January 22, 2019

In today’s digest read about Lactobacillus mulieris sp. nov. isolated from healthy female urinary tract, diversity of Escherichia coli phages in the Danish wastewater, PLate Coverage Algorithm (PLCA) in culture-enriched metagenomics, and more. Happy reading!

General microbiome

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions – Sara L. Jackrel – mBio

Gut microbiome

Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition – Rita A. Oliveira – Nature Microbiology

Long-term impact of fecal transplantation in healthy volunteers – Oleg V. Goloshchapov – BMC Microbiology

Efficacy of faecal microbiota transplantation in Crohn’sdisease: a new target treatment?– Liyuan Xiang – Microbial Biotechnology

Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner – bioRxiv

Microreview: Causalities of war: The connection between type VI secretion system and microbiota – Luke P. Allsopp – Cellular Microbiology

Urinary microbiome

*Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group – Joana Rocha – International Journal of systematic and evolutionary microbiology

Vaginal microbiome

Vaginal Microbiota Transplantation: The Next Frontier – Kevin DeLong – The Journal of Law, Medicine, & Ethics

Respiratory microbiome

*Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota – Fiona J. Whelan – Nature Microbiology

A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-levels– Zhang Wang – bioRxiv

Eye microbiome

The closed eye harbors a unique microbiome in dry eye disease – Kent A. Willis – medRxiv

Plant/root/soil microbiome

Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants – Yan Chen – Microbiome

Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community– Jiajie Feng – Microbiome

Microbiome composition differs in hybrid and inbred maize – Maggie R. Wagner – bioRxiv

Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum – Zuluaga Mya – PlosOne

Water microbiome

Molecular Characteristics of Dissolved Organic Nitrogen and Its Interaction with Microbial Communities in a Prechlorinated Raw Water Distribution System – Hang Xu – Environmental Science and Technology

Effects of geographic location and water quality on bacterial communities in full-scale biofilters across North America – Ben Ma – FEMS Microbiology Ecology

Phages and viruses

*Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species – Nikoline S. Olsen – bioRxiv

Bioinformatics

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences – Nicole R. Narayan – BMC Genomics

Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes – Jake L. Weissman and Philip L. F. Johnson – mSystems

Review: Integrating Computational Methods to Investigate the Macroecology of Microbiomes – Rilquer Mascarenhas – Frontiers in Genetics

Assessment of single cell RNA-seq statistical methods on microbiome data – Matteo Calgaro – bioRxiv

January 8, 2019

Today’s digest features a retrospective mini-review of mothur, study on gut microbiomes of over 900 vertebrate species [Spoiler alert: birds and bats share similarities in their microbiome], findings of fifteen-thousand-year-old viruses in glacier ice, and more. Happy reading!

Gut microbiome

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform – Christian Munck – Nature Communications

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels – Mohammad Tauqeer Alam – Gut Pathogens

Gut dysbiosis induces the development of pre-eclampsia through bacterial translocation– Xia Chen – Gut

Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals – Aftab Ahmad – PlosOne

Alterations of human lung and gut microbiome in non-small cell lung carcinomas and distant metastasis – Hui Lu – bioRxiv

The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for human complex diseases – Fengzhe Xu – bioRxiv

Oral microbiome

Acquisition of Oral Microbiota is Driven by Environment, Not Host Genetics – Chiranjit Mukherjee – bioRxiv

Animal microbiome

*Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats– Se Jin Song – mBio

Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities – Nikola Palevich – Applied and Environmental Microbiology

Inside out: microbiota dynamics during host-plant adaptation of whiteflies – Diego Santos-Garcia – The ISME Journal

Blood Loss Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Gut Microbiome of Rabbits – Junjie Yang – Current Microbiology

Probiotics

In Vitro Probiotic Potential of Hemophilin-producing Strains of Haemophilus haemolyticus – Brianna Atto – bioRxiv

Quantifying and engineering mucus adhesion of probiotics – Zachary J. S. Mays – bioRxiv

Plant/root/soil microbiome

Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in super arid environments – Ashraf Al-Ashhab – bioRxiv

Secreted metabolite-mediated interactions between rhizosphere bacteria and Trichoderma biocontrol agents – Ningxiao Li – PlosOne

Water microbiome

Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses – Daehyun Daniel Kim – bioRxiv

Viruses

*Glacier ice archives fifteen-thousand-year-old viruses – Zhi-Ping Zhong – bioRxiv

Meeting report: Viruses in the Built Environment (VIBE) meeting report – Aaron J. Prussin – Microbiome

Bioinformatics

*Minireview: Reintroducing mothur: 10 Years Later – Patrick D. Schloss – Applied and Environmental Microbiology

FunGeCo : A web based tool for estimation of Functional potential of bacterial genomes and microbiomes using Gene Context information – Swadha Anand – Bioinformatics

December 23, 2019

In today’s digest read about the subway microbiome (from surface and air samples collected at 16 subway stations in Oslo, Norway), role of Staphylococcus epidermidis in healthy maturation of the nasal microbiome, effect of storage and time on urinary microbiome, and more. Happy Holidays!

General microbiome

The emergence of microbiome centres – Jennifer B. H. Martiny – Nature Microbiology

Subway microbiome

*The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities– Jostein Gohli – Microbiome

Gut microbiome

Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut– Pichet Praveschotinunt – Nature Communications

Urinary microbiome

*The urinary microbiota composition remains stable over time and under various storage conditions – Caspar Bundgaard-Nielsen – bioRxiv

Vaginal microbiome

Review: Genetic Heterogeneity and Taxonomic Diversity among Gardnerella Species – Joana Castro – Trends in Microbiology

Nasal microbiome

*Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production – Qian Liu – Cell Host & Microbes

Animal microbiome

Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China – Chunlai Wang – mSystems

Animal experiments

Altered microbiota composition reflects enhanced communication in 15q11-13 CNV mice– Dian Eurike Septyaningtrias – Neuroscience Research

Plant/root/soil microbiome

Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities – S. Emilia Hannula – mBio

Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland– Jie Yang – Scientific Reports

Water microbiome

Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge– Chenbing Ai – Microorganisms

Viruses

Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves – Victor Golyaev – Scientific Reports

Bioinformatics

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise – Valentina Peona – bioRxiv

Transcriptome assembly from long-read RNA-seq alignments with StringTie2– Sam Kovaka – Genome Biology

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework – Guo Liang Gan – BMC Bioinformatics

The Generalized Matrix Decomposition Biplot and Its Application to Microbiome Data – Yue Wang – mSystems

December 20, 2019

This may be our last edition of the Microbiome Digest before the holidays kick in. A rich and dynamic Digest brings you all things microbiome (apologies for the tight formatting). An encouraging report on how we can reduce antimicrobial resistance organically, an amazing recovery of a human genome and an oral microbiome from chewed birch pitch thousands of years ago, and a network analysis reveals four levels of hierarchical trophic interactions in the human gut microbiome. Enjoy Reading and Happy Holidays!
Events
BMC Medicine’s upcoming collection, New Frontiers in Diagnosis, Treatment and Management of Neuromuscular Disorders, is soliciting submissions.
Current Issue of The ISME Journal
The 9th Gut Microbiota for Health World Summit – March 7 and 8 2020 in Madrid, Spain
General microbiology
High-order interactions distort the functional landscape of microbial consortia – Sanchez-Gorostiaga & Bajić et al. – PLoS Biology
Antimicrobial resistance
Human skin microbiome
Human oral microbiome
** A 5700 year-old human genome and oral microbiome from chewed birch pitch – Theis Z. T. Jensen et al. – Nature Communications
Press: Ancient “Chewing Gum” Reveals a 5,700-Year-Old Microbiome – Jim Daley – Scientific American
Human respiratory microbiome
Press: Child asthma flare-ups coincide with microbiome changes – JULIA EVANGELOU STRAIT-WUSTL – Futurity
Human gut microbiome
Human vaginal microbiome
Human gut-microbiota-brain axis
Review: Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain – Kan Gao et al. – Advances in Nutrition
Cancer microbiome
Metabolomics
The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics
Animal experiments
Animal microbiome
Plant, root and soil microbiome
Root microbiomes as indicators of seagrass health – Belinda C Martin et al. – FEMS Microbiology Ecology
Water and extremophile microbiome
Phages and viruses
Technology
Manipulating rod-shaped bacteria with optical tweezers – Zheng Zhang et al. – Scientific Reports
Bioinformatics
** Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang et al. – PLoS Computational Biology
Microbes in the news
The microbiome is fundamental to both health and disease – Fabian Brockotter – Poultry World
Low FODMAP Diet Helps IDB Patients – Kenny Walter – MDMAG
Oral Health: Caring for the Other Microbiome – Julia Peterman – Whole Foods Magazine
Non-microbiology pick

 

November 6, 2019

Today’s Digest features a large study on the evolution of diet and microbiota in African animals, a review on how diet can alter gut microbiota to fight infectious diseases, and we might reverse specific antibiotic resistance by removing those antibiotics in the environment. Enjoy!

General microbiology

Letter to the Editor: A conceptual framework for the phylogenetically constrained assembly of microbial communities – Daniel Aguirre de Cárcer – Microbiome

Review: The engineering of spatially linked microbial consortia – potential and perspectives – Sami Ben Said et al. – Current Opinion in Biotechnology

Preprint: Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy – Donovan H. Parks et al. – bioRxiv

Antimicrobial resistance

** Rapid decline of bacterial drug-resistance in an antibiotic-free environment through phenotypic reversion – Anett Dunai et al. – eLife

Human respiratory microbiome

Interplay between host-microbe and microbe-microbe interactions in cystic fibrosis – Catherine R. Armbruster et al. – Journal of Cystic Fibrosis

Human gut microbiome

Review: Gastrointestinal Microbiota and Type 1 Diabetes Mellitus: The State of Art – Marilena Durazzo et al. – Journal of Clinical Medicine

Identification of a Shared Microbiomic and Metabolomic Profile in Systemic Autoimmune Diseases – Chiara Bellocchi et al. – Journal of Clinical Medicine

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity – Robert C. Kaplan et al. – Genome Biology

Food microbiome

Comparison of microbial communities and physiochemical characteristics of two traditionally fermented vegetables – Qianqian Guan et al. – Food Research International

Animal experiments

** Review: Diet–microbiome–disease: Investigating diet’s influence on infectious disease resistance through alteration of the gut microbiome – Erica V. Harris et al. – PLoS Pathogen

Supplementation of Sesamin Alleviates Stress-Induced Behavioral and Psychological Disorders via Reshaping the Gut Microbiota Structure – Qianxu Wang et al. – Journal of Agricultural and Food Chemistry

Animal microbiome

** Covariation of diet and gut microbiome in African megafauna – Tyler R. Kartzinel et al. – PNAS

Press: Study of African animals illuminates links between environment, diet and gut microbiome – Brown University – Phys.org

Plant, root and soil microbiome

Interactive Effects of Nitrogen-Fixing Bacteria Inoculation and Nitrogen Fertilization on Soybean Yield in Unfavorable Edaphoclimatic Environments – Carlos Felipe dos Santos Cordeiro & Fábio Rafael Echer – Scientific Reports

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil – Vanessa L. Brisson et al. – Scientific Reports

Microbial communities and soil chemical features associated with commercial production of the medicinal mushroom Ganoderma lingzhi in soil – Le-Qin Ke et al. – Scientific Reports

Feasibility of bioleaching of heavy metals from sediment with indigenous bacteria using agricultural sulfur soil conditioners – Chuncheng Wu et al. – Science of the Total Environment

Land management and microbial seed load effect on rhizosphere and endosphere bacterial community assembly in wheat – Tim H. Mauchline et al. – Frontiers in Microbiology

Water and extremophile microbiome

Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications – Jessica Chopyk et al. – Water Research

Strong seasonality in arctic estuarine microbial food webs – Colleen T. Kellogg et al. – Frontiers in Microbiology

Evaluation of degradation behavior over tetracycline hydrochloride by microbial electrochemical technology: Performance, kinetics, and microbial communities – Xinhong Peng et al. – Ecotoxicology and Environmental Safety

Groundwater microbial communities and their connection to hydrochemical environment in Golmud, Northwest China – Liang Guo et al. – Science of the Total Environment

Performance of enhanced anaerobic digestion with different pyrolysis biochars and microbial communities – Ruixia Shen et al. – Bioresource Technology

Technology

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads – Jon G. Sanders et al. – Genome Biology

Bioinformatics

Microbiota analysis optimization for human bronchoalveolar lavage fluid – Pierre H. H. Schneeberger et al. – Microbiome

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities – James J Davis et al. – Nucleic Acids Research

Microbes in the news

Gut microbiome of premature babies is associated with stunted growth – EurekAlert!

Shark Skin Microbiome Protects Wounds From Infection – SciTechDaily

Fiber-rich diet eases son’s asthma, launches professor’s interdisciplinary microbiome research – Jeff Dodge – Colorado State University

Researchers identify certain gut bacteria that may be involved in causing bowel cancer – University of Bristol

Some gut bacteria may increase bowel cancer risk, research suggests – Nicola Davis – The Guardian

Certain Gut Bacteria May Contribute to Bowel Cancer – Technnology Networks

China Approves Alzheimer’s Treatment that Targets the Microbiome – Kerry Grens – The Scientist

Microbes on the market

Loop Genomics launches long-read Microbiome sequencing service at short-read price – Loop Genomics – PR Newswire

October 23, 2019

A rich Digest today featuring the “Prime Editing” invented by the David R. Liu lab, which promises to correct 89% of point mutations, an ultra-deep metagenomic study of phages in aquatic systems and strain level interaction between bacteria and plants. Enjoy!

General microbiology

** Search-and-replace genome editing without double-strand breaks or donor DNA – Andrew V. Anzalone et al. – Nature

Resolving a piece of the archaeal lipid puzzle – Ann Pearson – PNAS

Antimicrobial resistance

Commentary: Surveillance and monitoring of antimicrobial resistance: limitations and lessons from the GRAM project – Jesse Schnall et al. – BMC Medicine

Preprint: In vitro Efficacy of Novel Glucan Synthase Inhibitor, Ibrexafungerp (SCY-078), Against Multidrug- and Pan-resistant Candida auris Isolates from the Outbreak in New York – Yan Chun Zhu et al. – bioRxiv
https://www.biorxiv.org/content/10.1101/811182v1.abstract

Review: Proteomics approach to understand bacterial antibiotic resistance strategies – Bo Peng et al. – Expert Review of Proteomics

Human oral microbiome

Subgingival Microbiota and Longitudinal Glucose Change: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) – R.T. Demmer et al. – Journal of Dental Research

Human gut microbiome

Review: Systems biology perspective for studying the gut microbiota in human physiology and liver diseases – Ozlem Altay et al. – EBioMedicine

Review: Intestinal microbiota and colorectal carcinoma: Implications for pathogenesis, diagnosis, and therapy – Ana Montalban-Arques & Michael Scharl – EBioMedicine

Perspective: Carbohydrate-based Prebiotics in Targeted Modulation of Gut Microbiome – Ka-Lung Lam & Peter Chi Keung Cheung – Journal of Agricultural and Food Chemistry

Metabolomics

Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics – Xiaoling Zang et al. – Journal of Proteome Research

Food microbiome

Peer pressure: Evolutionary responses to biotic pressures in wine yeasts – C. G. Conacher et al. – FEMS Yeast Research

Animal experiments

Disruption of gut integrity and permeability contributes to enteritis in a fish-parasite model: a story told from serum metabolomics – Ariadna Sitjà-Bobadilla et al. – Parasites & Vectors

Animal microbiome

Estimating the burden of dengue and the impact of release of wMel Wolbachia-infected mosquitoes in Indonesia: a modelling study – Kathleen M. O’Reilly et al. – BMC Medicine

Plant, root and soil microbiome

Preprint: Insights into the desert living skin microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA – Nuttapon Pombubpa et al. – bioRxiv

** Metabolites in the root exudates of groundnut change during interaction with plant growth promoting rhizobacteria in a strain-specific manner – Sravani Ankati & Appa Rao Podile – Journal of Plant Physiology

Environmental and biotic drivers of soil microbial β-diversity across spatial and phylogenetic scales – Loïc Chalmandrier et al. – Ecography

Soil hydrology drives ecological niche differentiation in a native prairie microbiome – James S Griffin et al. – FEMS Microbiology Ecology

Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species – Julien Massoni et al. – The ISME Journal

Effect of aridity and dune type on rhizosphere soil bacterial communities of Caragana microphylla in desert regions of northern China – Jiangli Gao et al. – PLoS One

Rhizosphere bacterial community in watermelon-wheat intercropping was more stable than in watermelon monoculture system under Fusarium oxysporum f. sp. niveum invasion – Hongjie Yu et al. – Plant and Soil

Phosphorus-acquisition strategies of canola, wheat and barley in soil amended with sewage sludges – C. Nobile et al. – Scientific Reports

Water and extremophile microbiome

Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs – Zachary S. Cooper et al. – FEMS Microbiology Ecology

Performance and microbial communities of different biofilm membrane bioreactors with pre-anoxic tanks treating mariculture wastewater – Huining Zhang et al. – Bioresource Technology

Do organic substrates drive microbial community interactions in Arctic snow? – Benoît Bergk Pinto et al. – Frontiers in Microbiology

Genomic signatures for sedimentary microbial utilization of phytoplankton detritus in a fast-flowing estuary – Mariya W. Smit et al. – Frontiers in Microbiology

pH control and microbial community analysis with HCl or CO2 addition in H2-based autotrophic denitrification – Wei Xing et al. – Water Research

Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs – Eva Spieck et al. – The ISME Journal

Phages and viruses

** Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics – Vinicius S. Kavagutti et al. – Microbiome

Review: Phage Therapy with a Focus on the Human Microbiota – Sharita Divya Ganeshan & Zeinab Hosseinidoust – Antibiotics

Technology

Preprint: Gene copy normalization of the 16S rRNA gene cannot outweigh the methodological biases of sequencing – Robert Starke & Daniel Morais – bioRxiv

Review: Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing – Lauren M. Petersen et al. – Journal Clinical Microbiology

Microbes in the news

Which foods are beneficial for a healthy gut microbiome? – Ana Sandoiu – Medical News Today

Microbiome: Untapped source of novel antimicrobials – Delthia Ricks – Medical Xpress

The Problem With Labeling Gut Troubles ‘Dysbiosis’ – Elizabeth Preston – Undark

Bacteria for beauty: why you need to start thinking about your skin microbiome – Hannah Ebelthite – Telegraph

Research Finds These Mediterranean Diet Foods Protect The Gut Microbiome – Jamie Schneider – Mind Body Green

Are undiscovered antibiotics ‘silently waiting’ in our own bodies? Researchers scour microbiome for helpful genes – Shelly Fan – Genetic Literacy Project

Reprogramming the microbiome: Antara Lifesciences targets the human health space with dual targeted formulation – Tingmin Koe – Food Navigator Asia

Transient and long-term disruption of gut microbes after antibiotics – Jeff Hansen – UAB News

Microbes on the market

Microba, Psomagen Partner to Launch Microbiome Test in US – GenomeWeb

October 16, 2019

Happy Wednesday! Today’s digest includes the human gut virome, microbiome recovery after antibiotics, and the fungi growing on museum skeletons. Enjoy!

Pregnancy and early life

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn’s gut colonization – Dobbler – World Journal of Microbiology and Biotechnology

Human skin microbiome

In vitro Antimicrobial Activity of Acne Drugs Against Skin-Associated Bacteria – Blaskovich – Scientific Reports

Human gut microbiome

Review: The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific – Shkoporov – Cell Host & Microbe

Review: Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System – Yue – Microorganisms

Individualized recovery of gut microbial strains post antibiotics – Koo – npj Biofilms and Microbiomes

Animal experiments

Depletion of dietary aryl hydrocarbon receptor ligands alters microbiota composition and function – Brawner – Scientific Reports

Rat H1 parvovirus infection leads to alterations in gut microbiota – Xiang – Pathogens and Disease

Positive effect of an electrolyzed reduced water on gut permeability, fecal microbiota and liver in an animal model of Parkinson’s disease – Bordoni – PLoS One

The Sulfate-Reducing Microbial Communities and Meta-Analysis of Their Occurrence during Diseases of Small–Large Intestine Axis – Kushkevych – Journal of Clinical Medicine

Plant, root, and soil microbiome

Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities – Sengupta – Biogeosciences

Water and extremophile microbiome

Diversity, Distribution, and Ecology of Fungi in the Seasonal Snow of Antarctica – Menezes – Microorganisms

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process – Zhang – Environmental Microbiology

Built environment

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale – Valencia-Agami – Microorganisms

Increased loading leads to convergence of microbial communities and high methane yield in adapted anaerobic co-digesters – Wang – Water Research

Skeleton bones in museum indoor environments offer niches for fungi and are affected by weathering and deposition of secondary minerals – Pinzari – Environmental Microbiology

Bioinformatics

Species abundance information improves sequence taxonomy classification accuracy – Kaehler – Nature Communications