February 5th, 2019

Today’s digest includes some new bioinformatics techniques to study the microbiome and some more cool papers about diet and the microbiome.

General Microbiome

Experimental evolution reveals microbial traits for association with the host gut. – Vega NM – PLoS Biology

Human gut Microbiome

The intestinal microbiota predisposes to traveler’s diarrhea and to the carriage of multidrug-resistant Enterobacteriaceae after traveling to tropical regions. – Leo S – Gut Microbes

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome – Jun Li – bioRxiv

Human Pregnancy/Infant Microbiome

Effect of Delivery Mode and Nutrition on Gut Microbiota in Neonates. – Akagawa S – Annals of Nutrition and Metabolism

Trait-based community assembly and succession of the infant gut microbiome – John Guittar – Nature Communications

Animal experiments

Modulation of Gut Microbiota Composition by Serotonin Signaling Influences Intestinal Immune Response and Susceptibility to Colitis. – Kwon YH – Cellular and Molecular Gastroenterology and Hepatology

Plant, root, water and soil Microbiome

Marine biofilms constitute a bank of hidden microbial diversity and functional potential – Weipeng Zhang – Nature Communications

Combined metabarcoding and co-occurrence network analysis to profile the bacterial, fungal and Fusarium communities and their interactions in maize stalks – Jose F. Cobo-Diaz – Frontiers in Microbiology



Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks. – Metwally AA – PLoS Computational Biology

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion – Sabine Koch – PLoS Computational Biology

Swathi’s non-microbiology picks

How Millennials Became The Burnout Generation – An article about work-life balance that I think is applicable to scientists and academia.




January 2nd, 2019

Happy New Year Everyone! Some cool new papers for the digest including multiple diet studies!

General Microbiome

Cultivated human vaginal microbiome communities impact Zika and Herpes Simplex Virus replication in ex vivo vaginal mucosal cultures – Megan H Amerson-Brown – Frontiers in Microbiology

Human gut Microbiome

In vivo screening of multiple bacterial strains identifies Lactobacillus rhamnosus Lb102 and Bifidobacterium animalis ssp. lactis Bf141 as probiotics that improve metabolic disorders in a mouse model of obesity – Le Barz M – FASEB Journal

Protective effects of Bacillus probiotics against high-fat diet-induced metabolic disorders in mice. – Kim B – PLoS One

NLRP1 restricts butyrate producing commensals to exacerbate inflammatory bowel disease. – Tye H – Nature Communications

Human Pregnancy Microbiome

Characterizing the Subgingival Microbiome of Pregnant African American Women. – Yang I – J Obstet Gynecol Neonatal Nurs

Animal experiments 

A Gut Commensal Bacterium Promotes Mosquito Permissiveness to Arboviruses. – Wu P – Cell Host Microbe

Plant, root, and soil Microbiome

Specific recruitment of soil bacteria and fungi decomposers following a biostimulant application increased crop residues mineralization. – Hellequin E – PLoS One

Mangrove facies drives resistance and resilience of sediment microbes exposed to anthropic disturbance – C Capdeville – Frontiers in Microbiology



Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur – Hiltemann SD – Gigascience

iVikodak–a platform and standard workflow for inferring, analyzing, comparing, and visualizing the functional potential of microbial communities – S Nagpal -Frontiers in Microbiology

Swathi’s non-microbiology picks

Issac Asimov on his predictions for 2019 – Issac Asimov



November 12, 2018

Papers on metabolism, cancer and dietary fiber in this digest!

General Microbiome

Translating microbiome futures – Taroncher-Oldenburg G et al. – Nature Biotechnology

Human gut Microbiome

Prolonged Antibiotic Treatment Generates a Fluoroquinolone Resistant Gut Microbiome and Collateral Multi-Drug Resistance – Dubinsky et al. – biorxiv

Shifts in microbial transcription patterns prior to onset of Necrotizing enterocolitis may indicate low oxygen levels in the gut – Sher et al. – biorxiv

Dietary metabolism, the gut microbiome, and heart failure. – Tang WHW – Nature Reviews Cardiology

Long term but not short term exposure to obesity related microbiota promotes host insulin resistance. – Foley KP – Nature Communications 

Stability of vitamin B12 with the protection of whey proteins and their effects on the gut microbiome. – Wang H – Food Chemistry

Tongue Coating Microbiota Community and Risk Effect on Gastric Cancer. – Wu J – Cancer

Human Pregnancy Microbiome

Perinatal antibiotic exposure alters composition of murine gut microbiota and may influence later responses to peanut antigen. – Boutin RCT – Allergy Asthma Clin Immunol.

Animal experiments 

Effects of dietary fiber supplementation on fatty acid metabolism and intestinal microbiota diversity in C57BL/6J mice fed with high fat diet. – Zhai X et al – Journal of Agricultural Food Chemistry

Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis. – Ma C – Microbiome

The prebiotic inulin modulates gut microbiota but does not ameliorate atherosclerosis in hypercholesterolemic APOE*3-Leiden.CETP mice. – Hoving LR et al – Scientific Reports

Plant, root, and soil Microbiome

Comparing DNA, RNA and protein levels for measuring microbial activity in nitrogen-amended soils  Orellana et al. – biorxiv

Water and Extremophile Microbiome

Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean. – Enav H et al. – Nature Communications

Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment. – Lang XL – Archaea



GutLogo: Agent-based modeling framework to investigate spatial and temporal dynamics in the gut microbiome. Lin C et al. – PLoS One

Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers’ diarrhea – Zhu Q – Microbiome

Swathi’s non-microbiology picks

Building a local community of practice in scientific programming for Life Scientists – Sarah L. R. Stevens – biorxiv



September 21, 2018

A lot of nutrition papers in todays digest! Along with some interesting papers on optimizing microbiome sample prep and modeling results. Also included is an article on gender bias in science. 

General microbiome

The microbiome and inborn errors of metabolism: Why we should look carefully at their interplay? – Colonetti K – Genetics and Molecular Biology

A Comparative Review on Microbiota Manipulation: Lessons From Fish, Plants, Livestock, and Human Research. – Brugman S – Frontiers in Nutrition

Human gut microbiome

Propionate-producing bacteria in the intestine may associate with skewed responses of IL10-producing regulatory T cells in patients with relapsing polychondritis. – Shimizu J – PLoS One

Ectopic Fat Accumulation in Distinct Insulin Resistant Phenotypes; Targets for Personalized Nutritional Interventions. -Trouwborst I – Frontiers in Nutrition

The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units. -Aguirre de Cárcer D. – Scientific Reports

Microbiota-sensitive epigenetic signature predicts inflammation in Crohn’s disease. – Kelly D – JCI Insight

Mannose Alters Gut Microbiome, Prevents Diet-Induced Obesity, and Improves Host Metabolism. – Sharma V – Cell Reports
The Effect of White Rice and White Bread as Staple Foods on Gut Microbiota and Host Metabolism. – Mano F – Nutrients

Human Oral microbiome

Child Weight Gain Trajectories Linked To Oral Microbiota Composition. – Crag SJC – Scientific Reports

Human Pregnancy microbiome

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. – Goltsman DSA – Genome Research

Animal experiments 

Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice. – Skalski JH – PLoS Pathogens

Impact of Cross-Contamination Concentrations of Doxycycline Hyclate on the Microbial Ecosystem in an Ex Vivo Model of the Pig’s Cecum. – De Mulder T – Microbial Drug Resistance

Micromanaging Immunity in the Murine Host vs. the Mosquito Vector: Microbiota-Dependent Immune Responses to Intestinal Parasites. – Yordanova IA – Frontiers in Cellular and Infection Microbiology

The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch. – Michel AJ – Microbiome

Plant, root, and soil microbiome

Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil. – Peng J – Microbiome

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. – Vavourakis CD – Microbiome



Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies. – Wang Z – Frontiers in Cellular and Infection Microbiology


Modelling microbiome recovery after antibiotics using a stability landscape framework – – Liam P. Shaw – bioRxiv


The role of adjuvant probiotics to attenuate intestinal inflammatory responses due to cancer treatments. – Thomas M – Beneficial Microbes

Swathi’s non-microbiology picks

How female scientists can confront gender bias in the workplace  – Kendall Powell – Nature


August 21, 2018

Papers on the human virome, inflammatory bowel disease and new methods to understanding the microbiome. Also included is a documentary by Derek Muller (Veritasium) about Vitamins and host health for anyone interested in nutrition and the microbiome. 


Microbiome Researcher – Clinical Microbiomics

General microbiome

Enteric virome of Ethiopian children participating in a clean water intervention trial E Altan – PLoS One

Human respiratory microbiome

Association of nasal microbiome and asthma control in patients with chronic rhinosinusitis. – Yang HJ – Clinical and Experimental Allergy

In vivo imaging of bacterial colonization of the lower respiratory tract in a baboon model of Bordetella pertussis infection and transmission  – Thibaut Naninck – Scientific Reports

Human gut microbiome

Introducing insoluble wheat bran as a gut microbiota niche in an in vitro dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community. – De Paepe K – Environmental Microbiology

Quorum sensing can be repurposed to promote information transfer between bacteria in the mammalian gut. – Kim S – ACS Synthetic Biology

A meta-analysis reveals universal gut bacterial signatures for diagnosing the incidence of shrimp disease.  – Yu W – FEMS Microbiology Ecology

The Microbial Composition of Bacteroidetes Species in Ulcerative Colitis Is Effectively Improved by Combination Therapy With Fecal Microbiota Transplantation and Antibiotics. – Ishikawa D – Inflammatory Bowel Disease

In vitro gut metabolism of [U‐13C]‐quinic acid, the other hydrolysis product of chlorogenic acid – Martine Naranjo Pinta – Molecular Nutrition and Food Nutrition

Bariatric surgery changes gut microbiota composition independent of operation type – Fernanda L Paganelli – bioRxiv

Human Skin microbiome

Antibacterial soap use impacts skin microbial communities in rural Madagascar. – Yu JJ – PLoS One

Animal experiments 

Effects of dietary supplementation of the lignocelluloses FibreCell and OptiCell on performance, expression of inflammation-related genes and the gut microbiome of broilers. – Zeitz JO – Poultry Science

Multi-strain probiotics enhance immune responsiveness and alters metabolic profiles in the New Zealand black-footed abalone (Haliotis iris) – R Grandiosa – Fish and Shellfish Immunology

Plant, root, and soil microbiome

Antibiotics and Antibiotic Resistance Genes in Bulk and Rhizosphere Soils Subject to Manure Amendment and Vegetable Cultivation – C Chen – Journal of Environmental Quality



A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. – Williamson IA

An integrated, high-throughput strategy for multi-omic systems level analysis – Danielle B. Gutierrez – Journal of Proteome Research

Swathi’s non-microbiology picks

A new Documentary on Vitamins by Derek Muller – Vitamania

August 1, 2018

Todays digest has some interesting papers on fungi and gut microbiota, inflammation in the gut and a Nature Communications paper on stability criteria for complex microbial communities. Also included is an interesting paper on a mind-controlling fungus!

General microbiome

Fungi as Part of the Microbiota and Interactions with Intestinal Bacteria. – Kapitan M – Current topics in Microbial Immunology

Stability criteria for complex microbial communities. – Butler S – Nature Communications

Human respiratory microbiome

Exploring Host-Microbe Interactions in Lung Cancer. – Zhao Y – American Journal of Respiratory and Critical Care Medicine

Nasal microbiota clusters associate with inflammatory response, viral load, and symptom severity in experimental rhinovirus challenge.– Lehtinen MJ – Scientific Reports

Human gut microbiome

Gut Microbial β-Glucuronidase Inhibition via Catalytic Cycle Interception. – Pellock SJ – ACS Central Science

Effects of medicines used to treat gastrointestinal diseases on the pharmacokinetics of coadministered drugs: a PEARRL Review. – Litou C – The Journal of Pharmacy and Pharmacology

Activated ATF6 Induces Intestinal Dysbiosis and Innate Immune Response to Promote Colorectal Tumorigenesis. – Coleman OI – Gastroenterology

Dietary intake of fat and fibre according to reference values relates to higher gut microbiota richness in overweight pregnant women – CORRIGENDUM. – Röytiö H – The British Journal of Nutrition

The Potential of Gut Commensals in Reinforcing Intestinal Barrier Function and Alleviating Inflammation. – Hiippala K – Nutrients

Enteric Microbiota⁻Gut⁻Brain Axis from the Perspective of Nuclear Receptors. – Duszka K – International Journal of Molecular Sciences

Animal experiments 

Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats. – Wasimuddin – The ISME Journal

Antibiotic-induced dysbiosis predicts mortality in an animal model of <i>Clostridium difficile</i> infection. – Burdet C – Antimicrobial Agents and Chemotherapy

Plant, root, and soil microbiome

Plant Species and Heavy Metals Affect Biodiversity of Microbial Communities Associated With Metal-Tolerant Plants in Metalliferous Soils. – Borymski S – Frontiers in Microbiology

Food Microbiology

What’s in a name? ‘Non-coeliac gluten or wheat sensitivity’: controversies and mechanisms related to wheat and gluten causing gastrointestinal symptoms or disease. – Potter MDE – Gut

Role of whole grains versus fruits and vegetables in reducing subclinical inflammation and promoting gastrointestinal health in individuals affected by overweight and obesity: a randomized controlled trial. – Kopf JC – Nutrition Journal


Swathi’s non-microbiology picks

Robust manipulation of the behavior of Drosophila melanogaster by a fungal pathogen in the laboratory – Carloyn Elya – eLife



July 10, 2018

A review on microbial connections to depression and anxiety, effects of anthocyanins and flavanoids on the gut, and a Nature Communications paper on  Gut microbiota associations with common diseases and prescription medications! Also included are some articles on Oliver Sacks who would have turned 85 yesterday.

General microbiome

Mechanisms of action of vitamin D in colon cancer – Ferrer-Mayorga G – Journal of  Steroid Biochemistry and Molecular Biology

A review of dietary and microbial connections to depression, anxiety, and stress. – Taylor AM – Nutritional Neuroscience

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always. – Bengtsson-Palme J – Microbiome

Human respiratory microbiome

Aerodigestive dysbiosis in children with chronic cough. – Kazachkov M – Pediatric Pulmonology

Human gut microbiome

Shifts of Faecal Microbiota During Sporadic Colorectal Carcinogenesis. – Mori G – Scientific Reports

Gut microbiota associations with common diseases and prescription medications in a population-based cohort. -Jackson MA – Nature Communications

Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity. – Nyangahu DD – Microbiome

Animal experiments 

Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis – Raúl Miranda-CasoLuengo – bioRxiv

Dietary fiber increases the butyrate-producing bacteria and improves growth performance of weaned piglets. – Zhao J – J Agric Food Chem

Early intervention with faecal microbiota transplantation: an effective means to improve growth performance and the intestinal development of suckling piglets. – Cheng CS – Animal

Plant, root, and soil microbiome

A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome – Quigley CTC -Journal of Applied Phycology

Food Microbiology

Consumption of Black Legumes Glycine soja and Glycine max Lowers Serum Lipids and Alters the Gut Microbiome Profile in Mice Fed a High-Fat Diet. – Jing C – Journal of Agricultural Food Chemistry

A systematic literature review of the effect of anthocyanins on gut microbiota populations. – Igwe EO – Journal of Human Nutrition and Dietetics


Probiotics / prebiotics

The Mechanisms behind the Biological Activity of Flavonoids. – Gonzalez-Paramas AM – Current Medicinal Chemistry



Swathi’s non-microbiology picks

In honor of Oliver Sacks who would have been 85 yesterday: