February 26, 2021

Pregnancy and early life

Multi-kingdom ecological drivers of microbiota assembly in preterm infants – Rao et al. – Nature

Human gut

[PREPRINT]A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota – Sommer et al. – bioRxiv

[PREPRINT]Fiber-associated Lachnospiraceae reduce colon tumorigenesis by modulation of the tumor-immune microenvironment – Almeida et al. – bioRxiv

Animal microbiome/experiments

NLRP6-associated host microbiota composition impacts in the intestinal barrier to systemic dissemination of Brucella abortus – Rungue et al. – PLOS Neglected Tropical Diseases

Effects of sodium butyrate supplementation on inflammation, gut microbiota, and short‐chain fatty acids in Helicobacter pylori‐infected mice – Huang et al. – Helicobacter

The porcine corneal surface bacterial microbiome: A distinctive niche within the ocular surface – Leis et al. – PLOS One

Dysbiosis of fecal microbiota in cats with naturally occurring and experimentally induced Tritrichomonas foetus infection – Bierlein et al. – PLOS One

Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis – Lan et al. – Nature Communications

Plant, root, and soil microbiome

The bacterial communities of Alaskan mosses and their contributions to N2-fixation – Holland-Moritz et al. – Microbiome

Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments – Wyness et al. – PLOS One

[PREPRINT]Rare genera differentiate urban green space soil bacterial communities in three cities across the world – Mills et al. – bioRxiv

Nitrogen and water addition regulate fungal community and microbial co-occurrence network complexity in the rhizosphere of Alhagi sparsifolia seedlings – Zhang et al. – Applied Soil Ecology

Metabolic profiling and antioxidant activity during flower development in Agastache rugosa – Yeo et al. – Physiology and Molecular Biology of Plants

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

Long-term dynamic changes in attached and planktonic microbial communities in a contaminated aquifer – Mujica-Alarcon, Thornton & Rolfe – Environmental Pollution

Phages and viruses

Virome composition in marine fish revealed by meta-transcriptomics – Geoghegan et al. – Virus Evolution

Bioinformatics

Comparison of beta diversity measures in clustering the high-dimensional microbial data – Chen et al. – PLOS One

February 17, 2021

General microbiome

Microbial diversity in homes and the risk of allergic rhinitis and inhalant atopy in two European birth cohorts – Hyytiäinen et al. – Environmental Research

Pregnancy and early life

Can we modulate the breastfed infant gut microbiota through maternal diet? – Sindi et al. – FEMS Microbiology Reviews

Human respiratory microbiome

The nasal microbiome, nasal transcriptome, and pet sensitization – Chun et al. – Journal of Allergy and Clinical Immunology

Human gut microbiome

The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota – Lim et al. – Microorganisms

[REVIEW]Inflammatory bowel disease: tri-directional relationship between microbiota, immune system and intestinal epithelium – Ahlawat et al. – Critical Reviews in Microbiology

Fecal Microbiota Transplantation Is a Promising Method to Restore Gut Microbiota Dysbiosis and Relieve Neurological Deficits after Traumatic Brain Injury – Du et al. – Oxidative Medicine and Cellular Longevity

The baseline gut microbiota directs dieting-induced weight loss trajectories – Jie et al. – Gastroenterology

Animal microbiome (for animals in the wild)

Bacterial microbiota similarity between predators and prey in a blue tit trophic network – Dion-Phenix et al. The ISME Journal

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

Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene – Capo et al. – Microorganisms

Profiling of Microbial Communities in the Sediments of Jinsha River Watershed Exposed to Different Levels of Impacts by the Vanadium Industry, Panzhihua, China – He et al. – Environmental Microbiology

Bioinformatics

HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes – Li et al. – Microbiome

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework – Mehta et al. – f1000

February 10, 2021

Hello from snowy Lübeck,
today we have selected, among others, some papers about soil microbiota, associations of bacteria in healthy humans across different populations (in gut) and a couple of bioinformatic papers. Happy reading!

General microbiome

[REVIEW]Blautia—a new functional genus with potential probiotic properties? – Liu et al. – Gut Microbes

The sum is greater than the parts: exploiting microbial communities to achieve complex functions – Zaramela et al. – Current Opinion in Biotechnology

Pregnancy and early life

Influence of Lactobacillus crispatus, Lactobacillus iners and Gardnerella vaginalis on bacterial vaginal composition in pregnant women – Witkin et al. – Archives of Gynecology and Obstetrics

Human gut microbiome

The faecal metabolome in COVID-19 patients is altered and associated with clinical features and gut microbes – Lv et al. – Analytica Chimica Acta

Bacterial associations in the healthy human gut microbiome across populations – Loftus, Hassouneh & Yooseph – Scientific Reports

The Pre‐treatment Gut Microbiome is Associated with Lack of Response to Methotrexate in New Onset Rheumatoid Arthritis – Artacho et al. – Arthitis & Rheumatology

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

Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models – Strati et al. – Microbiome

Black Current Anthocyanins Improve Lipid Metabolism and Modulate Gut Microbiota in High‐Fat Diet‐Induced Obese Mice – Song et al. – Molecular Nutrition & Food Research

Animal microbiome (for animals in the wild)

Japanese quail (Coturnix japonica) as a novel model to study the relationship between the avian microbiome and microbial endocrinology-based host-microbe interactions – Lyte et al. – Microbiome

Plant, root, and soil microbiome

Impacts of earthworm introduction and cadmium on microbial communities composition and function in soil – Ren et al. – Environmental Toxicology and Pharmacology

Tree‐induced alterations to soil properties and rhizoplane‐associated bacteria following 23 years in a common garden – Yates et al. – Plant and Soil

Influence of imidacloprid on bacterial community diversity of mango orchard soil assessed through 16S rRNA sequencing-based metagenomic analysis – Garg et al. – Environmental Monitoring and Assessment

Bioinformatics

[PREPRINT]Multi-Block Sparse Functional Principal Components Analysis for Longitudinal Microbiome Multi-Omics Data – Jiang et al. – arXiv.org

Model-based microbiome data ordination: A variational approximation approach – Zeng, Zhao & Wang – Journal of Computational and Graphical Statistics

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses – Guo et al. – Microbiome

February 03, 2021

Job market

Postdoctoral Associate in quantitative microbial dynamics in the Clark lab at Duke University

General microbiome

[COMMENT]Microbiome innovations for a sustainable future – D’Hondt et al. – Nature Microbiology

Kin selection explains the evolution of cooperation in the gut microbiota – Simonety & McNally – PNAS

[REVIEW]Crossing Kingdoms: How the Mycobiota and Fungal-Bacterial Interactions Impact Host Health and Disease – Santus, Devlin & Behnsen – Infection and Immunity

Pregnancy and early life

Pregnant women who develop preeclampsia have lower abundance of the butyrate-producer Coprococcus in their gut microbiota – Altemani et al. – Pregnancy Hypertension

Human oral microbiome

Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota – Blaustein et al. – Microbiome

The role of Saccharibacteria (TM7) in the subginival microbiome as a predictor for secondary cardiovascular events – Schulz et al. – International Journal of Cardiology

Human gut microbiome

The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns – Zhu et al. – BMC Genomics

The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut – Arnold et al. – Microbiome

[REVIEW]Priming for Life: Early Life Nutrition and the Microbiota-Gut-Brain Axis – Ratsika et al. – Nutrients

[REVIEW]Gut Microbial Signatures in Sporadic and Hereditary Colorectal Cancer – Mori & Pasca – Int. J. Mol. Sci.

Animal microbiome (for animals in the wild)

[REVIEW]Mechanisms underlying gut microbiota–host interactions in insects – Schmidt & Engel

Plant, root, and soil microbiome

[REVIEW]Plant microbiome structure and benefits for sustainable agriculture – dos Santos & Olivares – Current Plant Biology

A microbial gene catalog of anaerobic digestion from full-scale biogas plants – Ma et al. – GigaScience

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

Microbial intrusion and seasonal dynamics in the groundwater microbiome of a porous basaltic rock aquifer used as municipal water reservoir – Knobloch et al. – FEMS Microbiology Ecology

Bacterial Diversity and Community Composition Distribution in Cold-Desert Habitats of Qinghai–Tibet Plateau, China – Zhang et al. – Microorganisms

Food microbiology

Bacterial community dynamics during different stages of processing of smoked bacon using the 16S rRNA gene amplicon analysis – Li et al. – International Journal of Food Microbiology

Bioinformatics

[PREPRINT]PredicTF: a tool to predict bacterial transcription factors in complex microbial communities – Monteiro et al. – bioRxiv

tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R – Carpenter et al. – BMC Bioinformatics

Techniques

In vitro infection models to study fungal-host interaction – Last et al. – FEMS Microbiology Reviews

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

Exploring the Relationship Between the Microbiome, Precision Medicine and Cancer – Tom Williams – Technology Networks

January 29, 2021

Human gut microbiome

Gut microbiome dysbiosis and correlation with blood biomarkers in active-tuberculosis in endemic setting – Khaliq et al. – PLOS One

Gut microbiota profile of Indonesian stunted children and children with normal nutritional status – Surono et al. – PLOS One

[PREPRINT]Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition – Lou et al. – bioRxiv

Human metabolome

Umbilical cord blood metabolome differs in relation to delivery mode, birth order and sex, maternal diet and possibly future allergy development in rural children – Ross et al. – PLOS One

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

Innate gut microbiota predisposes to high alcohol consumption – Ezquer et al. – Addiction Biology

Animal microbiome

Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle – Liu et al. – Animal Microbiome

Plant, root, and soil microbiome

Investigation of the microbiota associated with ungerminated and germinated Norwegian barley cultivars with focus on lactic acid bacteria – Østlie et al. – International Journal of Food Microbiology

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

[PREPRINT]Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring – Rubin-Blum – bioRxiv

[PREPRINT]Deep-sea plastisphere: long-term colonization by plastic-associated bacterial and archaeal communities in the Southwest Atlantic Ocean – Agostini – bioRxiv

Food microbiology

Systematic assessment of oat β-glucan catabolism during in vitro digestion and fermentation – Bai et al. – Food Chemistry

Bioinformatics

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads – Valiente-Mullor et al. – PLOS Computational Biology

January 27, 2021

General microbiome

[REVIEW]The complexities of the diet-microbiome relationship: advances and perspectives – Leeming et al. – Genome Medicine

Human skin microbiome

A mixed community of skin microbiome representatives influences cutaneous processes more than individual members – Loomis et al. – Microbiome

Analysis of the Composition and Functions of the Microbiome in Diabetic Foot Osteomyelitis Based on 16S rRNA and Metagenome Sequencing Technology – Zou et al. – Diabetes

Human gut microbiome

Gut microbiota condition the therapeutic efficacy of trastuzumab in HER2-positive breast cancer – Di Modica et al. – Cancer Research

[REVIEW]Role of the gut microbiota in type 2 diabetes and related diseases – Yang et al. – Metabolism

Animal microbiome (for animals in the wild)

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas – Baniel et al. – Microbiome

Taxonomic and functional adaption of the gastrointestinal microbiome of goats kept at high altitude (4800 m) under intensive or extensive rearing conditions – Zhang et al. – FEMS Microbiology Ecology

Shifts in bacterial communities and antibiotic resistance genes in surface water and gut microbiota of guppies (Poecilia reticulata) in the upper Rio Uberabinha, Brazil – Jia et al. – Ecotoxicology and Environmental Safety

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

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing – Okazaki et al. – Microbiome

Microbiota entrapped in recently-formed ice: Paradana Ice Cave, Slovenia – Mulec et al. – Scientific Reports

Sea‐ice microbial communities in the Central Arctic Ocean: Limited responses to short‐term pCO2 perturbations – Torstensson et al. – Limnology and Oceanography

Built environment (subways, indoor surfaces)

Bacterial community assemblages in classroom floor dust of 50 public schools in a large city: characterization using 16S rRNA sequences and associations with environmental factors – Park et al. – Microbiome

[REVIEW]Plastics and the microbiome: impacts and solutions – Lear et al. – Environmental Microbiome

Bioinformatics

[REVIEW]Understanding the host-microbe interactions using metabolic modeling – Jansma & El Aidy – Microbiome

January 20, 2021

Good morning readers! Today we have two very interesting studies published in Nature Genetics. One focuses on host factors influencing human gut microbiome composition, the other shows the influence of ABO histo-blood groups on gut microbiome.

Human gut microbiome

Large-scale association analyses identify host factors influencing human gut microbiome composition – Kurilshikov et al. – Nature Genetics

Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome – Rühlemann et al. – Nature Genetics

Fecal microbiome and metabolome differ in healthy and food-allergic twins – Bao et al. – JCI

Hepatic steatosis relates to gastrointestinal microbiota changes in obese girls with polycystic ovary syndrome – Jobira et al. – PLOS One

Animal microbiome

Microbiota modulates gut immunity and promotes baculovirus infection in Helicoverpa armigera – Yuan et al. – Insect Science

Immunological design of commensal communities to treat intestinal infection and inflammation – Brown et al. – PLOS Pathogens

Ticks Resist Skin Commensals with Immune Factor of Bacterial Origin – Hayes et al. – Cell

Techniques

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology – Jeong et al. – Scientific Reports

January 13, 2021

Good morning! Today we have a rather short reading list. One study links gut microbiome and COVID19. A second study shows the impact of the gut microbiome on the peripheral immune response. Additionally, two preprints were selected.

Human gut microbiome

Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19 – Yeoh et al. – Gut

Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma – Behary et al. – Nature Communications

Animal microbiome (for animals in the wild)

[PREPRINT]Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus) – Minich et al. – bioRxiv

Bioinformatics

[PREPRINT]AncestralClust: Clustering of Divergent Nucleotide Sequences by Ancestral Sequence Reconstruction using Phylogenetic Trees – Pipes & Nielsen – bioRxiv

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

Gut Microbiome and COVID-19 Severity: New Evidence for Link – Molly Walker – MedpageToday

January 12, 2021

Good morning, today we have a quite divers selection of studies. Of special note are the results of the PREDICT 1 study, published in Nature Medicine (Asnicar et al.). Furthermore, we cover among others virome in pregnant women, gut microbiome and PD, some animal microbiome studies, water microbiome, and bioinformatic tools.

General microbiome

[Meeting Report]Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020 – LaPelusa et al. – Microbiome

Identifying background microbiomes in an evidence recovery laboratory: A preliminary study – Neckovic et al. – Science & Justice

Human vaginal microbiome/virome

Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis – Zhang et al. – Virology Journal

Human gut microbiome

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals – Asnicar et al. – Nature Medicine

Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease – Li et al. – Metabolites

Animal microbiome

The Combined Effects of Magnesium Oxide and Inulin on Intestinal Microbiota and Cecal Short-Chain Fatty Acids – Omori et al. – Nutrients

Effect of host breeds on gut microbiome and serum metabolome in meat rabbits – Ye et al. – BMC Veterinary Research

Differential response of digesta- and mucosa-associated intestinal microbiota to dietary insect meal during the seawater phase of Atlantic salmon – Li et al. – Animal Microbiome

Plant, root, and soil microbiome

Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages – Tong et al. – BMC Microbiology

Water microbiome

Eukaryotic community diversity and pathogenic eukaryotes in a full-scale drinking water treatment plant determined by 18S rRNA and metagenomic sequencing – Li et al. – Environmental Science and Pollution Research

Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes – Sonthiphand et al. – PeerJ

Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding – Ogaki et al. – Environmental Microbiology

Built environment

Comparative analysis of impact of human occupancy on indoor microbiomes – Cao et al. – Frontiers of Environmental Science & Engineering

Bioinformatics

Re-purposing software for functional characterization of the microbiome – Gardiner et al. – Microbiome

[PREPRINT]Mining underutilized whole-genome sequencing projects to improve 16S rRNA databases – Nolan et al. – bioRxiv

Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function – Jing et al. – BMC Genomics

Techniques

Exploring protocol bias in airway microbiome studies: one versus two PCR steps and 16S rRNA gene region V3 V4 versus V4 – Drengenes et al. – BMC Genomics

Quantitative image analysis of microbial communities with BiofilmQ – Hartmann et al. – Nature Microbiology

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

Do the bugs in our guts make us sick, sad and obese? – Sismondo – Toronto Star

New microbiome research finds associations between microbes, diet, and metabolic health – Krawiec – Nutritional outlook

January 08, 2021

Human gut microbiome

Altered diversity and composition of gut microbiota in Wilson’s disease – Cai et al. – Scientific Reports

Emotional well-being and gut microbiome profiles by enterotype – Lee et al. – Scientific Reports

The Composition and Concordance of Lactobacillus Populations of Infant Gut and the Corresponding Breast-Milk and Maternal Gut – Zhang et al. – Front. Mircobiol.

Lifestyle modifications result in alterations in the gut microbiota in obese children – Cho – BMC Microbiology

Animal microbiome

Nutritional combinatorial impact on the gut microbiota and plasma short-chain fatty acids levels in the prevention of mammary cancer in Her2/neu estrogen receptor-negative transgenic mice – Sharma et al. – PLOS One

Modeling dysbiosis of human NASH in mice: Loss of gut microbiome diversity and overgrowth of Erysipelotrichales – Carter et al. – PLOS One

Geography as non-genetic modulation factor of chicken cecal microbiota – Viso et al. – PLOS One

Intestinal microbial communities of rainbow trout (Oncorhynchus mykiss) may be improved by feeding a Hermetia illucens meal/low-fishmeal diet – Rimoldi et al. – Fish Physiology and Biochemistry

Dramatic shifts in intestinal fungal community between wintering Hooded Crane and Domestic Goose – Xiang et al. – Avian Research (BMC)

Bacterial diversity in intestinal mucosa of mice fed with Dendrobium officinale and high-fat diet – Li et al. – 3 Biotech

Shift of Maternal Gut Microbiota of Tibetan Antelope (Pantholops hodgsonii) During the Periparturition Period – Shi et al. – Current Microbiology

Plant, root, and soil microbiome

Bacterial seed endophyte shapes disease resistance in rice – Matsumoto et al. – Nature Plants

Environment

Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya – Muturi et al. – PLOS One

Wastewater treatment alters microbial colonization of microplastics – Kelly et al. – PLOS One

Bioinformatics

MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome – Patumcharoenpol et al. – PLOS Computational Biology

Techniques

Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types – Abundo et al. – PLOS One