January 18, 2021

Today’s articles primarily focus on the human gut microbiome, with one paper finding that artificial sweeteners may not be as bad for the gut as we think, and a link between the gut microbiome and chronic kidney disease by Yang et al. Another great paper also involved the use of biocontrol strains in plants to reduce wheat disease. Enjoy!

Human gut microbiome

Settlers of our inner surface – Factors shaping the gut microbiota from birth to toddlerhood. Laursen et al. FEMS Microbiology Reviews

Synbiotics alleviate the Gut Indole Load and Dysbiosis in Chronic Kidney Disease. Yang et al. Cells.

Effects of Transanal Irrigation on Gut Microbiota in Pediatric
Patients with Spina Bifida.
Furuta et al. Journal of Clinical Medicine.

High-dose saccharin supplementation does not induce gut microbiota changes or glucose intolerance in healthy humans and mice. Joan Serrano et al. Microbiome.

[Preprint] Listeria monocytogenes faecal carriage is common and driven by microbiota. Marc Garcia-Garceca et al. Bioxriv.

Modelling the effect of birth and feeding modes on the development of human gut microbiota. Xiong et al. Proceedings of the Royal Society b.

Gut microbiome partially mediates and coordinates the effects of genetics on anxiety-like behavior in Collaborative Cross mice. Jin et al. Scientific reports.

Plant, root and soil microbiome

Biocontrol of Two Bacterial Inoculant Strains and Their Effects on the Rhizosphere Microbial Community of Field-Grown Wheat. Wang et al. BioMed Research International


[preprint] Utilizing the Food-Pathogen Metabolome to Putatively Identify Biomarkers for the Detection of Shiga Toxin-Producing E. coli (STEC) from Spinach. Jadhav et al. Preprints.

A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis. Yan et al. Microbiome.

October 29, 2020

Good morning! The highlight today would be a trial detailing the use of faecal microbiota transplantation in diabetes – with some surprising findings. There is also an interesting paper on the role of iron uptake systems in intestinal virulence in the Escherichia genus to read!


[Preview] Identification of SARS-CoV-2 Inhibitors using Lung and Colonic Organoids. Han et al. Nature.

Human gut microbiome

Toplogical analysis reveals state transitions in human gut and marine bacterial communities. Chang et al. npj Biofilms and Microbiomes.

Faecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomised controlled trial. Groot et al. Gut.

[Review] A review of a potential and promising probiotic candidate ‐ Akkermansia muciniphila. Cheng and Xie. Journal of Applied Microbiology.

Vaginal microbiome

Vaginal microbiota and human papillomavirus infection among young Swedish women. Cheng et al. npj Biofilms and Microbiomes.

Animal Experiments

Correlation of gut microbiota and neurotransmitters in a rat model of post-traumatic stress disorder. Zhou et al. Journal of Traditional Chinese Medical Sciences.

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study. Galardini et al. PLOS genetics.

Campylobacter jejuni persistently colonizes gnotobiotic altered Schaedler flora C3H/HeN mice and induces mild colitis. Brand et al. FEMS Microbiology Letters.

Animal microbiome

Comparative Microbiome Analysis of Three Species of Laboratory-Reared Periplaneta Cockroaches Lee et al. Korean journal of Parasitology.

Plant, root and soil microbiome

Biological invasions alter environmental microbiomes: A meta-analysis. Malacrinó et al. PLOS one.

September 27, 2020

Good morning, a few interesting papers today. In particular one paper finding a link between the meconium microbiome and head circumference is a great read, and the paper on the package MicrobiomeExplorer for R.

Pregnancy and Early Life

Meconium microbiome and its relation to neonatal growth and head circumference catch-up in preterm infants. Terrazza Nutricioist et al. PLOS ONE.

Human mouth microbiome

Photobiomodulation modulates inflammation and oral microbiome: a pilot study. Zanotta et al. Biomarkers.

Human vaginal microbiome

Changes in Vaginal Microbiome in Pregnant and Nonpregnant Women with Bacterial Vaginosis: Toward Microbiome Diagnostics? Mohamed et al. OMICS: A Journal Of Integrative Biology.

Human gut microbiome

Role of Gut Microbiome and Microbial Metabolites in Alleviating Insulin Resistance After Bariatric Surgery. Wang et al. Obesity Surgery

[Pre-print] Multi-omic Characterization of the Taxa-function Relationship in Infant Gut Microbiomes. Nguyen et al. Research Square.


MicrobiomeExplorer: An R package for the analysis and visualization of microbial communities. Reeder et al. Bioinformatics

Animal experiments

[Pre-print] Preventive Antibiotic Treatment Increases Neonatal Chicks Susceptibility to Salmonella Infection Via Disrupting Gut Microbiota and Linoleic Acid Metabolism. Mei et al. Research Square.

Plant, root and soil microbiome

Rhizospheric microbiomes help Dongxiang common wild rice (Oryza rufipogon Griff.) rather than Leersia hexandra Swartz survive under cold stress. Xu et al. Archives of Agronomy and Soil Science

August 27, 2020

Good morning! Today has a great nature paper on bacterial metabolic crossfeeding that can result in altered egg laying and reproducing behaviour, and additionally a paper showing how bacterial probiotics induce anergy in mice with Cow’s Milk allergy.

General microbiome

Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour, Henriques et al, Nature.

The Impact of the Postpartum “Doing-the-Month” Practice on Human Milk Microbiota: A Pilot Study in Taiwan, Chen et al. Microorganisms.

Vaginal microbiota

Glycan cross-feeding supports mutualism between Fusobacterium and the vaginal microbiota, Agarwal et al, PLOS biology.

Human gut microbiome

How Serotonin Level Fluctuation Affects the Effectiveness of Treatment in Irritable Bowel Syndrome, Vahora et al. Cureus.

Animal experiments

Three Candidate Probiotic Strains Impact Gut Microbiota and Induce Anergy in Mice with Cow’s Milk Allergy. Esber et al. Public and environmental Health Microbiology.

Plant, root and soil microbiome

Role of environmental factors in shaping the soil microbiome, Islam et al. Environmental Science and Pollution research.


Predictive analysis methods for human microbiome data with application to Parkinson’s disease, Dong et al, PLOS One.

July 9, 2020

Good morning! Today there are not many papers, but there are two interesting highlights. The first being a COVID paper analysing the immunological profiles of patients, suggesting an immune-based therapeutic intervention may be the way to go. The second paper analysing the oral microbiome in oral cancer patients, showing significant alterations in diversity and specific genuses in these patients.



Immunological and inflammatory profiles in mild and severe cases of COVID-19. Song et al. Nature Communications.

Human microbiome

Oral microbial dysbiosis and its performance in predicting oral cancer. Su et al. Carcinogenesis.

Animal microbiome

Potential of indigenous Bacillus spp. as probiotic feed supplements in an extruded low‐fish‐meal diet for juvenile olive flounder, Paralichthys olivaceus. Niu et al. Journal of the World Aquaculture Society.

Animal experiments

Glyphosate-based herbicides influence antioxidants, reproductive hormones and gut microbiome but not reproduction: A long-term experiment in an avian model. Ruuskanen et al. Environmental pollution.

Evidence of Microbiome-Drug Interactions Between the Antimalarial Lumefantrine and Gut Microbiota in Mice. Ippolito et al. The American Journal of Tropical Medicine and Hygiene.

Plant, root and soil microbiome

The bacterial community and metabolome dynamics and their interactions modulate fermentation process of whole crop corn silage prepared with or without inoculants. Xu et al. Society for Applied Microbiology.

Water and extremophile microbiome

Host and environmental determinants of microbial community structure in the marine phyllosphere. Vogel et al. PLOS ONE.

May 16th, 2020

Good morning!

A few nice studies today, with highlights being utilising Streptomyces endophytes to aid in plant growth, a review on the gut-brain-axis with a focus on psychiatry, and a bioinformatics study looking into the role of pathogenic E.coli in cancer. Enjoy!


The coding capacity of SARS-CoV-2 Y.Finkel/O. Mizrahi et al. bioXriv.

Human vaginal microbiome

The study of host-bacterial relationships and immune function in different vaginal environments (Study in progress) A. berard et al. Journal of Obstetrics and Gynaecology Canada.

Human gut microbiome

Relationship between the composition of the digestive microbiota and the concentrations of opportunistic pathogens in intensive care patients. C. Fontaine et al. bioXriv.

Animal microbiome

Evaluation of fecal Lactobacillus populations in dogs with idiopathic epilepsy: a pilot study. Karen R. Muñana et al. Animal microbiome.

Plant, root and soil microbiome

Streptomyces endophytes promotes the growth of Arabidopsis thaliana S. F Worsley et al. bioXriv.

Water and extremophile microbiome

Deciphering a marine bone degrading microbiome reveals a complex community effort E. Borchert et al. bioRxiv.


Human microbiome and homeostasis: insights into the key role of prebiotics, probiotics and symbiotics. B. Salehi et al. Critical Reviews in Food Science and Nutrition.

Probiotics and the Microbiota-Gut-Brain Axis: Focus on Psychiatry. Mörkl S. Current Nutrition Reports.


Novel Discoveries Targeting Pathogenic Gut Microbes and New Therapies in Pancreatic Cancer: Does Pathogenic E. coli Infection Cause Pancreatic Cancer Progression Modulated by TUBB/Rho/ROCK Signaling Pathway? A Bioinformatic Analysis. W. Luo et al. BioMed Research international.

April 13, 2020

Hi everyone!

In today’s digest there is a range of exciting papers. The first paper looks into using a COVID-19 RBD vaccine on rodents. You will also find a great study on utilising Myxobacterium to fight cucumber wilt – even as an avid cucumber hater I appreciated this one! A third highlight is an exciting clinical study of heat-inactivated Bifidobacterium in reducing patient IBD symptoms.


Preprint: The SARS-CoV-2 receptor-binding domain elicits a potent neutralizing response without antibody-dependent enhancement – Quinlan et al.

Preprint: Comparison of SARS-CoV-2 infections among 3 species of non-human primates – Lu et al.

Preprint: Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence – Leary et al.

Human gut microbiome

Preprint: Short-chain fatty acid production by gut microbiota from children with obesity is linked to bacterial community composition and prebiotic choice – Holmes et al.

Short Review: In sickness and health: Effects of gut microbial metabolites on human physiology – Glowacki & Martens. PLOS Pathogens.

Animal experiments

Evaluation of microbiome-host relationships in the zebrafish
gastrointestinal system reveals adaptive immunity is a target of bis(2-ethylhexyl) phthalate (DEHP) exposure
– Adamovsky et al. Environmental Science & Technology.

Abnormal gut microbiota composition is associated with experimental autoimmune prostatitis‐induced depressive‐like behaviors in mice – Du et al. The Prostate.

Plant, root and soil microbiome

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios – P. Braga et al. Microbiome.

Predatory myxobacterium controls cucumber fusarium wilt by regulating soil microbial community – Ye et al. Microbiome.

Food Microbiology

Green tea polyphenols boost gut-microbiota-dependent mitochondrial TCA and urea cycles in Sprague–Dawley rats – Zhou et al. The Journal of Nutritional Biochemistry.


Heat-inactivated Bifidobacterium bifidum MIMBb75 (SYN-HI-001) in the treatment of irritable bowel syndrome: amulticentre, randomised, double-blind, placebo-controlled clinical trial – Andresen et al. The Lancet Gastroentrology & Hepatology.