Category Archives: Waste and pollution

August 28, 2024

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Human gut microbiome

[REVIEW] Feeding gut microbes to nourish the brain: unravelling the diet–microbiota–gut–brain axis – Elizabeth Schneider et al – Nature Metabolism

Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes – Jordy Evan Sulaiman et al – Nature Communications

Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients – Anna K. Hartikainen et al – NPJ Biofilms & Microbiomes

Impact of probiotics on gut microbiome of extremely preterm or extremely low birthweight infants – Lauren C. Beck et al – Nature Pediatric Research

Effect of Helicobacter pylori on sleeve gastrectomy and gastric microbiome differences in patients with obesity and diabetes – Yong Suk Park et al – International Journal of Obesity

Mining human microbiomes reveals an untapped source of peptide antibiotics – Marcelo D.T. Torres et al – Cell

Both pathogen and host dynamically adapt pH responses along the intestinal tract during enteric bacterial infection – Sarah E. Woodward et al – PLOS Biology

Examination of sex-specific interactions between gut microbiota and host metabolism after 12-week combined polyphenol supplementation in individuals with overweight or obesity – Kelly M. Jardon et al – Gut Microbes

Human vaginal microbiome

The potential of residual clinical Group B Streptococcus swabs for assessing the vaginorectal microbiome in late pregnancy – Laura K. Boelsen et al – Scientific Reports

Animal models

Sex-dependent effects of a high fat diet on metabolic disorders, intestinal barrier function and gut microbiota in mouse – Candice Lefebvre et al – Scientific Reports

Animal microbiome

16S rRNA metabarcoding for the identification of tick-borne bacteria in ticks in the Republic of Korea – Badriah Alkathiri et al – Scientific Reports

The bacterial microbiome and resistome of house dust mites in Irish homes – Amal Aljohani et al – Scientific Reports

Social environment influences microbiota and potentially pathogenic bacterial communities on the skin of developing birds – Ester Martínez-Renau – BMC Animal Microbiome

16S amplicon-based microbiome biomapping of a commercial broiler hatchery – Michael J. Rothrock Jr. et al – BMC Animal Microbiome

Phages & viruses

[REVIEW] Renewed insights into Ackermannviridae phage biology and applications – Anders Nørgaard Sørensen & Lone Brøndsted – NPJ Viruses

Adaptation strategies of giant viruses to low-temperature marine ecosystems – Marianne Buscaglia et al – ISME Journal

Targeted viromes and total metagenomes capture distinct components of bee gut phage communities – Dino Lorenzo Sbardellati et al – BMC Microbiome

Plant, root & soil microbiome

Soil health is associated with higher primary productivity across Europe – Ferran Romero et al – Nature Ecology & Evolution

Pathogen-driven Pseudomonas reshaped the phyllosphere microbiome in combination with Pseudostellaria heterophylla foliar disease resistance via the release of volatile organic compounds – Qing-Song Yuan et al – BMC Environmental Microbiome

Water & extremophile microbiome

Impact of temperature and water source on drinking water microbiome during distribution in a pilot-scale study – Fien Waegenaar et al – NPJ Clean Water

Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa – Anthony M. Smith et al – PLOS One

Nitrite-oxidizing bacteria adapted to low oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones – Samantha G Fortin et al – ISME Journal

Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments – Chyrene Moncada et al – ISME Journal

Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica – Hanbyul Lee et al – BMC Environmental Microbiome

Tools & methods

Intestinal organ chips for disease modelling and personalized medicine – Alican Özkan et al – Nature Reviews Gastroenterology & Hepatology

MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using Machine lEarning Techniques – Edoardo Bizzotto et al – BMC Environmental Microbiome

refMLST: reference-based multilocus sequence typing enables universal bacterial typing – Mondher Khdhiri et al – BMC Bioinformatics

Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization – Weixian Liu et al – BMC Bioinformatics

August 14, 2024

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Human microbiome

Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs – Eugeni Belda et al – BMC Medical Genomics

The impact of breastfeeding on the preterm infant’s microbiome and metabolome: a pilot study – Keriann Schulkers Escalante et al – Nature Pediatric Research

[REVIEW] The human microbiome in space: parallels between Earth-based dysbiosis, implications for long-duration spaceflight, and possible mitigation strategies – Sofia Etlin et al – Clinical Microbiology Reviews

MASS cohort: Multicenter, longitudinal, and prospective study of the role of microbiome in severe pneumonia and host susceptibility – Xin Wei et al – iMeta

Distinctive duodenal microbiomes and bile acid profiles in duodenal tumor patients revealed by prospective observational study – Yoko Kubosawa et al – Nature Scientific Reports

Elucidating the dynamics and impact of the gut microbiome on maternal nutritional status during pregnancy, effect on pregnancy outcomes and infant health in rural Pakistan: study protocol for a prospective, longitudinal observational study – Yaqub Wassan et al – BMJ Open

Time-varying ambient air pollution exposure is associated with gut microbiome variation in the first 2 years of life – Tianlai Qiu et al – Environmental Pollution

Animal experiments

Gut Microbiota-Induced Modulation of the Central Nervous System Function in Parkinson’s Disease Through the Gut-Brain Axis and Short-Chain Fatty Acids – Yiting Ni et al – Molecular Neurobiology

Animal microbiome

Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria – Junbo Tang et al – Nature Communications

Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata – Gagandeep Brar et al – Applied & Environmental Microbiology

Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition – Lingyan Ma & Wentao Lyu et al – iMeta

Meconium microbiota in naturally delivered canine puppies – Alessia Bertero et al – BMC Veterinary Research

Gut microbiome perturbation and its correlation with tylosin pharmacokinetics in healthy and infected pigs – Eon-Bee Lee et al – Nature Scientific Reports

Beneficial microbes, compounds, & foods

Restriction of growth and biofilm formation of ESKAPE pathogens by caprine gut-derived probiotic bacteria – Prerna Saini et al – Frontiers in Microbiology

[REVIEW] Polyphenols improve non-alcoholic fatty liver disease via gut microbiota: A comprehensive review – Kimia Mohammadhasani et al – Food Science & Nutrition

[REVIEW] Exploring the Potential of Postbiotics for Food Safety and Human Health Improvement – Folayemi Janet Isaac-Bamgboye et al – Journal of Nutrition & Metabolism

Transcriptomics and gut microbiome analysis of the edible herb Bidens pilosa as a functional feed additive to promote growth and metabolism in tilapia (Oreochromis spp.) – Che-Chun Chen et al – BMC Genomics

[REVIEW] A comprehensive review of the characterization, host interactions, and stabilization advancements on probiotics: Addressing the challenges in functional food diversification – Eskindir Getachew Fentie et al – Comp. Rev. in Food Science & Safety

Effects of kefir consumption on gut microbiota and health outcomes in women with polycystic ovary syndrome – Merve Esra Çıtar Dazıroğlu – Food Science & Nutrition

Plant, root, & soil microbiome

Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species – Anastasiia Fetsiukh et al – Nature Scientific Reports

Differences in the constituents of bacterial microbiota of soils collected from two fields of diverse potato blackleg and soft rot diseases incidences, a case study – Weronika Babinska-Wensierska et al – Nature Scientific Reports

Variations of soil metal content, soil enzyme activity and soil bacterial community in Rhododendron delavayi natural shrub forest at different elevations – Li Wang et al – BMC Microbiology

Effective microorganism combinations improve the quality of compost-bedded pack products in heifer barns: exploring pack bacteria-fungi interaction mechanisms – Zhenbin Zhang et al – BMC Microbiology

Global patterns in the growth potential of soil bacterial communities – Ernest D. Osburn et al – Nature Communications

Microplastic-contamination can reshape plant community by affecting soil properties – Mengzuan He et al – Ecotoxicology & Environmental Safety

Water & extremophile microbiome

Microbial Succession on Microplastics in Wastewater Treatment Plants: Exploring the Complexities of Microplastic-Microbiome Interactions – Klaudia Kwiatkowska & Paulina Ormaniec – Microbial Ecology

Microbial ecology

Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology – Oscar Gallardo-Navarro et a – Heliyon

Antibiotic resistance

[NEWS FEATURE] Five ways science is tackling the antibiotic resistance crisis – Amber Dance – Nature

Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life – Pål Trosvik et al – Nature Scientific Reports

Bioinformatics tools

MetaBakery: a Singularity implementation of bioBakery tools as a skeleton application for efficient HPC deconvolution of microbiome metagenomic sequencing data to machine learning ready information – Boštjan Murovec et al – Frontiers in Microbiology

July 24, 2024

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Human microbiome

Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease – Xiangge Tian et al – BMC Microbiome

The Role of Gut Microbiota in the Neuroprotective Effects of Selenium in Alzheimer’s Disease – Anatoly V. Skalny et al – Molecular Neurobiology

[REVIEW] The oral–gut microbiome axis in health and disease – Benoit J. Kunath – Nature Reviews Microbiology

Enhancing gut microbiota and microbial function with inulin supplementation in children with obesity – Chonnikant Visuthranukul et al – International Journal of Obesity

Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder – Zaiquan Dong et al – Journal of Affective Disorders

Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health – Na Han et al – Frontiers in Microbiology

Skin locations inference and body fluid identification from skin microbial patterns for forensic applications – Litao Huang et al – Forensic Science International

Animal experiments

Improving insulin resistance by sulforaphane via activating the Bacteroides and Lactobacillus SCFAs–GPR–GLP1 signal axis – Sicong Tian et al – Food & Function

Gastroprotective and microbiome-modulating effects of ubiquinol in rats with radiation-induced enteropathy – Walaa A. Eraqi et al – BMC Animal Microbiome

Animal microbiome

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses – Mason R. Stothart et al – Nature Communications

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale – Shuai Du et al – Environmental Science & Technology

Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages – Marwa Mamdouh Tawfik et al – BMC Animal Microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Laura Glendinning et al – BMC Microbiome

Water & extremophile microbiome

Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton – Tianyi Chang et al – BMC Microbiome

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake – Arianna I. Krinos et al – BMC Microbiome

Built environment microbiome

[PREPRINT] Utilizing the biosimulator to analyze the environmental microbiome within the intensive care units of a hospital – Sunil Thomas et al – ResearchSquare

Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system – Dou Wang et al – BMC Microbiome

Plant, root, & soil microbiome

Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China – Jie-Liang Liang et al – BMC Microbiome

Bioinformatics tools

MIDASim: a fast and simple simulator for realistic microbiome data – Mengyu He et al – BMC Microbiome

March 13, 2024

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Human gut microbiome

Gut microbiota–tryptophan metabolism–GLP-1 axis participates in β-cell regeneration induced by dapagliflozin – Yafei Jiang et al – Diabetes

Inhibition of inosine metabolism of the gut microbiota decreases testosterone secretion in the testis – Lei Tang et al – mSystems

[REVIEW] Exploring the gut microbiota and its potential as a biomarker in gliomas – Dana Aljarrah et al – Biomedicine & Pharmacotherapy

Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin and acacia gum in Kenyan infant gut microbiota during iron supplementation – Paula Momo Cabera et al – ISME Communications

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Ekaterina Buzun et al – Cell Host and Microbe

Animal Microbiome

Dietary carbohydrate sources differently prime the microbial ecosystem but not the epithelial gene expression profile along the complete gut of young calves – Thomas Hartinger et al – BMC Animal Microbiome

Multi-omics reveals that alkaline mineral water improves the respiratory health and growth performance of transported calves – Jiancheng Qi et al – BMC Microbiome

Efficacy of a novel multi-enzyme feed additive on growth performance, nutrient digestibility and gut microbiome of weanling pigs fed corn-wheat or wheat-barley based diet – Ayodeji S Aderibigbe et al – Journal of Animal Science

Plant and soil microbiome

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition – Jia Wang et al – mSystems

Plasma Treatment Modifies Element Distribution in Seed Coating and Affects Further Germination and Plant Growth through Interaction with Soil Microbiome – Tetiana Kalachova et al – Journal of Agricultural and Food Chemistry

Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils – Prinpida Sonthiphand et al – Bulletin of Environmental Contamination and Toxicology

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria – Katarina Hrovat et al – ISME Communications

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process – Liqun Jiang et al – Microbiology Spectrum

Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes – Ziguo Zhang et al – mSystems

Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis – Eliza P.-I. Loo et al – Cell Host and Microbe

Built environment microbiome

Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station – Tomoro Warashina et al – Applied and Environmental Microbiology

Bioinformatics and Techniques

The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes – Thibaut Dumas et al – BMC Microbiome

Proportion-based normalizations outperform compositional data transformations in machine learning applications – Aaron Yerke et al – BMC Microbiome

A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria – Geraldine J. Sullivan et al – mSystems

[PREPRINT] Bacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach – Federica Palma et al – bioRXiv

February 28, 2024

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Human gut microbiome

Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging – Shalini Singh – BMC Microbiome

Safety, feasibility, and impact on the gut microbiome of kefir administration in critically ill adults – Vinod K. Gupta – BMC Medicine

Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip – Jeeyon Lee – Advanced Science

Animal experiments

CRB1-associated retinal degeneration is dependent on bacterial translocation from the gut – Shanzhen Peng – Cell

Amino acid formula induces microbiota dysbiosis and depressive-like behavior in mice – Ji Hu – Cell Reports

Bacteroides fragilis aggravates high-fat diet-induced non-alcoholic fatty liver disease by regulating lipid metabolism and remodeling gut microbiota – Yumei Huang – Microbiology Spectrum

Animal microbiome

Gut microbiota modulation enhances the immune capacity of lizards under climate warming – Jing Yang – BMC Microbiome

Gut microbiota contribute to variations in honey bee foraging intensity – Cassondra L Vernier – ISME Journal

Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis – Run-Ze Ye – BMC Microbiome

Multi-omics reveal mechanisms of high enteral starch diet mediated colonic dysbiosis via microbiome-host interactions in young ruminant – Chunjia Jin – BMC Microbiome

Plant, root, and soil microbiome

[PREPRINT] Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils – Valerie A Seitz – Research Square

Stronger compensatory thermal adaptation of soil microbial respiration with higher substrate availability – Lingrui Qu – ISME Journal

Built environment

Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants – Yulin Zhang – mSystems

Water and extremophile microbiome

Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics – Lauren F. Messer – BMC Microbiome

Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides – Feng-Qing Wang – BMC Microbiome

Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea – Tianshuo Zu – Microbial Ecology

Beneficial microbes

[PREPRINT] Enhancing Recovery from Gut Microbiome Dysbiosis and Alleviating DSS-Induced Colitis in Mice with a Consortium of Rare Short-Chain Fatty Acid-Producing Bacteria – Achuthan Ambat – bioRxiv

Neuroprotective Effects of Bifidobacterium animalis subsp. lactis NJ241 in a Mouse Model of Parkinson’s Disease: Implications for Gut Microbiota and PGC-1α – Yuxuan Dong – Molecular Neurobiology

February 21, 2024

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Human nasal microbiome

[PREPRINT]Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Zhao et al. – bioRxiv

Human oral microbiome

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases – Bazzani et al. – npj Biofilms and Microbiomes

Human gut microbiome

Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity – Behling et al. – Microbiome

Animal microbiome

Psychological stress-induced microbial metabolite indole-3-acetate disrupts intestinal cell lineage commitment – Wei et al. – Cell Metabolism

Gut microbiota contributes to bisphenol A-induced maternal intestinal and placental apoptosis, oxidative stress, and fetal growth restriction in pregnant ewe model by regulating gut-placental axis – Zhang et al. – Microbiome

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

Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones – Sun et al. – Microbiome

Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge – Li et al. – PeerJ

The exometabolome of microbial communities inhabiting bare ice surfaces on the southern Greenland Ice Sheet – Doting et al. – Environmental Microbiology

Searching for microbial contribution to micritization of shallow marine sediments – Garuglieri et al. – Environmental Microbiology

Food microbiology

Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing – Rana et al. – Scientific Reports

Phages and viruses

[PREPRINT]Fecal Virome Transplantation (FVT) from healthy humans remodels the gut bacteriome and virome and reduces metabolic syndrome in mice – Cervantes-Echeverría et al. – bioRxiv

[PREPRINT]Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Zolfo et al. – bioRxiv

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Why addressing how our brain and our gut talk to each other matter for IBS – Gut microbiota for health

May 5, 2023

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Today’s microbiome digest is a grab bag that includes ten simple rules for working with other people’s code, an article examining Wolbachia infections in native cockroach populations, and an article examining the role in lactic acid in shaping the human microbiome. Also highlighted is an article focused on human viruses residing within our cells and tissues, which demonstrated a unique virome in nine different human organs through targeted-enrichment viral metagenomics and virus specific qPCRs.

Happy reading!

General microbiome

The structure of prevacuolar compartments in Neurospora crassa as observed with super-resolution microscopy – Bowman – PLOS One

Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences – Nakano et al. – PLOS One

***Unmasking the tissue-resident eukaryotic DNA virome in humans – Pyöriä et al. – Nucleic Acids Research

Predicting partner fitness based on spatial structuring in a light-driven microbial community – Sakkos et al. – PLOS Computational Biology

Multi-site human microbiome

Evaluation of alcohol-free mouthwash for studies of the oral microbiome – Yano et al. – PLOS One

A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome – Zhang et al. – Microbiome

Human gut microbiome

Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment – Hao et al. – Microbiome

Animal microbiome

Wolbachia infection in native populations of Blattella germanica and Periplaneta americana – Choubdar et al. – PLOS One

Plant, root, and soil microbiome

Bacterial and fungal community composition and community-level physiological profiles in forest soils – Kunito et al. – PLOS One

Water and extremophile microbiome

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks – Liu et al. – Microbiome

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes – Muñoz-Marín et al. – PLOS One

Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages – Tong et al. – Microbiome

Bioinformatics

Ten simple rules for working with other people’s code – Pilgrim et al. – PLOS Computational Biology

Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier – Raza et al. – PLOS One

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria – Roux et al. – PLOS Biology

February 18th, 2023

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Bonjour from Paris, France !

In today’s digest you will find a broad range of amazing preprints and published papers! An amazing read is a fresh preprint from Fritz and collaborator describing an exciting method of sampling in difficult to reach environments. The authors used army ants of the genus Dorylus which are foragers to survey the viral diversity of plants, vertebrate and invertebrates of the tropical forest!

Today’s non-microbiology pick is an opinion piece on the current state and limitation of viral taxonomy. In this piece, Simmonds and collaborators, provide concrete recommendations to guide the development of a coherent and comprehensive virus taxonomy.

Have a great Saturday!

Pregnancy and early life

The investigation of the association of pregnancy weight gain on maternal and neonatal gut microbiota composition and abundance using 16sRNA sequencing – Song and Liu – BMC Pregnancy and Childbirth

Human gut microbiome

The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population – Bourdeau-Julien et al. – Microbiome

Review: Conversations in the Gut: The Role of Quorum Sensing in Normobiosis – Markus et al. – International Journal of Molecular Sciences

Review: Gut Microbiome and Neurodevelopmental Disorders: A Link Yet to Be Disclosed – Illiodromiti et al. – Microorganisms

Natural Green Spaces, Sensitization to Allergens, and the Role of Gut Microbiota during Infancy – Buchholz et al. – mSystems

Animal experiments

Mimicking seasonal changes in light-dark cycle and ambient temperature modulates gut microbiome in mice under the same dietary regimen – Matsumoto et al – Plos One

Animal microbiome

Preprint: Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta – Moeller et al. – BioRxiV

Plant, root, and soil microbiome

Preprint: Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype – Simonin et al. – BioRxiV

Preprint: Viral but not bacterial community succession is characterized by extreme turnover shortly after rewetting dry soils – Santos-Medellin et al. – BioRxiV

Ecological drivers and potential functions of viral communities in flooded arsenic-contaminated paddy soils – Gao et al. – Science of the total environment

Water and extremophile microbiome

Preprint: Redefinition of archetypal phytoplankton-associated bacteria taxa based on globally distributed dinoflagellates and diatoms – Yang et al. – BioRxiV

Preprint: Plastic Leachate Exposure Drives Antibiotic Resistance and Virulence in Marine Bacterial Communities – Vlaanderen et al. – BioRxiV

Phages and viruses

Preprint: African army ants at the forefront of virome surveillance in a remote tropical forest – Fritz et al. – BioRxiV

Techniques

Preprint: Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction – Simon et al. – BioRxiV

Preprint: The long and short of it: Benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies – Cook et al. – BioRxiV

Non microbiology pick

Opinion: Four principles to establish a universal virus taxonomy – Simmonds et al. – PLoS Biology

December 9, 2022

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Today’s digest features global antimicrobial resistance, comammox and anammox bacteria in wastewater treatment, mOTUs3, and more. Check out Elisa Granato & Christoph Ziegenhain’s story about postdoc life. Happy Friday and see you next week at #MVIF!

Global microbiome & resistome

Experimental temperatures shape host microbiome diversity and composition – Jingdi Li – Global Change Biology

Global biogeography and projection of soil antibiotic resistance genes – Zheng et al. – Science Advances

*Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance – Patrick Munk – Nature Communications

Blood microbiome

No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C.S. Tan – bioRxiv

Gut microbiome

Effects of dog ownership on the gut microbiota of elderly owners – Chaona Jiang – Plos One

Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases – Yoshihiko Tomofuji – Cell Genomics

Gut microbiome-wide association study of depressive symptoms – Djawad Radjabzadeh – Nature Communications

Development of non-alcoholic steatohepatitis is associated with gut microbiota but not oxysterol synthesis – Jacqueline Wyss – bioRxiv

The microbiome’s fiber degradation profile and its relationship with the host diet – Yotam Cohen & Elhanan Borenstein – BMC Biology

Animal microbiome

Lactobacillus reuteri improves the development and maturation of fecal microbiota in piglets through mother-to-infant microbe and metabolite vertical transmission – Gang Wang – Microbiome

Live biotherapeutics

Development of a live biotherapeutic throat spray with lactobacilli targeting respiratory viral infections – Irina Spacova – Microbial Biotechnology

Soil/root/plant microbiome

Differential microbial assembly processes and co-occurrence networks in the soil-root continuum along an environmental gradient – Yangquanwei Zhong – iMeta

Water microbiome

*Co-occurrence and cooperation between comammox and anammox bacteria in a full-scale attached growth municipal wastewater treatment process – Katherine J Vilardi – bioRxiv

Full-scale activated sludge transplantation reveals a highly resilient community structure – Giulia Dottorini – Water Research

Bioinformatics

Towards complete representation of bacterial contents in metagenomic samples – Xiaowen Feng, Heng Li – arXiv

*Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments – Hans-Joachim Ruscheweyh – Microbiome

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023 – CNCB-NGDC Members and Partners – Nucleic Acids Research

Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes – Lei Liu – Microbiome

November 7, 2022

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Human and General Microbiome

Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure – Matthew R Stutz – Nature Communications

Taxonomic Abundance in Primary and Secondary Root Canal Infections – Ronald Ordinola-Zapata – International Endodontic Journal

Review: The intestinal barrier in disorders of the central nervous system – Carolina Pellegrini – The Lancet. Gastroenterology & Hepatology

Review: Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution – Emma Slack – Mucosal Immunology

Correspondence: A critical analysis of eating disorders and the gut microbiome – Sydney M Terry – Journal of Eating Disorders

Beneficial Microbes and Compounds

Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity – Gihyeon Kim – Microbiome

Lactobacillus rhamnosus GG supernatant promotes intestinal mucin production through regulating 5-HT4R and gut microbiota – Yu Gu – Food & Function

Animal Model Microbiome

Genetic and environmental circadian disruption induce weight gain through changes in the gut microbiome – Baraa Altaha – Molecular Metabolism

Strains producing different short-chain fatty acids alleviate DSS-induced ulcerative colitis by regulating intestinal microecology – Shuo Yang – Food & Function

Non-Model Animal Microbiome

Microbiome assembly and maintenance across the lifespan of bumble bee workers – Tobin J Hammer – Molecular Ecology

The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone – Danny P Nielsen – Ecology Letters

Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition – Ziyue Zhang – Archives of Microbiology

Forensic Microbiome

Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes – Thomas Clarke – Scientific Reports

Plant Microbiome

Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation – Hetty KleinJan – Molecular Ecology

Built Environment Microbiome

Review: Microplastics in urban waters and its effects on microbial communities: a critical review – Saber Entezari – Environmental Science and Pollution Research International

Microbiome Analysis and Techniques

Assessing the Dark Field of Metaproteome – Haonan Duan – Analytical Chemistry