July 13, 2022

Today’s digest features studies on the leaf-microbiome of 🍅 and 🍓 plants (+ bumblebees and mites), human gut and wastewater resistome, and more. Happy reading!

Reproductive tract

Female reproductive tract microbiota and recurrent pregnancy loss: a nested case-control study – Pirkko Peuranpää – Reproductive BioMedicine Online

Gut microbiome

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties – Sudarshan A. Shetty – Journal of the International Society for Microbial Ecology

*Within-patient evolution of plasmid-mediated antimicrobial resistance – Javier DelaFuente – bioRxiv

An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species – Sigal Leviatan – Nature Communications

Animal microbiome

Carpenter Bees (Xylocopa) Harbor a Distinctive Gut Microbiome Related to That of Honey Bees and Bumble Bees – Jo-anne C. Holley – Applied and Environmental Microbiology

Animal experiments

Gardnerella Exposures Alter Bladder Gene Expression and Augment Uropathogenic Escherichia coli Urinary Tract Infection in Mice – Nicole M. Gilbert – Frontiers in Cellular and Infection Microbiology

Plant microbiome

*The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites – Marie Legein – Microbiology Spectrum

Food microbiome

Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities – Christina C. Saak – bioRxiv

New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria – Muhammad Yasir – Food Research International

Water microbiome

*High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent – Kevin Kaibond Chau – bioRxiv

Pilot investigation on biostability of drinking water distribution systems under water source switching – Kejia Zhang – Applied Microbiology and Biotechnology

Bioinformatics

*BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J. Pavia – bioRxiv

getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories – Vincent Moco – BMC Bioinformatics

baseLess: Lightweight detection of sequences in raw MinION data – Ben Noordijk – bioRxiv

July 12, 2022

Human and General Microbiome

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections – Paula Hayakawa Serpa – Genome Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Man Kit Cheung – Journal of Gastroenterology and Hepatology

Altered Pattern of Immunoglobulin A-Targeted Microbiota in Inflammatory Bowel Disease After Fecal Transplantation – Wen-Qi Huang – Frontiers in Microbiology

16S rRNA gene sequencing reveals an altered composition of gut microbiota in children with Mycoplasma pneumoniae pneumonia treated with azithromycin – Qiong Deng – The Journal of General and Applied Microbiology

Clinical and metagenomic profiling of hormonal acne-prone skin in different populations – Nina Hrapovic – Journal of Cosmetic Dermatology

Microbiota diversity in nonalcoholic fatty liver disease and in drug-induced liver injury – Cristina Rodriguez-Diaza – Pharmacological Research

Beneficial Microbes and Compounds

Review: The potential role of prebiotics, probiotics, and synbiotics in adjuvant cancer therapy especially colorectal cancer – Zahoor Alam – Journal of Food Biochemistry

Review: Probiotics, prebiotics and postbiotics for better sleep quality: a narrative review – J E Haarhuis – Beneficial Microbes

Review: Gut Microbiota: A Novel Therapeutic Target for Parkinson’s Disease – Manlian Zhu – Frontiers in Immunology

Animal Model Microbiome

Obesity enriches for tumor protective microbial metabolites and treatment refractory cells to confer therapy resistance in PDAC – Kousik Kesh – Gut Microbes

Profiling of d-alanine production by the microbial isolates of rat gut microbiota – Cindy J. Lee – The FASEB Journal

Non-Model Animal Microbiome

Within-community variation of interspecific divergence patterns in passerine gut microbiota – Jan Kubovčiak – Ecology and Evolution

Bacteriophages

Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria – Brian Y. Hsueh – Nature Microbiology

Bioinformatics and Microbiome Analysis

Preprint: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning – Alex Chklovski – biorXiv

Cancer type classification using plasma cell-free RNAs derived from human and microbes – Shanwen Chen – eLife

Temporal Alignment of Longitudinal Microbiome Data – Ran Armoni – Frontiers in Microbiology

A Bottom-up Approach to Testing Hypotheses That Have a Branching Tree Dependence Structure, with Error Rate Control – Yunxiao Li – Journal of the American Statistical Association

July 9, 2022

Have a nice weekend! 

Human and General Microbiome

Review: Bladder cancer, inflammageing and microbiomes – Austin Martin – Nature Reviews. Urology

Review: Gut associated metabolites and their roles in Clostridioides difficile pathogenesis – Andrea Martinez Aguirre – Gut Microbes

Oral and gut dysbiosis leads to functional alterations in Parkinson’s disease – Sungyang Jo – NPJ Parkinson’s Disease

Transcriptional programming in a Bacteroides consortium – Brian D Huang – Nature Communications

Gut microbiota composition in colorectal cancer patients is genetically regulated – Francesca Colombo – Scientific Reports

Relative contributions of the host genome, microbiome, and environment to the metabolic profile – Kangjin Kim – Genes & Genomics

Beneficial Microbes and Compounds

Effects of probiotic Lactiplantibacillus plantarum IMC 510 supplementation on metabolic factors in otherwise healthy overweight and obese individuals – Maria Magdalena Coman – Journal of Applied Microbiology

Grape seed and skin extract, a potential prebiotic with anti-obesity effect through gut microbiota modulation – Mohamed Mokrani – Gut Pathogens

Lactobacillus acidophilus LA85 ameliorates cyclophosphamide-induced immunosuppression by modulating Notch and TLR4/NF-κB signal pathways and remodeling the gut microbiota – Liangyu Xue – Food & Function

Animal Model Microbiome

Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis – Anshul Sinha – Microbiome

Non-Model Animal Microbiome

Rickettsia helvetica infection is associated with microbiome modulation in Ixodes ricinus collected from humans in Serbia – Apolline Maitre – Scientific Reports

Environmental Microbiome

Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms – Javier Edo Varg – Environmental Microbiome

Estuarine plastisphere as an overlooked source of N(2)O production – Xiaoxuan Su – Nature Communications

Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics – Joon-Yong Lee – Journal of Proteome Research

Other

Privacy Risks in Microbiome Research: Public Perspectives before and during a Global Pandemic – Andrea Shin – Ethics & Human Research

Bioinformatics and Experimental Microbiome Analysis

Review: Metagenomics Approaches to Investigate the Neonatal Gut Microbiome – Zakia Boudar – Frontiers in Pediatrics

Editorial: Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes – Arwyn Edwards – Microbiology

A Bayesian method for identifying associations between response variables and bacterial community composition – Adrian Verster – PLoS Computational Biology

GenBank as a Source to Monitor and Analyze Host-Microbiome Data – Vivek Ramanan – Bioinformatics

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies – Hayley B Hassler – Microbiome

July 8, 2022

A selection of some great microbiome research and I’ve highlighted some resources for spatial transcriptomics for my non-microbiome picks.

General microbiome

Host control and the evolution of cooperation in host microbiomes – Sharp & Foster. Nature Communications

Effect of Helicobacter pylori Eradication on Gastric Cancer Prevention: Updated Report From a Randomized Controlled Trial With 26.5 Years of Follow-up – Yan et al. Gastroenterology

Gut microbiome

Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome – Xu et al. Microbiome

Long-Term Effects of Developmental Exposure to Oxycodone on Gut Microbiota and Relationship to Adult Behaviors and Metabolism – Lyu et al. mSystems

Biogeographic variation and functional pathways of the gut microbiota in celiac disease – Constante et al. Gastroenterology.

Animal experiments

Akkermansia muciniphila prevents cold-related atrial fibrillation in rats by modulation of TMAO induced cardiac pyroptosis – Luo et al. eBioMedicine

Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome – Machado et al. Cell Reports.

Virome

Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome – Jonge et al. Nature Communications

Respiratory microbiome

Host lung microbiota promotes malaria-associated acute respiratory distress syndrome – Mukherjee et al. Nature Communications

Bioinformatics

Super-taxon in human microbiome are identified to be associated with colorectal cancer – Dai et al. BMC Bioinformatics

Non-microbiome picks

As spatial transcriptomics grows in popularity you might be interested in some recent reviews & examples of the technology in use

An introduction to spatial transcriptomics for biomedical research – Williams et al. Genome Medicine

Deciphering tissue structure and function using spatial transcriptomics – Walker et al. Communications biology

Method of the Year: spatially resolved transcriptomics – Marx. Nature Methods

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays – Chen et al. Cell (The recent famous Cell cover using Stereo-Seq)

Museum of spatial transcriptomics – Moses & Pachter. Nature Methods

July 5, 2022

Highlights!

A volatile from the skin microbiota of flavivirus-infected hosts promotes mosquito attractiveness – Hong Zhang – Cell → The production of acetophenone, a potent attractant for mosquitoes, is induced by Flavivirus by a microbiota-based mechanism. This finding shows an interesting example of the interplay between certain viral agents and the microbiota to influence host susceptibility to interact with other species. 

Human and General Microbiome

Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID-19 and its Association with Microbiota in the Gut – Yifei Shen – Advanced Science

Interaction of n-3 polyunsaturated fatty acids with host CD36 genetic variant for gut microbiome and blood lipids in human cohorts – Zelei Miao – Clinical Nutrition 

A weight-loss model based on baseline microbiota and genetic scores for selection of dietary treatments in overweight and obese population – Amanda Cuevas-Sierra – Clinical Nutrition

Beneficial Microbes and Compounds

Restoration of cefixime-induced gut microbiota changes by a prebiotic blend in a mouse model – Jingyi Yuan – Applied Microbiology and Biotechnology

A synbiotics, long chain polyunsaturated fatty acids, and milk fat globule membranes supplemented formula modulates microbiota maturation and neurodevelopment – Tomás Cerdó – Clinical Nutrition

Animal Model Microbiome

Multi-omics data reveals the disturbance of glycerophospholipid metabolism caused by disordered gut microbiota in depressed mice – Tian Tian – Journal of Advanced Research

C-section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [clostridium] scindens in mice – Sean H Adams – Physiological Reports

A single respiratory tract infection early in life reroutes healthy microbiome development and affects adult metabolism in a preclinical animal model – Soner Yildiz – NPJ Biofilms and Microbiomes

Non-Model Animal Microbiome

Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis – Laura Baldassarre – Nature Communications

Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis – Ana Carolina Borsanelli – Microbial Ecology

Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria – Anna Voulgari-Kokota – Scientific Reports

Plant and Soil Microbiome

Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area – Gargi Das – Current Microbiology

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning – Kendra E Walters – The ISME Journal

Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.) – Davide Francioli – Scientific Reports

Bioinformatics and Microbiome Analysis

MB-SupCon: Microbiome-based predictive models via Supervised Contrastive Learning – Sen Yang – Journal of Molecular Biology

July 2, 2022

Have a nice weekend!

Highlights!

Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides – Miriam N. Ojima – The ISME Journalthis paper contributes to the understanding of the configuration of different bifidobacteria in response to human milk oligosaccharides. 

Genomes of six viruses that infect Asgard archaea from deep-sea sediments – Ian M. Rambo – Nature MicrobiologyBy using metagenomics, authors describe six relatively large viral genomes, capable to infect members of the Asgard superphylum. The paper remarks on the strange features found in those viral genomes.

TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila – Yaojiang Liu – MicrobiomeThis article demonstrates the existence of “a novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses”. 

Human and General Microbiome

Review: The microbiome and gut homeostasis – Jee-Yon Lee – Science 

Review: The role of microbiome: a novel insight into urolithiasis – Sen-Yuan Hong – Critical Reviews in Microbiology

Review: Symbiosis: the other cells in development – Tyler J Carrier – Development 

Dysbiosis of the Gut Microbiome Is Associated With Histopathology of Lung Cancer – Xiong Qin – Frontiers in Microbiology

Beneficial Microbes and Compounds

Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions – Sean M Gibbons – Advances in Nutrition

Akkermansia muciniphila Alters Gut Microbiota and Immune System to Improve Cardiovascular Diseases in Murine Model – Xin He – Frontiers in Microbiology

Impact of probiotics use on clinical outcomes of immune checkpoint inhibitors therapy in cancer patients – Luying Wan – Cancer Medicine

Review: The gut microbiome as possible mediator of the beneficial effects of very low calorie ketogenic diet on type 2 diabetes and obesity: a narrative review – G Defeudis – Eating and Weight Disorders

Animal Microbiome

The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction – Weiquan Wang – Nature Ecology & Evolution

Milk microbiomes of three great ape species vary among host species and over time – Sally L Bornbusch – Scientific Reports

Plant Microbiome

Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions – Malick Bill – Journal of Applied Microbiology

Environmental Microbiome

Review: Priorities for ocean microbiome research – the Tara Ocean Foundation – Nature Microbiology

Microbiome Analysis Techniques and Tools

Protocol for correlation analysis of the murine gut microbiome and meta-metabolome using 16S rDNA sequencing and UPLC-MS – Xiaoqing Li – STAR Protocols

microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization – Yang Cao – Bioinformatics

July 1, 2022

We made it to the end of the week, we made it through the end of June. To celebrate, check out the two (!) articles about the pig gut microbiome, try out a new tool for network analysis (MicNet Toolbox), or enjoy an NPR Short Waves podcast episode about Agar Art. Or maybe you’re spending the afternoon preparing a research talk or fieldwork event? If that’s the case, check out the article presenting 10 rules for improving communication among scientists or the one on the hidden labor of managing threats to safety by women in fieldwork.

General microbiome

Assessment of disinfectant efficacy in reducing microbial growth – Alajlan et al. – PLOS One

Animal experiments

Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses – Apiwatsiri et al. – PLOS One

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig – Gaio et al. – PLOS One

Preprint: Using axenic and gnotobiotic insects to examine the role of different microbes on the development and reproduction of the kissing bug Rhodnius prolixus (Hemiptera: Reduviidae) – Gilliland et al. – bioRxiv

Bioinformatics

MicNet toolbox: Visualizing and unraveling a microbial network – Favila et al. – PLOS One
Techniques

Evaluating the impact of sample storage, handling, and technical ability on the decay and recovery of SARS-CoV-2 in wastewater – Beattie et al. – PLOS One

Microbes in the news

NPR’s Short Wave Podcast: Let’s Get Crafty With Agar Art (11 minute episode)!

Science, publishing, and career

Ten simple rules for improving communication among scientists – Bautista et al. – PLOS Computational Biology

You can’t report your feelings: The hidden labor of managing threats to safety by women in global public health fieldwork – McAuliffe et al. – PLOS Global Public Health

June 29, 2022

General microbiome

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station – Urbaniak et al. – Microbiome

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology – Lai, Hayashi & Lu – Current Opinion in Chemical Biology

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom – Thomas et al. – Nature Communications

Human oral microbiome

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women – Kato et al. – BMC Oral Health

Human urinary microbiome

Concordance of Urinary Microbiota Detected by 16S rRNA Amplicon Sequencing Versus Expanded Quantitative Urine Culture – Vaughan et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Dietary variety relates to gut microbiota diversity and abundance in humans – Huang et al. – European Journal of Nutrition

The gut microbiota composition in patients with right- and left-sided colorectal cancer and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing – Suga et al. – BMC Gastroenterology

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis – Troci et al. – Molecular Nutrition & Food Research

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – Münzker et al. – Microbiome

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

Perinatal transmission of a probiotic Bifidobacterium strain protects against early life stress-induced mood and gastrointestinal motility disorders – Zhu et al. – Food & Function

Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder – Xu et al. – Microbiology Spectrum

Animal microbiome (for animals in the wild)

Gut microbiome of century-old snail specimens stable across time in preservation – Chalifour, Elder & Li – Microbiome

Plant, root, and soil microbiome

Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense – Zhang et al. – Microbiome

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

A genome and gene catalog of glacier microbiomes – Liu et al. – Nature Biotechnology

Bioinformatics / Data

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans – Lemos et al. – Scientific Data

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota – Campos et al. – Poultry Science

[PREPRINT]Predicting metabolomic profiles from microbial composition through neural ordinary differential equations – Wang et al. – bioRxiv

June 25, 2022

Highlights!

Microbiome-associated human genetic variants impact phenome-wide disease risk – Robert H George Markowitz – PNASIn this paper, the use of an integrative framework of case-control studies and extensive health records, authors could find associations between microbiome-associated variants (MAVs) and different phenotypes associated with human diseases.

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – Julia Münzker – Microbiome This study presents evidence for the role of the gut microbiome in the weight loss and metabolic success of gastric bypass surgery. The increment of taurine-conjugated bile acid species can activate systemic TGR5 signaling to stimulate adaptive thermogenesis, with consequences on the host metabolism.

Human and General Microbiome

Human gut microbiota composition and its predicted functional properties in people with western and healthy dietary patterns – Anna M Malinowska – European Journal of Nutrition

Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut – Kyung Hyun Kim – mSystems

Characteristics and interplay of esophageal microbiota in esophageal squamous cell carcinoma – Zheng Lin – BMC Cancer

Interactions among the mycobiome, bacteriome, inflammation, and diet in people living with HIV – María José Gosalbes – Gut Microbes

Disentangling the relationship of gut microbiota, functional gastrointestinal disorders and autism: a case-control study on prepubertal Chinese boys – Oscar W H Wong – Scientific Reports

Beneficial Microbes and Compounds

Dietary supplementation with biogenic selenium nanoparticles alleviate oxidative stress-induced intestinal barrier dysfunction – Lei Qiao – NPJ Science of Food

Non-Model Animal Microbiome

Glyphosate-based herbicide exposure: effects on gill microbiota of rainbow trout (Oncorhynchus mykiss) and the aquatic bacterial ecosystem – Laure Bellec – FEMS Microbiology Ecology

Social microbiota and social gland gene expression of worker honey bees by age and climate – Kirk E Anderson – Scientific Reports

Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research – T G Sumithra – Applied Microbiology and Biotechnology

Concept: Inter-individual variation in parasite manipulation of host phenotype: a role for parasite microbiomes? – Robert Poulin – The Journal of Animal Ecology

Environmental Microbiome

Review: A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses – Jean Legeay – Microbial Ecology

The influence of bioclimate on soil microbial communities of cork oak – Daniela Costa – BMC Microbiology

Techniques

Liposome Delivery of Nucleic Acids in Bacteria: Toward In Vivo Labeling of Human Microbiota – Luís Moreira – ACS Infectious Diseases

Other

Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics – Mayank Baranwal – eLife

June 24, 2022

Today we have a report in Science on bacterium which is 1cm long, a great review of the gut virome in human health, and a meta-analysis of mycobiota signatures in colorectcal cancer among some other great papers.

General microbiology

A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles – Volland et al. – Science

Virome

Filamentous bacteriophage delays healing of Pseudomonas-infected wounds – Bach et al. – Cell Reports Medicine

[REVIEW] The gut virome: A new microbiome component in health and disease – Cao et al. – eBioMedicine

Gut Microbiome

Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function – Mayneris-Perxachs et al. – ISME

Altered mycobiota signatures and enriched pathogenic Aspergillus rambellii are associated with colorectal cancer based on multi-cohort fecal metagenomic analyses – Lin et al. – Gastroenterology

[REVIEW] Small molecules in the big picture of gut microbiome-host cross-talk – Ma et al. – eBioMedicine

Maternal gut microbiome–induced IgG regulates neonatal gut microbiome and immunity – Sanidad et al. – Science Immunology

Non-Microbiome picks

Time for better time-restricted eating trials to lessen the burden of metabolic diseases – Taub and Panda – Cell Reports Medicine

What SARS-CoV-2 does to our brains – Aschman et al. – Immunity