July 30th, 2021

Today’s papers are primarily plant and environment related, but there’s also a great couple papers on the humanmicrobiome – discussing streptococci’s ability to colonise the ear, as well as a mini-review discussing oral microbial transplantation in improving COVID-19 outcomes. Have a great day!

Human general microbiome

Competitive advantage of oral streptococci for colonization of the middle ear mucosa. Jacob et al. bioRxiv.

Human gut microbiome

Utilizing machine learning with knockoff filtering to extract significant metabolites in Crohn’s disease with a publicly available untargeted metabolomics dataset – Bin Masud et al- PLOS one.

Human vaginal microbiome

Modeling the temporal dynamics of cervicovaginal microbiota identifies targets that may promote reproductive health – Munoz et al – Microbiome.

Human respiratory microbiome

The forgotten oral microbial transplantation for improving the outcomes of COVID-19 – AbdelMassih et al – New microbes and New Infections. [Mini-review]

Plant, root and soil microbiome

Metabolomics and microbiome reveal impacts of rhizosphere metabolites on alfafa continuous cropping – Wang et al -bioRxiv.

Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient – Seitz et al – bioRxiv.

Unraveling negative biotic interactions determining soil microbial community assembly and functioning -Romdhane et al -The ISME journal.

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups – Langwig et al -The ISME journal.

Impact of microecological agents on water environment restoration and microbial community structures of trench system in a Baiyangdian wetland ecosystem – Li et al – Journal of Applied Microbiology.

July 15, 2021

Good morning!

There are two particularly exciting papers today; a metagenomic analysis of the genera Akkermansia, providing evidence this is a primarily human microbiota member, and a paper aiming to further understand our knowledge of antibiotic exposure – finding significant alterations in neuronal gene expression in mouse pups.

Human gut microbiome

Development of a prebiotic blend to influence in vitro fermentation effects, with a focus on propionate, in the gut. Collins et al. FEMS Microbiology Ecology.

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Karcher et al. Genome Biology.

Pregnancy and Early life

Effects of early-life penicillin exposure on the gut microbiome and frontal cortex and amygdala gene expression. Volkova et al. iScience.

Animal experiments

Altered milk yield and rumen microbial abundance in response to concentrate supplementation during the cold season in Tibetan sheep. Lin-Sheng Gui et al. Electronic journal of Biotechnology.

Plant, root and soil microbiome

Time outweighs the effect of host developmental stage on microbial community composition. Dibner et al. FEMS Microbiology Ecology.

Food microbiology

Dynamics of dark fermentation microbial communities in the light of lactate and butyrate production. Detman et al. Microbiome.


A metabolomics pipeline for the mechanistic interrogation of the gut microbiome. Han et al. Nature.

May 10, 2021

Good morning! Today’s papers are mainly focused on the gut microbiota. A particular highlight is Li et al’s study, involving a network analysis of ulcerative colitis patient microbiotas, showing their potential role as opportunistic pathogens. Enjoy!

Gut microbiome

Iron status influences non-alcoholic fatty liver disease in obesity through the gut microbiome. Mayneris-Perxachs et al. Microbiome.

Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC). Li et al. BMC microbiology.

A meta-analysis of Gut Microbiota in Children with Autism. Andreo-Martinéz et al. Journal of autism and developmental disorders.

Pregnancy and early life

Deviations in the gut microbiota of neonates affected by maternal group B Streptococcus colonization. Li et al. BMC microbiology.

Animal experiments

Preprint: Longitudinal changes in diet cause repeatable and largely reversible shifts in gut microbial communities of laboratory mice and are observed across segments of the entire intestinal tract. Low et al. Bioxriv.

Cage environment regulates gut microbiota independent of toll-like receptors. Lipinski et al. Infection and Immunity.

Changes of gut microbiome composition and metabolites associated with hypertensive heart failure rats. Li et al. BMC microbiology.

Plant, root and soil microbiome

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field. Cadot et al. Microbiome.

Water and Extremophile Microbiome

Preprint: A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere. R. Osburn et al. Bioxriv.


geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response. Minot et al. Genome Biology.

April 25th, 2021

Today’s digest shows some great papers, with two highlights. The first being the value of a ketogenic diet on treating drug-resistant epilepsy in children, suggesting gut microbial dysbiosis is responsible for the drug resistance. the second is a thorough analysis of both the developing microbiota in goats using metagenomics and metatranscriptomics by Pan et al. Enjoy!

Gut microbiome

(Preprint) Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients – Moreira-Rosário et al. Bioxriv.

HPV infection and bacterial microbiota in the semen from healthy men. – Tuomimen et al. BMC Infectious Diseases.

(Review) Gastrointestinal dysfunction in Parkinson’s disease: molecular pathology and implications of gut microbiome, probiotics, and fecal microbiota transplantation – Metta et al. Journal of Neurology.

Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets – Gong et al. Microbial pathogenesis.

Vaginal microbiome

Oral administration of Lactobacillus crispatus M247 to papillomavirus-infected women: results of a preliminary, uncontrolled, open trial – Di Pierro et al. Minerva Obstrestics and Gynecology.

Animal experiments

(Preview) Bugs R Us: Restoring sociability with microbiota in autism. – Bellone and Lüscher. Cell reports medicine.

Anti-aging effects of a functional food via the action of gut microbiota and metabolites in aging mice – Zhang et al. Aging.

Animal microbiome

Dynamics of rumen gene expression,microbiome colonization, and their interplay in goats – Pan et al. BMC Genomics.

Evolution of rumen and oral microbiota incalves is influenced by age and time of weaning – Amin et al. Animal Microbiome

Plant, root and soil microbiome

(Review) Impacts of wildfire on soil microbiome in Boreal environments – Köster et al. Current opinion in Environmental Science & Health.

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.