August 4, 2020

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

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

General microbiome

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

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

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

Multi-site human microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

August 3, 2020

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

Covid-19

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

Human Microbiome: brain, gut, fecal and oral

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

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

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

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

Plant, root and soil microbiome

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

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

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

Environmental microbiology

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

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

August 1, 2020

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

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

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

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

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

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

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

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

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


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

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


Plant, root, and soil microbiome

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

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

July 24, 2020

Good afternoon all!

Today’s digest is a bit on the lighter side, nevertheless, there are some great papers to sink your teeth into.

Those with an interest in tropical diseases will want to read an investigation into the three-way relationship between humans, their microbiotas and the protozoan cause of Chagas disease.

History buffs, and fans of the epic novel ‘Romance of the Three Kingdoms’ may be interested by an analysis of the soil microbiome of the Jinsha relic, which is found at the site of the former Chinese Shu state capital.

For those more philosophically inclined, there is an interesting discussion on the impact of human space activity on the search for extra-terrestrial life. So that’s ancient history and space-age wizardry all covered in today’s rather modest digest. What more could you want?!

COVID-19

Preprint: Rapid in vitro assays for screening neutralizing antibodies and antivirals against SARS-CoV-2 – Oark et al.

Preprint: The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner – Ogawa et al.

Preprint: Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants – Weisblum et al.

General microbiome

Mapping of host-parasite-microbiome interactions reveals metabolic determinants of tropism and tolerance in Chagas disease – Hossain et al.Science Advances

Animal experiments

Host immunity and the colon microbiota of mice infected with Citrobacter rodentium are beneficially modulated by lipid-soluble extract from late-cutting alfalfa in the early stages of infection – Fries-Craft et al.PLOS One

Plant, root, and soil microbiome

Diversity and structure of soil microbiota of the Jinsha earthen relic – Yang et al.PLOS One

Quantitative detection of economically important Fusarium oxysporum f. sp. cubense strains in Africa in plants, soil and water – Matthews et al. – PLOS One

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina – Ettinger and Eisen – PLOS One

Techniques

Majority sensing in synthetic microbial consortia – Alnahhas et al. – Nature Communications

Microbes in the news

Should we disinfect outer space?: Jenna Sutela and Sophia Roosth in conversation – Sutela and Roosth – Art in America

July 23, 2020

In today’s digest – duodenal microbiota linked to stunting in children, differential effects of germfree and antibiotic treated mouse models on social behavior, microbial metabolite receptor GPBAR and its interaction with bile acids, review article on engineering microbes to treat diseases and many more…happy reading!

General microbiome

The Microbiota-Gut-Immune-Glia (MGIG) Axis in Major Depression – Leszek Rudzki – Molecular Neurobiology

Engineering the gut microbiota to treat chronic diseases – Noura S. Dosoky – Applied Microbiology and Biotechnology

Human microbiome

Acute and chronic improvement in postprandial glucose metabolism by a diet resembling the traditional Mediterranean dietary pattern: Can SCFAs play a role? – Marilena Vitale – Clinical Nutrition

Linking the duodenal microbiota to stunting in a cohort of undernourished Bangladeshi children with enteropathy – Robert Y. Chen – New England Journal of Medicine

Enterobacterales Infection after Intestinal Dominance in Hospitalized Patients – Krishna Rao – mSphere

Differences in the gut Firmicutes to Bacteroidetes ratio across age groups in healthy Ukrainian population – Alexander Vaiserman – BMC Microbiology

Preprint- Association of gut microbiota with cerebral cortex and cerebrovascular abnormality in human mild traumatic brain injury – Lijun Bai – BioRxiv

Real-world study in infants fed an infant formula with two human milk oligosaccharides – Enriqueta Román – Nutricion Hospitalaria

Animal experiments

Gut microbiome composition differences among breeds impact feed efficiency in swine – Matteo Bergamaschi – Microbiome

Opposing effects of antibiotics and germ-free status on neuropeptide systems involved in social behaviour and pain regulation – Katerina V. A. Johnson – BMC Neuroscience

Local Necrotic Cells Trigger Systemic Immune Activation via Gut Microbiome Dysbiosis in Drosophila – Hina Kosakamoto – Cell Reports

Peanut skin extract ameliorates the symptoms of type 2 diabetes mellitus in mice by alleviating inflammation and maintaining gut microbiota homeostasis – Lan Xiang – Aging

Preprint- Community composition and development of the post-weaning piglet gut microbiome – D. Gaio – BioRxiv

Gut microbiota regulate tumor metastasis via circRNA/miRNA networks – Zhuxian Zhua – Gut Microbes

Porcine circovirus type 2 (PCV2) and Campylobacter infection induce diarrhea in piglets: Microbial dysbiosis and intestinal disorder – Gang Yang – Animal Nutrition

Plant, root and soil microbiome

Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota – Sarah Huet – Frontiers in Plant Science

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat – Aymé Spor – Scientific Reports

Water microbiome

Preprint- Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs – A. Meziti – BioRxiv

Preprint- Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing – Kimothy L. Smith – BioRxiv

Phages and Viruses

Preprint- Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract – Sabrina I. Green – BioRxiv

Techniques
Structural basis of GPBAR activation and bile acid recognition – Fan Yang – Nature

Microbes in News

Machine learning analysis reveals less diverse microbiome in children with type 1 diabetes – Healio

July 22, 2020

Human microbiome

The Urinary Tract Microbiome in Older Women Exhibits Host Genetic and Environmental Influences – Adebayo et al. – Cell Host & Microbe

The vaginal microbiome as a predictor for outcome of in vitro fertilization with or without intracytoplasmic sperm injection: a prospective study – Koedooder et al. – Human reproduction

Comparison of Meconium Microbiome in Dizygotic and Monozygotic Twins Born by Caesarean Section (CS) – Yang et al. – Frontiers in Microbiology

Gut microbiome

Autoreactivity in naïve human fetal B cells is associated with commensal bacteria recognition – Chen et al. – Science

Prenatal stress increases IgA coating of offspring microbiota and exacerbates necrotizing enterocolitis-like injury in a sex-dependent manner – Brawner et al. – Brain, Behavior, and Immunity

General microbiome

* Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts – McLean et al. – Cell Reports

July 21, 2020

Hello! We are in the midst of an unprecedented heat wave here in Western New York and I hope everyone is enjoying summer in the northern hemisphere. In todays post there is an interesting article by Kyung-Eon Lee, et al on the extracellular vesicle of a gut microbe Paenalcaligenes hominis as a risk factor for vagus nerve-mediated cognitive impairment. There also is a preprint on parthenogenesis in weevils as a possible Wolbachia-density dependent trait to ponder as well as a look at the experimental approaches to investigating the vaginal biofilm microbiome. Enjoy!

COVID-19

Preprint: ACE2-independent interaction of SARS-CoV-2 spike protein to human epithelial cells can be inhibited by unfractionated heparin. Lynda J Partridge, et al. bioRxiv

SARS-CoV-2 is not present in the vaginal fluid of pregnant women with COVID-19. MM Aslan, et al. – The Journal of Maternal…

GENERAL MICROBIOME

Preprint: Targeting methionine synthase in a fungal pathogen causes a metabolic imbalance that impacts cell energetics, growth and virulence. Jennifer Scott, et al. bioRxiv

HUMAN SKIN MICROBIOME

News Article: All-Natural Soap For Nourished And Balanced Microbiome Product Launched

HUMAN VAGINAL MICROBIOME

Experimental approaches to investigating the vaginal biofilm microbiome. PubMed – NIH

HUMAN GUT MICROBIOME

The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment. Kyung-Eon Lee, et al. Microbiome

Evolution of Gut Microbiome and Metabolome in Suspected Necrotizing Enterocolitis. MDPI

[PDF] Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study. T Sainz,et al. – Nutrients

ANIMAL MICROBIOME

Preprint: Parthenogenesis in weevils of the tribe Naupactini (Coleoptera, Curculionidae): a Wolbachia-density dependent trait?Marcela Silvina Rodriguero, et al. bioRxiv

PLANT, ROOT AND SOIL MICROBIOME

Preprint: Humic acids enrich the plant microbiota with bacterial candidates for the suppression of pathogens. Maura SRA Silva, et al. bioRxiv

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt. J Yuan, et al. – The ISME Journal

ANIMAL EXPERIMENTS

The gut microbiota of brood parasite and host nestlings reared within the same environment: disentangling genetic and environmental effects. CY Lee, et al. – The ISME Journal

TECHNIQUES

Two possible candidate enzymes from Ulva lactuca-associated epiphytic bacteria obtained through PCR and functional evaluation. JS Ruiz-Toquica, et al. – Universitas Scientiarum

WATER AND EXTREMOPHILE MICROBIOME

Genomic insights into the salt tolerance and cold adaptation of Planococcus halotolerans SCU63 T. L Gan, et al. – Archives of Microbiology

PROBIOTICS / PREBIOTICS

The Benefits of Probiotic Interventions in Maternal-Fetal Health: An Appraise Review. P Dhillon, et al. – PharmaNutrition

PHAGES AND VIRUSES

[PDF] Low Host Abundance and High Temperature Determine Switching from Lytic to Lysogenic Cycles in Planktonic Microbial Communities in a Tropical Sea (Red Sea). R Abdulrahman Ashy, et al. – Viruses

July 18, 2020

Have a nice weekend! Today, in this Digest: microbiome in psoriasis, cancer and a set of papers about vaginal microbiome.  

Human and General Microbiome

The cutaneous and intestinal microbiome in psoriatic disease – Stephanie T. Lea – Clinical Immunology

Microbiome-induced antigen presenting cell recruitment coordinates skin and lung allergic inflammation – Niki D. Ubags – Journal of Allergy and Clinical Immunology

Butyrate, but not Propionate, Reverses Maternal Diet-Induced Neurocognitive Deficits in Offspring – Linchao Yu – Pharmacological Research

Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function – Devin R. Leopold – Current Biology

Characterization of gut contractility and microbiota in patients with severe chronic constipation – Dina R. Yarullina – PLoS ONE

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron – Daniel Ryan – Nature Communications 

Bacteria pathogens drive host colonic epithelial cell promoter hypermethylation of tumor suppressor genes in colorectal cancer – Xiaoxuan Xia – Microbiome

Vaginal microbiome analysis of healthy women during different periods of gestation – Dan Li – Bioscience Reports

The Gut Microbiome as a Component of the Gut-Brain Axis in Cognitive Health – Wen Gao – Biological Research For Nursing 

The Effect of Gut Microbiome on Carcinogenic DNA Damage – Yun-Chung Hsiao – Chemical Research in Toxicology

The effect of curative resection on fecal microbiota in patients with colorectal cancer: a prospective pilot study – Sung Sil Park – Annals of Surgical Treatment and Research

Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer – Travis T Sims – International Journal of Gynecological Cancer

Gut microbial composition changes in bladder cancer patients: A case-control study in Harbin, China – Canxia He –  Asia Pacific Journal of Clinical Nutrition

Beneficial Microbes, Interventions, and Compounds

A 4-strain Probiotic Supplement Influences Gut Microbiota Composition and Gut Wall Function in Patients with Ulcerative Colitis – Jonas Ghyselinck – International Journal of Pharmaceutics

Systematic Review: Probiotics for induction of remission in Crohn’s disease – Berkeley N Limketkai – Cochrane Systematic Review

Human milk and mucosa-associated disaccharides impact on cultured infant fecal microbiota – Antonio Rubio-del-Campo – Scientific Reports 

YYFZBJS ameliorates colorectal cancer progression in ApcMin/+ mice by remodeling gut microbiota and inhibiting regulatory T-cell generation – Hua Sui – Cell Communication and Signaling 

Challenges of Screening Prospective Stool Donors for Fecal Microbiota Transplantation – Nancy E. Dubois – Biological Research For Nursing

Effects of banana powder (Musa acuminata Colla) on the composition of human fecal microbiota and metabolic output using in vitro fermentation – Dan‐Dan Tian – Journal of Food Science

COVID-19 Papers

ACE2 and TMPRSS2 expression by clinical, HLA, immune, and microbial correlates across 34 human cancers and matched normal tissues: implications for SARS-CoV-2 COVID-19 – Riyue Bao – Journal of ImmunoTheraphy of Cancer

July 17, 2020

Human microbiome

Covid-19: disinfectants and sanitisers are changing microbiomes. Ajit Singh.
BMJ.

Probiotics and COVID-19: one size does not fit all. Joyce WY Mak. The Lancet Gastroenterology & Hepatology.

Probiotics and COVID-19. Eric Giannoni. The Lancet Gastroenterology & Hepatology.

Animal microbiome
The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid-Type I IFN Signaling Axis. Emma S. Winkler.Cell

Built-in environment
Bed bugs shape the indoor microbial community composition of infested homes. Madhavi L.Kakumanua. Science of the Total Environment.

Pre-print
Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. Laura Glendinning. bioRxiv.

Microbial Diversity of Co-occurring Heterotrophs in Cultures of Marine Picocyanobacteria. Sean Michael Kearney. bioRxiv

Microbes in the news
The human microbiome: Everything you need to know about the 39 trillion microbes that call our bodies home. Mun-Keat Looi. ScienceFocus

July 16, 2020

Greeting everyone from the boiling hell southern Spain tourns every Summer.

Today we have a lot of soil microbiome in general. Also PARGT, a new software tool for predicting antimicrobial resistance in bacteria. And new insight in the relatioship between blood type and bacteria.

General microbiome

Blood type and the microbiome- untangling a complex relationship with lessons from pathogens – Kathleen L Arnolds et al. – Current Opinion in Microbiology

In vivo synthesis of bacterial amyloid curli contributes to joint inflammation during S. Typhimurium infection – Amanda L. Miller et al. – PLOS PATHOGENS

Human respiratory microbiome

Proteomic advances in salivary diagnostics – Eftychia Pappa et al. – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

Human gut microbiome

The Influence of Gut and Tumor Microbiome on Pancreatic Cancer Outcomes – Natalia Khalaf MD et al. – Gastroenterology

Animal microbiome

Inulin alleviates hypersaline-stress induced oxidative stress and dysbiosis of gut microbiota in Nile tilapia (Oreochromis niloticus) – Li Zhou et al. – Aquaculture

Water and extremophile microbiome

Microbial Community Composition and Function in Sediments from the Pearl River Mouth Basin – Ye Chen et al.Journal of Ocean University of China

Protist Interactions and Seasonal Dynamics in the Coast of Yantai, Northern Yellow Sea of China as Revealed by Metabarcoding – Yingjun Fu etl al. – Journal of Ocean University of China volume

Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming – Zhen-Zhen Zheng et al. – Nature Communications

Pre-print Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance – Ankita Kothari et al. – bioRxiv

Plant, root, and soil microbiome

Review – Can interaction between silicon and non–rhizobial bacteria benefit in improving nodulation and nitrogen fixation in salinity–stressed legumes? A review – Hassan Etesami – Rhizosphere

Reductive soil disinfestation incorporated with organic residue combination significantly improves soil microbial activity and functional diversity than sole residue incorporation – Jun Zhao et al. – Applied Microbiology and Biotechnology

Microbial clicks and combobulation: integrating microbes without passports and visas for managing soilborne diseases – Sanogo Soum –
Archives of Phytopathology and Plant Protection

Arbuscular mycorrhizal fungi improve mineral nutrition and tolerance of olive tree to Verticillium wilt – Boutaj Hanane – Archives of Phytopathology and Plant Protection

Responses of microbial communities and metabolic activities in the rhizosphere during phytoremediation of Cd-contaminated soil – Chenjing Liu et al. – Ecotoxicology and Environmental Safety

MnO2/tourmaline composites as efficient cathodic catalysts enhance bioelectroremediation of contaminated river sediment and shape biofilm microbiomes in sediment microbial fuel cells – Wei Li et al. – Applied Catalysis B: Environmental

Reductive soil disinfestation incorporated with organic residue combination significantly improves soil microbial activity and functional diversity than sole residue incorporation – Jun Zhao et al. Applied Microbiology and Biotechnology

Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond – Wen-hua Zhou et al. – Applied Microbiology and Biotechnology

Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses – Mary Donato et al. – PLOS ONE

Built environment

Identification of sulfate-reducing and methanogenic microbial taxa in anaerobic bioreactors from industrial wastewater treatment plants using next-generation sequencing and gene clone library analyses – Jantharadej, Krittayapong et al. – Journal of Environmental Science and Health

Determination of the inhibitory concentration level of fat, oil, and grease (FOG) towards bacterial and archaeal communities in anaerobic digestion – Muhammad Usman et al. – Renewable and Sustainable Energy Reviews

Bioinformatics

PARGT: a software tool for predicting antimicrobial resistance in bacteria – Abu Sayed chowdhury et al. – Scientific Reports

Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing – Phillip R. Myer et al. – PLOS ONE