Review: Metal and organic pollutants bioremediation by extremophile microorganisms – Patricia Giovanella – Journal of Hazardous Material

Animal microbiome

*Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala – Michaela D. J. Blyton – Animal microbiome

Impact of pine leaf biochar amendment on bacterial dynamics and correlation of environmental factors during pig manure composting – Jiao Li – Bioresource Technology

Animal experiment

Potential roles of gut microbiome and metabolites in modulating ALS in mice – Eran Blacher – Nature

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Inhibitory and nutrient use phenotypes among co‐existing Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil – Adil Essarioui – Environmental Microbiology

Phages and viruses

*The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites – Heng Li – Virology Journal

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July 29, 2019

Good Morning! Highlights of today’s digest include a revisited study that showed a significant alterations in the gut microbiome by the consumption of low/no-calorie sweeteners (LNCS), such as Splenda, and raising safety concerns, another work tells us development of Burkholderia-free host plant model to show how Burkholderia helps plant development, and finally a study finds a mechanistic link between the gut microbiome and early childhood asthma as shown with highthened expression of bacterial genes that make 12,13-diHOME which alters immune response.

Human gut microbiome

***Revisited: Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota – Susan S. Schiffman et al. – Food and Chemical Toxicology

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Fabian Frost et al. – PLOS ONE

Human respiratory microbiome

Chronic obstructive pulmonary disease upper airway microbiome is associated with select clinical characteristics – Alexa A. Pragman et al. – PLOS ONE

Animal experiments

***Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance – Sophia R. Levan et al. – Nature Microbiology

Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets – Tadele G. Kiros et al. – PLOS ONE

Low-dose inoculation of Escherichia coli achieves robust vaginal colonization and results in ascending infection accompanied by severe uterine inflammation in mice – Valerie P. O’Brien – PLOS ONE

Probiotic strains improve high-fat diet-induced hypercholesterolemia through modulating gut microbiota in ways different from atorvastatin – Dun Su et al. – bioRxiv

Host Genotype-shaped Gut Microbiome Modulate Atherosclerosis Development in Mice – Kazuyuki Kasahara et al. – Arteriosclerosis, Thrombosis, and Vascular Biology

Animal microbiome

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Osiris Gaona et al. – PLOS ONE

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis – Emilie Lejal et al. – bioRxiv

Characterization of the gastrointestinal bacterial microbiome of farmed juvenile and adult white Cachama (Piaractus brachypomus) – Victor Alfonso et al. – Aquaculture

Biosynthesis and Characterization, Antioxidant and Antimicrobial Activities
of Selenium Nanoparticles from Ethanol Extract of Bee Propolis
– Shubharani R. et al. – Journal of Nanomedicine & Nanotechnology

Plant, root and soil microbiome

The role of inoculum dispersal and plant species identity in the assembly of leaf endophytic fungal communities – Kevin D. Ricks et al. – PLOS ONE

***Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant – Arne Sinnesael et al. – PLOS ONE

AOA and AOB communities respond differently to changes of soil pH under long-term fertilization – Rubio Sun et al. – Soil Ecology Letters

***Negative plant-microbiome feedback limits productivity in aquaponics – Jessica A. Day et al. – bioRxiv

Do plant–microbe interactions and aluminum tolerance influence
alpine sedge species’ responses to nitrogen deposition?
– Teal S. Potter et al. – Ecosphere

Plant diversity and fertilizer management shape the belowground microbiome of native grass bioenergy feedstocks – Daniel Revillini et al. – Frontiers in Plant Science

Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location – Yunshi Li et al. – PeerJ

Responses of plant growth, physiological, gas exchange parameters of super and non-super rice to rhizosphere temperature at the tillering stage – Shuying Li at al. – Nature Scientific Reports

Influence of introduced arbuscular mycorrhizal fungi and phosphorus sources on plant traits, soil properties, and rhizosphere microbial communities in organic legume-flax rotation – Yunliang Li et al. – Plant and Soil

Effects of arbuscular mycorrhizal fungi on inoculated seedling growth and rhizosphere soil aggregates – Zhongfeng Zhang et al. – Soil and Tillage Research

Properties of bacterial community in the rhizosphere soils of Achyranthes bidentata tolerant to consecutive monoculture – Juanying Wang et al. – Plant Growth Regulation

The role of volatile organic compounds and rhizosphere competence in the mode of action of the non-pathogenic Fusarium oxysporum FO12 towards Verticillium wilt – Mulero-Aparicio et al. – Frontiers in Microbiology

Dynamic changes in soil chemical properties and microbial community structure in response to different nitrogen fertilizers in an acidified celery soil – Yuping Wu et al. – Soil Ecology Letters

Improved rhizoremediation for decabromodiphenyl ether (BDE-209) in E-waste contaminated soils – Jiayin Feng et al. – Soil Ecology Letters

Review: Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization – Peng Cai et al. – Soil Ecology Letters

Organic amendment effects on nematode distribution within aggregate fractions in agricultural soils – Xiaoke Zhang et al. – Soil Ecology Letters

Water and extermophile microbiome

Book chapter: New Perspectives on the Distribution and Roles of Thermophilic Fungi – Miriam I. Hutchinson et al. – Fungi in Extreme Environments: Ecological Role and Biotechnological Significance

Diversity and biogeography of eukaryotic microorganism in the deepsea sediment of the Eastern Indian Ocean – Xiaoxia Ma et al. – International Journal of Science

Phages and viruses

Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames – Stefania Pacini et al. – bioRxiv

Techniques

Modelling approaches for studying the microbiome – Manish Kumar et al. – Nature Microbiology

Guest Editorial: Beyond sequencing: fast and easy microbiome profiling by flow cytometry – Charlotte Esser at al. – Archives of Toxicology

View Point: Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation – Pablo Carbonell et al. – ACS Synthetic Biology

Microbes in the News

***Elevated Concentration of Lipid in Neonatal Microbiome Predicts Later Risk for Asthma, Allergy – Allison Inserro – AJMC Newsroom

Friday, July 19th

Happy Friday! Today’s digest includes the microbiome of plankton, viral diversity of ticks, and a review of microbiome engineering. Enjoy!

General microbiome

Homeorhesis and ecological succession quantified in synthetic microbial ecosystems – Chuang – PNAS

Human nearly-sterile sites

Insights into the Microbiome of Breast Implants and Periprosthetic Tissue in Breast Implant-Associated Anaplastic Large Cell Lymphoma – Walker – Scientific Reports

Human gut microbiome

Review: Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes – Lam – Cell Host & Microbe

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Frost – PLoS One

Animal experiments

Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus – Tan – PLoS One

Animal microbiome

Cicadae pupa promotes metabolites synthesis of Isaria cicadae, a dominant species in cicada flowers microbiota – Chunyu – Journal of Agricultural and Food Chemistry

Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice – Moeller – mSphere

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Gaona – PLoS One

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection – Kolody – ISME

Plant, root, and soil microbiome

Preprint: Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity – Cobo-Diaz – BioRxiv

Water and extremophile microbiome

Impacts of continuous inflow of low concentrations of silver nanoparticles on biological performance and microbial communities of aerobic heterotrophic wastewater biofilm – Alizadeh – Journal of Agricultural and Food Chemistry

Phages and viruses

Preprint: Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake – Okazaki – BioRxiv

Preprint: Identification and evolution of avian endogenous foamy viruses – Chen – BioRxiv

Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago – Sameroff – Scientific Reports

Bioinformatics

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences – Mallick – Nature Communications

Heterogeneity spacers in 16S rDNA primers improve analysis of mouse gut microbiomes via greater nucleotide diversity – Jensen – BioTechniques

July 2, 2019

This Tuesday, read about the fecal microbial transplantation for cardiometabolic syndrome treatment, oral microbiome of early stage Parkinson’s disease, Finnish Health and Early Life Microbiota (HELMi) project, and more. Happy reading!

General microbiome

Review: Defining Division of Labour in Microbial Communities – Samir Giri – JMB

Review: Selective pressures during chronic infection drive microbial competition and cooperation – Jiwasmika Baishya & Catherine A. Wakeman – Biofilms and Microbiomes

Gut microbiome

*Review: Fecal Microbial Transplantation and Its Potential Application in Cardiometabolic Syndrome – Avner Leshem – Frontiers in Immunology

Review: The Microbiome and Irritable Bowel Syndrome – A Review on the Pathophysiology, Current Research and Future Therapy – Pei Pei Chong – Frontiers in Microbiology

Alterations of the bile microbiome in primary sclerosing cholangitis – Timur Liwinski – BMJ Gut Microbiota

Selective and suppressive effects of antibiotics on donor and recipient bacterial strains in gut microbiota determine transmission efficiency of blaNDM-1-bearing plasmids – Lianwei Ye – Journal of Antimicrobial Chemotherapy

Pregnancy and early life

Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve – Kattayoun Kordy – bioRxiv

Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota – Mari Hagbø – Paediatric research

*Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort – Katri Korpela – BMJ Paediatrics

Oral microbiome

*The oral microbiome of early stage Parkinson’s disease and its relationship with functional measures of motor and non-motor function – Dragos Mihaila – PlosOne

Phages and viruses

What is (not) known about the dynamics of the human gut virome in health and disease – Leen Beller Jelle Matthijnssens – Current Opinion in Virology

Water and extremophile microbiome

Characterization of indigenous bacteria from radon-rich groundwater and their tolerance to physicochemical stress – T. Nayak – International Journal of Environmental Science and Technology

Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes – Nachiket P. Marathe – Microbiome

Techniques

Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities – Shi Ming Tan – Biofilms and microbiomes

Bioinformatics

Use and abuse of correlation analyses in microbial ecology – Alex Carr – ISME Journal

Education

From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training – Annette McGrath – Plos Computational Biology

Ten quick tips for effective dimensionality reduction – Lan Huong Nguyen and Susan Holmes – Plos Computational Biology

June 29, 2019

Happy Saturday! Today, in this Digest: a review about the relationship between hypertension and the gut (including the microbiome as a key player) and a systematic review of the associations between vaginal microbiota, HPV and cervical dysplasia. Today we have also several papers about bioinformatic tools, methods, and techniques associated with microbiome research, including the analysis of well-to-well contamination during microbiome research. And of course, many more papers!

 

Human or General Microbiome

Review: Hypertension as a Metabolic Disorder and the Novel Role of the Gut – Masami Tanaka – Current Hypertension Reports

Minireview: Antibiotics and immunotherapy in gastrointestinal tumors: Friend or foe? – Cong Yan – World Journal of Clinical Cases

Review: Proton pump inhibitors and dysbiosis: Current knowledge and aspects to be clarified – Giovanni Bruno – World Journal of Gastroenterology

Systematic Review: The vaginal microbiota, HPV and cervical dysplasia: a systematic review and network meta-analysis – Johanna Norenhag – BJOG

Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy – Azza Abdel-Gadir – Nature Medicine

Exploration of the Vaginal and Gut Microbiome in African American Women by Body Mass Index, Class of Obesity, and Gestational Weight Gain: A Pilot Study – Mary Ann Faucher - American Journal of Perinatology

Banking feces: a new frontier for public blood banks? – Simon Mark Dahl Jørgensen – Transfusion

Diet-microbiota-metabolite interaction networks reveal key players in inflammatory bowel disease – Yijie Weng – Journal of Digestive Diseases

The microbiome of calcium-based urinary stones – Ryan A. Dornbier – Urolithiasis

Scientometric analysis of the term “microbiota” in research publications (1999-2017): A second youth of a century-old concept – Lesya Baudoin – FEMS Microbiology Letters

Microbiome analysis as a platform R&D tool for parasitic nematode disease management – Glenn Hogan – The ISME Journal

Is the Oral Microbiome Associated with Blood Pressure in Older Women? – Joshua H. Gordon – High Blood Pressure & Cardiovascular Prevention

An untargeted fecal and urine metabolomics analysis of the interplay between the gut microbiome, diet and human metabolism in Indian and Chinese adults – Abhishek Jain – Scientific Reports

Gut Microbiota Alteration is Characterized by a Proteobacteria and Fusobacteria Bloom in Kwashiorkor and a Bacteroidetes Paucity in Marasmus – Thi-Phuong-Thao Pham – Scientific Reports

The effects of perineal disinfection on infant’s oral microflora after transvaginal examination during delivery – Hongping Li – BMC Pregnancy and Childbirth

Metagenomic analysis of bile salt biotransformation in the human gut microbiome – Promi Das – BMC Genomics

 

Animal Microbiome / Animal Experiments

Metagenomic assessment of the Cebus apella gut microbiota – Jenni Firrman – American Journal of Primatology

Multipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial Perspective – Marta Turon – mSystems

Arthropod-bacteria interactions influence assembly of aquatic host microbiome and pathogen defense – Sasha E. Greenspan – Proceedings of the Royal Society B

Intestinal microbiota contributes to altered glucose metabolism in simulated microgravity mouse model – Yifan Wang – The FASEB Journal

Impact of Low-dose Ionising Radiation on the Composition of the Gut Microbiota of Mice – Xiaodan Liu – Toxicological Sciences

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats – Melissa R. Ingala – Ecology and Evolution

 

Microbiome and Therapeutics (Compounds, Microbes or Procedures)

Review: Effects of Fish n-3 PUFAs on Intestinal Microbiota and Immune System – Cinzia Parolini – Marine Drugs

Review: Updates in Treatment of Recurrent Clostridium difficile Infection – Tanveer Singh – Journal of Clinical Medicine Research

Synbiotics suppress colitis-induced tumorigenesis in a colon-specific cancer mouse model – Yasufumi Saito – PLOS One

Roles of Chinese Medicine and Gut Microbiota in Chronic Constipation – Zhenyuan Xu – Evidence-Based Complementary and Alternative Medicine

Increasing the Dose and/or Repeating Faecal Microbiota Transplantation (FMT) Increases the Response in Patients with Irritable Bowel Syndrome (IBS) – Magdy El-Salhy – Nutrients

Interleukin-37 sensitize the elderly type 2 diabetic patients to insulin therapy through suppressing the gut microbiota dysbiosis – Tianyi Li – Molecular Immunology

Skin microbiome modulation induced by probiotic solutions – Bernhard Paetzold – Microbiome

Evaluation of Predation Capability of Periodontopathogens Bacteria by Bdellovibrio Bacteriovorus HD100. An in Vitro Study – Romeo Patini – Materials

 

Bioinformatics, Methods and Techniques

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research – Jeremiah J. Minich – mSystems

Associated commentary: A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses – Alan W. Walker – mSystems

redbiom: a Rapid Sample Discovery and Feature Characterization System – Daniel McDonald – mSystems

Review: Methods and basic concepts for microbiota assessment – Marcio Costa – The Veterinary Journal

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system – Vincent Somerville – BMC Microbiology

Robust biomarker discovery for microbiome-wide association studies – Qiang Zhu – Methods

A Method for Comprehensive Proteomic Analysis of Human Faecal Samples to Investigate Gut Dysbiosis in Patients with Cystic Fibrosis – Griet Debyser – Emerging Sample Treatments in Proteomics

metaQuantome: An integrated, quantitative metaproteomics approach reveals connections between taxonomy and protein function in complex microbiomes – Caleb W. Easterly – Molecular & Cellular Proteomics

Review: The dark side of technological advances in analysis of microbial ecosystems – Mick Bailey – Journal of Animal Science and Biotechnology

June 4, 2019

General microbiome
Rigorous Statistical Methods for Rigorous Microbiome Science – Amy D. Willis – mSystems

Understanding microbial community dynamics to improve optimal microbiome selection – Robyn J. Wright – Microbiome

Toward a Better Understanding of Species Interactions through Network Biology – Ryan S. McClure – mSystems

Human respiratory microbiome
Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus – Hyun Jik Kim – Microbiome

Human gut microbiome
A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans – Alfonso Benítez-Páez – mSystems

Gut microbiome identifies risk for colorectal polyps – Ezzat Dadkhah – BMJ Open Gastroenterology

Yogurt improves insulin resistance and liver fat in obese women with nonalcoholic fatty liver disease and metabolic syndrome: a randomized controlled trial – Yang Chen – American Journal of Clinical Nutrition

Preprint: Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids – Robert A Quinn – bioRxiv

Animal models
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model – Limei Lin – Microbiome

Missing Links: the Role of Primates in Understanding the Human Microbiome – Katherine R. Amato – mSystems

Plant, root, and soil microbiome
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays – Frank Reith – Annals of Botany

Water and extremophile microbiome
Effects of sulfamethoxazole and sulfamethoxazole-degrading bacteria on water quality and microbial communities in milkfish ponds – Bea-Ven Chang – Environmental Pollution

Preprint: Temporal dynamics of Bacteria, Archaea and protists in equatorial coastal waters – Caroline Chénard – bioRxiv

Built environment
Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area – Miles Richardson – Microbiome

Phages and viruses
Preprint: The human gut virome is highly diverse, stable and individual-specific – Andrey Shkoporov – bioRxiv

Bioinformatics
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language – Luis Pedro Coelho – Microbiome

Science, publishing, and career
Preprint: The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Rochelle E. Tractenberg – bioRxiv

Alyson’s non-microbiology picks
Why Your Metro Commute Is So Insanely Windy – Julie Bogen – The Atlantic

The 2019 Wellcome photography prize: close focus on the human condition – Sean O’Hagan – The Guardian

May 31, 2019

Happy Friday!! Today’s digest contains reviews on the role of microbiota in immune memory formation and bioinformatic tools for soil microbiome analysis

General microbiome

*Review: The microbiome and immune memory formation – Kathy D. McCoy – Immunology and Cell biology

Preprint – Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing – Emily Crawford – bioRxiv

Animal experiments

Response of Fish Gut Microbiota to Toxin-Containing Cyanobacterial Extracts: A Microcosm Study on the Medaka (Oryzias latipes) – Sébastien Duperron – Environmental Science & Technology Letters

Plant, root, and soil microbiome

*Book chapter : Bioinformatics Tools for Soil Microbiome Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Belowground Microbial Communities: Key Players for Soil and Environmental Sustainability – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Single-Cell Genomics and Metagenomics for Microbial Diversity Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

In vitro digestion and fermentation of three polysaccharide fractions from Laminaria japonica and their impact on lipid metabolism-associated human gut microbiota – Jie Gao – Journal of Agricultural and Food Chemistry

Preprint – Biogeographical patterns in soil bacterial communities across the Arctic region – Lucie A Malard – bioRxiv

Water and extremophile microbiome

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient – Marie Simonin – Environmental Microbiology

Phages and viruses

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages – Jakub Barylski – Systematic Biology

Techniques

Protocol: Analysis of Microbial Siderophores by Mass Spectrometry – Tomas Pluhacek – Part of the Methods in Molecular Biology

Review: A guide to visualizing the spatial epigenome with super‐resolution microscopy – Jianquan Xu – The FEBS Journal