January 29, 2026

Animal microbiome

Host genetic background and environment have different effects on the establishment and structure of the adult worker honey bee gut microbiota – Breven Stark – PLOS ONE

Microbiota discovered in scorpion venom – Barbara Murdoch – PLOS ONE


Animal experiments / Disease models

Intestinal decontamination with rifaximin attenuates LSEC dysfunction and liver fibrosis in mice – Tingting Su – PLOS ONE

Periplaneta americana extract ameliorates recurrent oral ulcers in rats by enhancing the intestinal epithelial barrier and regulating gut microbiota – Kailing Li – PLOS ONE

Formononetin ameliorates SP-induced urticaria in mice via suppressing TAK1/MAK signaling pathway -Yan Wu –PLOS ONE

Lipopolysaccharide induced mouse depression model can better simulate changes in peripheral blood FFAs in alMDD -Jincai Pan –PLOS ONE


Human microbiome (gut & reproductive)

Stool and vaginal microbiome profiles patterns among Black and White endometrial cancer survivors: A pilot study in North Carolina – Mu Jin – PLOS ONE


Infection, immunity & host–microbe interactions

Examining the role of IgA in a persistent model of Staphylococcus aureus colonization – Yunys Perez-Betancourt – PLOS Pathogens

Diversify and conquer: How effector diversity is shaped by host–microbe co-evolution -Marion C Müller – PLOS Pathogens

Oo-No: Ophidiomyces ophidiicola–bacterial interactions and the role of skin lipids in development of ophidiomycosis – Jason W Dallas – PLOS Pathogens


Probiotics & food microbiology

In-vitro evaluation of probiotic potential of gut microbes isolated from retail chicken – Sangram Biswas – PLOS ONE


Antimicrobial resistance & clinical microbiology

Extended-spectrum β-lactamase and carbapenemase-producing Enterobacterales among adult patients and their family members at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia – Dessie Abera – PLOS ONE


Microbiome methods & bioinformatics

PCR bias impacts microbiome ecological analyses – Dharmik R Rathod – PLOS Computational Biology

CoSMIC: A hybrid approach for large-scale, high-resolution microbial profiling of novel niches – Maor Knafo – PLOS ONE


Environmental & applied microbiology

Developing a simple, cost-effective proof-of-concept vaccine candidate against EHEC for cattle – Cecilia M Duarte – PLOS ONE

Preventive effect of bentonite against pyoderma via direct binding capability of staphylococci – Mao Kaneki – PLOS ONE

Ultraviolet light and polyethylene glycol as environmental cleaning agents to reduce contamination of Pseudogymnoascus destructans in bat hibernacula – Alyssa J Stulberg – PLOS ONE


Water, pollution & human exposure

Micro- and nanoplastics in biological samples following a drinking water intervention in Barcelona, Spain – Emma Calikanzaros – PLOS Water


Human disease & biomarkers

Evidence of an allostatic response by intestinal tissues following induction of joint inflammation – Meghan M Moran – PLOS ONE

Multi-modal data to identify key factors influencing lung injury in ARDS patients undergoing invasive mechanical ventilation: A prospective multi-center observational study protocol – Zhimei Duan – PLOS ONE

Integrative genomic analysis reveals DHX58 as a key player in gastric cancer – Yan Li – PLOS ONE

Identifying biomarkers for diagnosis and disease activity monitoring in PSC-IBD and UC through proteomic profiling: A prospective study protocol – Ondrej Fabian – PLOS ONE

S100-alarmins, antenatal corticosteroids and the risk of late-onset sepsis in preterm infants – Gloria Kessler – PLOS ONE

Exploring the role of the key gene TNFAIP3 between periodontitis and influenza A through bioinformatic analysis and molecular docking – Mingxiang Xu – PLOS ONE

GC-MS based bioactive profiling of Phyllanthus niruri and its antibacterial potential – Zubair Khalid Labu – PLOS ONE

December 04, 2025

Human & Clinical Microbiome

Modifiable risk factors for inflammatory bowel disease in KuwaitReem Alhasan – PLOS ONE


Host–Pathogen Interactions (Human-focused)

Pharmacokinetic profiles of Moutan Cortex after single and repeated administration in a colitis modelJin-Hwa Kim – PLOS ONE

ceRNA regulatory network and immune-neurodegenerative mechanisms of peripheral CD4+ T cells in Parkinson’s diseaseLijun Guo – PLOS ONE

Safety profile of TNF-α inhibitors in pediatric patientsYanmo Yang – PLOS ONE


Animal Microbiome

Gut bacteria induce heterologous immune priming in Rhodnius prolixusCarissa A Gilliland – PLOS Pathogens

A reliable in vitro rumen culture system for screening anti-methanogenic compoundsPhilip P Laric – PLOS ONE

High-Resolution Melting assays for discrimination of fungal pathogens causing Grapevine Trunk DiseasesFilipe Azevedo-Nogueira – PLOS ONE

Bimodal expression of Type III Secretion System 2 enables cooperative virulence in Salmonella TyphimuriumMilada Pospíšilová – PLOS Pathogens


Animal Experiments (disease models)

The female reproductive tract–gut axis in gastrointestinal parasitic infectionOlivia Shorthouse – PLOS Pathogens

Toxoplasma gondii disrupts intestinal microbiota and host metabolism in ratsJi-Xin Zhao – PLOS NTDs

Sarcopenia modelling by portal vein ligation inducing hyperammonemia in ratsMaria Nadinskaia – PLOS ONE

Evogliptin prevents ceramide-induced pyroptosis via NLRP3/GSDM-D pathwayRazia Rashid Rahil – PLOS ONE

Mechanistic insight into the antidiabetic effects of Ficus hispida fruitsNusaiba Jahan – PLOS ONE


Computational Microbiology & Modeling

Identification of dynamic models of microbial communitiesAna Paredes-Vázquez – PLOS Computational Biology

Accuracy of the Lotka–Volterra model fails in strongly coupled microbial systemsMichael P Mustri – PLOS Computational Biology


Plant, Soil & Ecological Microbiome

Distinct S-adenosylmethionine synthases link phosphatidylcholine to mitochondrial functionAthena L Munden – PLOS Biology

Microbiome digest, 31 October 2014

Happy Halloween! Today we have fungal communities in mammals, more on the TMAO story, some microbiome reviews, honey bee colonization, and microbophobia papers.

General human/mammalian microbiome

* Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease – Lisa Rizzetto, Carlotta De Filippo and Duccio Cavalieri – European Journal of Immunology

“In this review, we describe the ecology and the human niches of our fungal “fellow travelers” in both health and disease, discriminating between passengers, colonizers, and pathogens based on the interaction of these fungi with the human immune system.”

Prognostic Value of Elevated Levels of Intestinal Microbe-Generated Metabolite Trimethylamine-N-Oxide in Patients With Heart Failure – Refining the Gut Hypothesis – W.H. Wilson Tang – Journal of the American College of Cardiology

“High TMAO levels were observed in patients with HF, and elevated TMAO levels portended higher long-term mortality risk independent of traditional risk factors and cardiorenal indexes.”

* Deciphering the human microbiome using next-generation sequencing data and bioinformatics approaches – Yihwan Kim – Methods

“This review examines computational methods that are valuable for the analysis of human microbiome, and highlights the results of several large-scale human microbiome studies.”

Human gut microbiome

Novel opportunities for the exploitation of host–microbiome interactions in the intestine – Ingmar JJ Claes – Current Opinion in Biotechnology

“New sequencing technologies have dramatically increased our knowledge on the composition of the human intestinal microbiota in health and disease. ”

Animal microbiome

* Routes of Acquisition of the Gut Microbiota of the Honey Bee Apis mellifera – J. Elijah Powell – Applied and Environmental Microbiology

“Colonization patterns were evaluated using quantitative real-time PCR (qPCR) to assess community sizes and using deep sequencing of 16S rRNA gene amplicons to assess community composition.”

Soil microbiome 

Landscape-scale Variation in Pathogen-suppressive Bacteria in Tropical Dry Forest Soils of Costa Rica – Kristen K. Becklund – Biotropica

“To estimate the potential for disease suppression among Streptomyces communities in tropical dry forests, we cultured soil-borne Streptomyces from plots in two forests in northwestern Costa Rica (Santa Rosa and Palo Verde)”

Microbes in the news

More scary than Halloween: this month in germophobia microbophobia – Jonathan Eisen – MicroBEnet

“It seems that any time a holiday comes around in the US, the press starts to ramp up the writing of stories about evil microbes that are lurking all around us. “

MSU and Detroit analyze tiny bacteria to investigate murders – Kate Wells – Michigan Rado

““Can we use these communities to identify whether a person is from a certain location or if they’ve been to a location?” asks Benbow”

Science and career

Satire: Sixth Person Dies As Another “Dance Your PhD” Video Goes Wrong – The Allium

“Principal Investigator, Professor Tom Morrow (61) slipped as he was mimicking a helix-turn-helix motif as part of a much larger transcription factor protein.”

10 Creative Careers That Rely on Science and Math – Alexandra Ossola – The Atlantic

“Knowledge of STEM subjects isn’t just essential for physicists or computer engineers. Fashion designers, zookeepers, and deep-sea divers also use it every day.”

Bik’s Picks

Lava Flow In Hawaii Spares Homes, But Threatens To Cut Off Community – Scott Neuman – NPR

“Officials in Hawaii are sending National Guard troops to the town of Pahoa on the Big Island, where a lava flow is creeping toward a main road, threatening to cut off the community.”

100-Year-Old Time Capsule Discovered – Clapway

“A 100-year old time capsule was found at Baltimore’s Washington Monument during a restoration project. And it seems officials are hesitant to even open it because of how old it is.”

Researchers: Science says girls’ sexualized Halloween costumes are scary – Rebecca C Bigler and Sarah McKenney – Dallas News

“Parents could also foster girls’ creativity by encouraging them to make their own costumes. “

And, related to the post above, make sure to read the hilarious comments here:
Delicious Women’s Phd Darling Sexy Costume – Amazon

“Sexy graduation gown is a micro mini with zip up front. Gold sash, hat, and diploma included”

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