November 4, 2022

Today’s digest features a 30-color colorblind friendly color palette and functions for mapping color to hierarchical/nested data, ecosystem-specific reference databases, stoma samples for a very effective way of small intestinal microbiome characterization, and a reminder that 16S rRNA gene sequencing is NOT metagenomics. Happy Friday!

Join the next #MVIF when Sarah Lebeer will talk about citizen science and vaginal microbiome!!

Global resistome

Sharing of Antimicrobial Resistance Genes between Humans and Food Animals – Huiluo Cao – mSystems

Gut microbiome

Host-microbiome interactions: Gut-Liver axis and its connection with other organs – Swadha Anand & Sharmila S. Mande – npj Biofilms and Microbiomes

Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment – Alice Chen-Liaw – bioRxiv

Effects of different amoxicillin treatment durations on microbiome diversity and composition in the gut – Katrine Lekang – Plos One

The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons – Joseph J. Bruckner – Plos Biology

Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants – Lauren C. Beck – Nature Microbiology

*Plasticity of the adult human small intestinal stoma microbiota – Bahtiyar Yilmaz – Cell Host & Microbe


Bioinformatics

MIDAS2: Metagenomic Intra-species Diversity Analysis System – Chunyu Zhao – Bioinformatics

Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data – Matteo Ciciani – Nature Communications

*microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data – Erin M. Dahl – Microbiology Resource Announcements

*Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling – Christina Karmisholt Overgaard – Frontiers in Microbiology


November 02, 2022

General microbiome

[RETRACTION]Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake – Ahmad et al. – PLOS One

Pregnancy and early life

A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning – Vatanen et al. – Clee

Multi-site human microbiome

[REVIEW]Recent advances in systemic lupus erythematosus and microbiota: from bench to bedside – Zhan et al. –

Human vaginal microbiome

Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics – France et al. – PLOS One

Human gut microbiome

Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia – Bernard-Raichon et al. – Nature Communications

Gut microbiota and myocardial fibrosis – Xu, Yang & Bao – European Journal of Pharmacology

Assessing the relationship between physical activity and the gut microbiome in a large, population-based sample of Wisconsin adults – Holzhausen et al. – PLOS One

Challenges and costs of donor screening for fecal microbiota transplantations – Bernard et al. – PLOS One

Animal microbiome

Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses – Cuesta et al. – Cell Host & Microbe

Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals – Koziol et al. – Microbiology Open

Understanding the Dynamic of POMS Infection and the Role of Microbiota Composition in the Survival of Pacific Oysters, Crassostrea gigas – Delisle et al. – Microbiology Spectrum

Changes in Gut Microbiota Structure: A Potential Pathway for Silver Nanoparticles to Affect the Host Metabolism – Wang et al. – ACS Nano

Skin microbiota of oxazolone-induced contact hypersensitivity mouse model – Mäenpää et al. – PLOS One

Effects of a farm-specific fecal microbial transplant (FMT) product on clinical outcomes and fecal microbiome composition in preweaned dairy calves – Slanzon et al. – PLOS One

Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes – Gil & Hird – Microbiology Spectrum

Uropygial gland microbiota differ between free-living and captive songbirds – Grieves et al. – Scientific Reports

Plant, root, and soil microbiome

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere – Muscatt et al. – Microbiome

Bioinformatics

CRAMdb: a comprehensive database for composition and roles of microbiome in animals – Lei et al. – NAR

Techniques

DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes – Brauer & Bengtsson – Microbiology Open

synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing – Zaramela et al. – mSystems

October 26, 2022

General microbiome

[BOOK]Human Microbiome in Health and Disease – Part B – Progress in Molecular Biology and Translational Science

Pregnancy and early life

Relationships of the very low birth weight infant microbiome with neurodevelopment at 2 and 4 years of age – Sarkar et al. – Developmental Psychobiology

Human respiratory microbiome

The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis – Knudsen et al. – Microbiome

Human gut microbiome

Profiling the fungal microbiome after FMT for graft-versus-host disease: insights from a phase 1 interventional study – van Lier et al. – Transplantation and Cellular Therapy

Colorectal cancer, Vitamin D and microbiota: A double-blind Phase II randomized trial (ColoViD) in colorectal cancer patients – Bellerba et al. – Neoplasia

Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome – Piancone et al. – Scientific Reports

Animal microbiome

[DATA]Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages – Feng et al. – Scientific data

Tick transmission of Borrelia burgdorferi to the murine host is not influenced by environmentally acquired midgut microbiota – Narasimhan et al. – Microbiome

Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis – Bianchimano et al. – Microbiome

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds – Navine et al. – Molecular Ecology

Impact of Germinated Brown Rice and Brown Rice on Metabolism, Inflammation, and Gut Microbiome in High Fat Diet-Induced Insulin Resistant Mice – Zhao et al. – J. Agric. Food Chem.

Dietary Lactobacillus reuteri prevent from inflammation mediated apoptosis of liver via improving intestinal microbiota and bile acid metabolism – Lin et al. – Food Chemistry

Plant, root, and soil microbiome

Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin – Wen et al. – Microbiome

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction – Tom et al. – Microbiome

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

Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary – Guo et al. – Science of The Total Environment

Bioinformatics

LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis – Özkurt et al. – Microbiome

Techniques

[PREPRINT]Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes – McCully et al. – bioRxiv

A novel metagenome-derived viral RNA polymerase and its application in a cell-free expression system for metagenome screening – Han et al. – Scientif Reports

October 24, 2022

Human and General Microbiome

The Association Between Microplastics and Microbiota in Placentas and Meconium: The First Evidence in Humans – Shaojie Liu – Environmental Science & Technology

The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations – Xinwei Ruan – NPJ Biofilms and Microbiomes

Role of mucus-bacteria interactions in Enterotoxigenic Escherichia coli (ETEC) H10407 virulence and interplay with human microbiome – Thomas Sauvaitre – NPJ Biofilms and Microbiomes

Commensal oral microbiota impacts ulcerative oral mucositis clinical course in allogeneic stem cell transplant recipients – Julia S Bruno – Scientific Reports

Review: Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications – Raphaela I Lau – Nature Reviews. Gastroenterology & Hepatology

Review: The microbiota and aging microenvironment in pancreatic cancer: Cell origin and fate – Zhou Chen – Biochimica et Biophysica Acta

Review: New perspectives into the vaginal microbiome with systems biology – Christina Y Lee – Trends in Microbiology

Beneficial Microbes and Compounds

Oral supplementation with selected Lactobacillus acidophilus triggers IL-17-dependent innate defense response, activation of innate lymphoid cells type 3 and improves colitis – Jiří Hrdý – Scientific Reports

Animal Model Microbiome

The Benefits of Switching to a Healthy Diet on Metabolic, Cognitive and Gut Microbiome Parameters are Preserved in Adult Rat Offspring of Mothers Fed a High-Fat, High-Sugar Diet – Michael D Kendig – Molecular Nutrition & Food Research

Jatrorrhizine alleviates ulcerative colitis via regulating gut microbiota and NOS2 expression – Jia Ling Zhang – Gut Pathogens

Non-Model Animal Microbiome

Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan – Yoshiaki Sato – Microbes and Environments

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium – Yui Sato – Microbiome

Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages – Lei Feng – Scientific data

Screening Salamanders for Symbionts – Elli Vickers – Methods in Molecular Biology

Gut microbiota differs between two cold-climate lizards distributed in thermally different regions – Jun-Qiong Chen – BMC Ecology and Evolution

Microbial community in resistant and susceptible Churra sheep infected by Teladorsagia circumcincta – Verónica Castilla Gómez de Agüero – Scientific Reports

Genome Evolution of a Symbiont Population for Pathogen Defence in Honeybees – Karl Dyrhage – Genome Biology and Evolution

Plant Microbiome

Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome – Jonathan M Conway – Nature Microbiology

Phytohormones producing rhizobacteria alleviate heavy metals stress in soybean through multilayered response –  Husna – Microbiological Research

Review: Linking plant functional genes to rhizosphere microbes: a review – Qi Liu – Plant Biotechnology Journal

Bioinformatics and Microbiome Analysis Techniques 

Resampling-based inferences for compositional regression with application to beef cattle microbiomes – Sujin Lee – Statistical Methods in Medical Research

Review: Methods used for the study of endophytic fungi: a review on methodologies and challenges, and associated tips – Jefferson Brendon Almeida Dos Reis – Archives of Microbiology

October 12, 2022

General microbiome

Global airborne bacterial community—interactions with Earth’s microbiomes and anthropogenic activities – Zhao et al. – PNAS

Tumor microbiome links cellular programs and immunity in pancreatic cancer – Cancer Cell – Ghaddar et al. – Cancer Cell

Human wound microbiome

The Wound Microbiome – White & Grice – Cold Spring Harbor Perspectives in Biology

Human gut microbiome

Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke – Zhou et al. – Journal of Translational Medicine volume

Gut-Testis Axis: Microbiota Prime Metabolome To Increase Sperm Quality in Young Type 2 Diabetes – Yan et al. – Microbiology Spectrum

Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups – West et al. – Scientific Reports

[REVIEW]The role of the gut microbiota in health and cardiovascular diseases – Wang et al. – Molecular Biomedicine

Animal microbiome

Airborne polystyrene microplastics and nanoplastics induce nasal and lung microbial dysbiosis in mice – Zha et al. – Chemosphere

Effects of urban particulate matter on gut microbiome and partial schizophrenia-like symptoms in mice: Evidence from shotgun metagenomic and metabolomic profiling – Yi et al. – Science of The Total Environment

Lactococcus lactis’ Effect on the Intestinal Microbiota of Streptococcus agalactiae-Infected Zebrafish (Danio rerio) – Tan et al. – Microbiology Spectrum

Exploring AI-2-mediated interspecies communications within rumen microbial communities – Liu et al. – Microbiome

Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions – Martinez-Alvaro et al. – Microbiome

Chicken intestinal microbiota modulation of resistance to nephropathogenic infectious bronchitis virus infection through IFN-I – Yin et al. – Microbiome

Plant, root, and soil microbiome

[CORRESONDENCE]Functionally-explicit sampling can answer key questions about the specificity of plant–microbe interactions – Fleishman et al. – Environmental Microbiome

Dissecting the cotranscriptome landscape of plants and their microbiota – Nobori et al. – EMBO Reports

Bioinformatics

MiMeDB: the Human Microbial Metabolome Database – Wishart et al. – NAR

gutMDisorder v2.0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions – Qi et al. – NAR

October 10, 2022

Human and General Microbiome

The hallmarks of dietary intervention-resilient gut microbiome – Natalia S Klimenko – NPJ Biofilms and Microbiomes

Nutrition and Microbiome Interactions in Human Cancer – Phillip J Daschner – Journal of the Academy of Nutrition and Dietetics

Differences in the microbiota of oral rinse, lesion, and normal site samples from patients with mucosal abnormalities on the tongue – Yawaka Shitozawa – Scientific Reports

Dynamic changes in host immune system and gut microbiota are associated with the production of SARS-CoV-2 antibodies – Maozhen Han – Gut

Antibiotics and probiotics impact gut antimicrobial resistance gene reservoir in COVID-19 patients – Qi Su – Gut Microbes

Fibre is good for the microbiome: but what is the evidence? – Kevin Whelan – The Lancet. Gastroenterology & Hepatology

Model Animal Microbiome

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities – Afrizal Afrizal – Cell Host & Microbe

Non-Model Animal Microbiome

Convergent evolution of the gut microbiome in marine carnivores – Xibao Wang – Ecology and Evolution

Gut microbiota shift in layer pullets fed on black soldier fly larvae-based feeds towards enhancing healthy gut microbial community – Evalyne W Ndotono – Scientific Reports

Succession of the intestinal bacterial community in Pacific bluefin tuna (Thunnus orientalis) larvae – Akito Taniguchi – PloS One

Plant Microbiome

Bacterial community in soil and tree roots of Picea abies shows little response to clearcutting – Tijana Martinović – FEMS Microbiology Ecology

Environmental Microbiome

Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea – Jianchang Tao – Scientific Data

Food Microbiome

Microbiome of rehydrated corn and sorghum grain silages treated with microbial inoculants in different fermentation periods – Mariele Cristina Nascimento Agarussi – Scientific Reports

Microbiome Analysis

Quantification and characterization of mouse and human tissue-resident microbiota by qPCR and 16S sequencing – Bingqing Yao – STAR Protocols

October 3, 2022

Human and General Microbiome

Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease – Eiko Hayase – Cell

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions – Lian Narunsky-Haziza – Cell

A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors – Anders B Dohlman – Cell

Gut microbiota of hepatitis B virus-infected patients in the immune-tolerant and immune-active phases and their implications in metabolite changes – Ya-Nan Li – World Journal of Gastroenterology

Streptococcus mutans promotes tumor progression in oral squamous cell carcinoma – Ming-Shao Tsai – Journal of Cancer

Short-chain fatty acid concentrations in the incidence and risk-stratification of colorectal cancer: a systematic review and meta-analysis – Ehsan Alvandi – BMC Medicine

Mycobacterium potentiates protection from colorectal cancer by gut microbial alterations – Yu-Mi Kim – Immunology

Nutrition, Immunosenescence, and Infectious Disease: An Overview of the Scientific Evidence on Micronutrients and on Modulation of the Gut Microbiota – Philip C Calder – Advances in Nutrition 

Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients – Heather K Armstrong – Gastroenterology

Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects – Andrea McDowell – Experimental & Molecular Medicine

Microbiome ethics, guiding principles for microbiome research, use and knowledge management – Lene Lange – Environmental Microbiome

Review: The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly – Fen Zhang – The Lancet. Microbe

Beneficial Microbes and Compounds

Review: Tailoring gut microbiota with a combination of Vitamin K and probiotics as a possible adjuvant in the treatment of rheumatic arthritis: a systematic review – Luciana Pereira – Clinical Nutrition ESPEN

Dietary Isoflavones Alter Gut Microbiota and Lipopolysaccharide Biosynthesis to Reduce Inflammation – Sudeep Ghimire – Gut Microbes

Bacteroides thetaiotaomicron rough-type lipopolysaccharide: The chemical structure and the immunological activity – Molly Dorothy Pither – Carbohydrate Polymers

Animal Microbiome

Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis – Aida Daugaliyeva – Scientific Reports

Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi – Corey C Holt – Microbiome

Plant Microbiome

Review: Microbiomes in agroecosystem: Diversity, function and assembly mechanisms – Chao Xiong – Environmental Microbiology Reports

Bioinformatics and Microbiome Analysis

Integrating Phylogenetic and Functional Data in Microbiome Studies – Gavin M Douglas – Bioinformatics 

Higher off-target amplicon detection rate in MiSeq v3 compared to v2 reagent kits in the context of 16S-rRNA-sequencing – Mari-Lee Odendaal – Scientific Reports

September 28, 2022

General microbiome

[Personal View]Causal discovery for the microbiome – Corander, Hanage & Pensar – The Lancet Microbe

Integrative functional analysis uncovers metabolic differences between Candida species – Begum et al. – Communications Biology

Human skin microbiome

Evolution of the facial skin microbiome during puberty in normal and acne skin – Schneider et al. – JEADV

Human gut microbiome

[REVIEW]Harnessing Microbiota to Improve Immunotherapy for Gastrointestinal Cancers – Goc & Sonnenberg – Cancer Immunol Res

[REVIEW]Gut microbiome in multiple sclerosis-related cognitive impairment – Ghadiri et al. – Multiple Sclerosis and Related Disorders

[REVIEW]The Microbiome in Gastrointestinal Cancers – White & Wargo – Gastroenterology Clinics of North America

Human gut microbiota and its metabolites impact immune responses in COVID-19 and its complications – Nagata et al. – Gastroenterology

Gut microbial fermentation promotes the intestinal anti-inflammatory activity of Chinese yam polysaccharides – Bai et al. – Food Chemistry

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

The preventive effects of probiotic Akkermansia muciniphila on D-galactose/AlCl3 mediated Alzheimer’s disease-like rats – He et al. – Experimental Gerontology

Characterizing the chicken gut colonization ability of a diverse group of bacteria – Poudel et al. – Poultry Science

Obesity induced gut dysbiosis contributes to disease severity in an animal model of multiple sclerosis – Shahi et al. – Front. Immunol.

Animal microbiome (for animals in the wild)

Impact of aluminum exposure on oxidative stress, intestinal changes and immune responses in red swamp crayfish (Procambarus clarkii) – Zhang et al. – Science of The Total Environment

Network analysis reveals significant joint effects of microplastics and tetracycline on the gut than the gill microbiome of marine medaka – Liao et al. – Journal of Hazardous Materials

Xenobiotic estradiol-17ß alters gut microbiota of hatchling American Alligators (Alligator mississippiensis) – Murphy et al. – Environmental Microbiology

Sustained Drought, but Not Short-Term Warming, Alters the Gut Microbiomes of Wild Anolis Lizards – Williams et al. – Applied and Environmental Microbiology

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

Microbial Composition of Freshwater Marsh Sediment Responds more Strongly to Microcosm Seawater Addition than Simulated Nitrate or Phosphate Eutrophication – Weingarten & Jackson – Microbial Ecology

Built environment (subways, indoor surfaces)

Microbial community regulation and performance enhancement in gas biofilters by interrupting bacterial communication – Wang et al. – Microbiome

Bioinformatics

Identification of microbial features in multivariate regression under false discovery rate control – Srinivasan, Xue and Zhan – Computational Statistics & Data Analysis

Techniques

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oyewole et al. – Microbiome

September 24, 2022

Human and General Microbiome

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients – Thomas Vogl – Science Advances

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oluwaseun Rume-Abiola Oyewole – Microbiome

Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis – Victoria M Martin – Microbiome

Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism – Peter Spanogiannopoulos – Nature Microbiology

Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome – Rebecca C Simpson – Nature Medicine

Advances in the gut microbiome and mood disorders – Sabrina Mörkl – Current Opinion in Psychiatry

Review: Modulation of the intestinal microbiota impacts the efficacy of immunotherapy in cancer patients – A recent literature survey – Stella Ziegler – European Journal of Microbiology & Immunology

Animal Microbiome

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome – Tina Keller-Costa – Microbiome

Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis – Qian Zhou – Microbiome

Plant Microbiome

Response of soil microecology to different cropping practice under Bupleurum chinense cultivation – Li Liu – BMC Microbiology

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland – Jie Li – Microbiology Spectrum

Review: Investigating plant-microbe interactions within the root – Yuniar Devi Utami – Archives of Microbiology

Food Microbiome

Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation – Yuwei Tan – Microbiology Spectrum

More Microbes

A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis – Simon Mills – NPJ Biofilms and Microbiomes

Bioinformatics and Microbiome Analysis

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes – Lin Zhang – PLoS Computational Biology

September 22, 2022

Happy almost Friday! Today’s digest includes a time series tracking changes after fecal transplant, biofilm-formation analysis from isolations from swine slaughterhouses as well as techniques to improve computational notebooks, rapid genotyping, and more.

Enjoy!

Human gut microbiome

Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains – Koo & Morrow – PLOS One

Animal experiments

Microbiome complexity shapes metabolism – Litichevskiy & Thaiss – PLOS Biology

Minimal overall divergence of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes despite potential adaptive enrichment for scale-eating – Heras & Martin – PLOS One

Molecular characterization and biofilm-formation analysis of Listeria monocytogenes, Salmonella spp., and Escherichia coli isolated from Brazilian swine slaughterhouses – Santos et al. – PLOS One

Animal microbiome

Ecology and distribution of Leptospira spp., reservoir hosts and environmental interaction in Sri Lanka, with identification of a new strain – Sluydts et al. – PLOS Neglected Tropical Diseases

Techniques

A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research – Figueiredo et al. – PLOS Computational Biology

Bacterial concentration and Campylobacter spp. quantification differ when fresh or ultra-frozen samples are analysed over time using molecular biology and culture-based methods – Khattak et al. – Plos One

Robust inference of population size histories from genomic sequencing data – Upadhya & Steinrücken – PLOS Computational Biology

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data – Váradi et al. – PLOS One

Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods – Xue & Marco – PLOS ONE