November 14, 2018

Today’s digest is about how dietary shifts and low gluten diet changes the intestinal microbiome, fecal microbiota transplant in intestinal disorders, characterization of the most abundant bacteriophage family in the human gut, and Raman spectroscopy based method for fast identification of antibiotic resistance bugs.

Human gut microbiome

Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis – Yinghong Wang – Nature Medicine

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults – Lea BS Hansen – Nature Communications

Resilience of human gut microbial communities for the long stay with multiple dietary shifts – Hong Liu – Gut

Microbiome and its relation to gestational diabetes – Ramon V. Cortez – Endocrine

Effect of bifidobacterium breve A-1 on anxiety and depressive symptoms in schizophrenia: A proof-of-concept study – Ryo Okubo – Journal of Affective Disorders

Fecal Akkermansia muciniphila Is Associated with Body Composition and Microbiota Diversity in Overweight and Obese Women with Breast Cancer Participating in a Presurgical Weight Loss Trial – Andrew D Fruge – Journal of the Academy of Nutrition and Dietetics

An Open-Labeled Study on Fecal Microbiota Transfer in Irritable Bowel Syndrome Patients Reveals Improvement in Abdominal Pain Associated with the Relative Abundance of Akkermansia Muciniphila – Cruz-Aguliar RM – Digestion

Animal experiments

Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids – Shi-Jun Yue – American Journal of Physiology Endocrinology and Metabolism

Air microbiome

A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations – Joan Cáliz – PNAS

Phages and viruses

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis – Andrey N Shkoporov – Nature Communications


Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples – Yuan Gao – Nature Methods

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts – Justin D Silverman – Microbiome

Microbes in the news

Chinese scientists develop novel instrument for rapid profiling of antimicrobial resistance – EurekaAlert

Microbes on the market

Chr. Hansen Receives Joint Innovation Fund Grant to Develop Next Generation Microbial Solutions for Agriculture – Microbiome times

Non-microbiology picks

Remission of Human Type 2 Diabetes Requires Decrease in Liver and Pancreas Fat Content but Is Dependent upon Capacity for β Cell Recovery – Roy Taylor – Cell Metabolism



October 25, 2018

Roller coaster of fantastic articles today! Two sister articles from TEDDY cohort about development of the gut microbiota in early childhood and type-1 diabetes. Another article on association of the early gut microbiota with body mass index later in life in a Norwegian cohort. A multi-omics study of the rumen microbiota and insight into how human gut microbiota recovers following antibiotic exposure. And many more, keep reading…

Human gut microbiome

Recovery of gut microbiota of healthy adults following antibiotic exposure – Albert Palleja – Nature Microbiology

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study – Tommi Vatanen – Nature

Temporal development of the gut microbiome in early childhood from the TEDDY study – Christopher J. Stewart – Nature

Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort – Maggie A. Stanislawski – mBio

Human gut microbe co-cultures have greater potential than monocultures for food waste remediation to commodity chemicals – Matthew A. Perisin – Scientific Reports

Animal experiments

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem – Lindsey M. Solden – Nature Microbiology

A gut microbial factor modulates locomotor behaviour in Drosophila – Catherine E. Schretter – Nature

Dietary fibers inhibit obesity in mice, but host responses in the cecum and liver appear unrelated to fiber-specific changes in cecal bacterial taxonomic composition – Janice E. Drew – Scientific Reports

Plant, root, and soil microbiome

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes – Joshua Ladau – mSystems


Intestinal barrier dysfunction orchestrates the onset of inflammatory host–microbiome cross-talk in a human gut inflammation-on-a-chip – Woojung Shin – PNAS

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon – Anna Cusco – BioRxiv

Microbes in the news

3 million common procedures in England could become ‘life threatening’ without antibiotics – CNN

Antibiotic plus probiotic combination may kill off superbugs – Medical News Today

Microbes on the market

Microbiotica Attracts Equity Investment from Seventure’s Health for Life Capital Fund – Microbiome Times

Rebiotix and Microbiome Insights Collaborate on a Microbiome IBD Tool for Clinical Development – Microbiome Times

APC Microbiome Ireland pool resources to lead maternity probiotic venture –

Non-microbiology picks

How should autonomous vehicles be programmed? – ScienceDaily

February 2, 2017

Did you ever wonder about vitamin B12 role in microbiome organization and function? using a chemical probe mimic of vitamin B12, the authors reveal a light- and B12-dependent DNA regulator and predict that organismal interdependencies for B12 may be critical to microbiome stability and overall function.  On the extremophiles front, a study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the salt-secreting desert tree Tamarix aphylla.  An interesting paper reinforced linkages between the colonization of the foodborne pathogen E. coli O157:H7 in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders. And as for future generations, if you want to get your kids or students excited about microbiology, try an interactive tool created by Stanford bioengineers: the 3D printed microscope powered by your smartphone.

Continue reading

The new Microbiome Digest team

Microbiome Digest proudly presents: the New Microbiome Digest Team! From now on, Microbiome Digest will be taken over by a team of 21 enthusiastic scientist from all over the world.

I have tried to make this change as smoothly as possible, but I still anticipate some unanticipated SNAFU’s in the beginning. As we all need to adapt to this new style of publishing, there will probably be some irregularity in posting, some duplicate entries, or formatting issues. Or maybe you won’t notice anything at all!

Let’s give a warm welcome to the new Microbiome Digest team. Here is a short introduction to the new members (I am very short on time) – I will make a decent page with a better description in the near future.

Welcome on board!

Screen Shot 2017-01-15 at 5.03.00 PM.png

Help wanted for Microbiome Digest

Quick update on January 10: Thank you for an inbox full of applications! I will try to write back to each of you personally and set up a rotating publication scheme. I hope I have time to set something up over the upcoming weekend!

I’ve been running my Microbiome Digest blog almost continuously for 2.5 years. And it will come as no surprise that this has been slowly taking more and more of my time. So today’s post is about realizing that I will be needing some help to keep on running it.

The first Microbiome Digest post was on May 21, 2014. Click on the link to see how short it is, and compare that with the posts from the last couple of days. It took me more than 4 hours to prepare Thursday’s post!

The microbiome field has been growing a lot over the past few years, and I get more and more alerts and numbers of new papers to go through every day. Just look at the steady increase of the number of papers in the microbiome field on Pubmed. There is no sign that it’s slowing down anytime soon!

2000-2016 graph pubmed.png

Before Microbiome Digest was online, I had already been sending out nearly daily literature update emails to my Stanford coworkers for a couple of months. So in the past 3 years, I have been going through my alerts and preparing posts almost every day. After long days of lab work or data analysis. When I was writing a grant proposal. In the weekends. While traveling for work. On vacations. When I was sick. After the funeral of my sister. After burying my cat. At 1 AM. In hotel rooms and at airports, but usually at home.

Preparing the daily Digest has gradually taken away all my free time. I have not watched TV in years. I have no idea what Game of Thrones is. Or West World. No time. The Digest always came first. On some days, it was easy. Just 30 papers to scan. On others, it was hundreds. There were days when I cried to see 10 new long Google Scholar alerts come in. But I always kept on going, because I did not want to disappoint my readers. However, the amount of work is starting to take away my 8 hours of sleep, and the past months have been very tough, and I’ve decided that I need to delegate some work to someone else.

So: I am looking for a couple of people who can help me run my blog. It would involve going through the alerts I have set up, selecting interesting papers, checking if they have already been posted in the previous days, sorting them in categories, getting the links to the papers, and write and publish a blog post via Wordpress. Ideally, we would have enough people in our team so we could all take turns, only have to do this once a week, with the flexibility to switch in case of the occasional travel or illness. I usually do the work at night to prepare for the next morning, but it could also be done in the early morning. As long as we can continue to post every day around 9am Pacific time.

The ideal person to do this job would be / have:

  • Graduate student or postdoc
  • Working on human, animal, plant, or environmental microbiome
  • Can commit to a block of 2-4 hours on a set day of the week
  • Experience using PubMed and Google Scholar
  • Reliable person with reliable access to computer and internet
  • Interest in science writing/science communication

Just to make sure, this is a voluntary, unpaid position. But it will help you to stay on top of the microbiome literature, never run out of papers to contribute for Journal Club, broaden your network, and expand your resume and experience.

Please contact me at my gmail address (see below), using “Microbiome Digest Help” as the subject line – the ability to follow instructions will be part of the selection process 😀   – and only contact me if you can seriously commit to at least one night per week. Just a one-paragraph description of who you are, what your topic of research is, and why you would love to be part of this new team is enough. No need to send a resume or CV. Thanks!


Screen Shot 2017-01-08 at 12.03.20 PM.png




October 1, 2016

Microbiome of tonsils in kidney disease, poisonous salamanders,  Kruger National Park, drought tolerance of plants, and human milk microbiota.

Pregnancy and birth

Distinct patterns in human milk microbiota and fatty acid profiles across specific geographic locations – Himanshu Kumar – Frontiers in Microbiology

ReviewSystematic Review of the Human Milk Microbiota – John L. Fitzstevens – Nutrition in Clinical Practice

Human respiratory microbiome

Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy – Hirofumi Watanabe – Nephrology Dialysis Transplantation

Human skin microbiome

Microbiota is a primary cause of pathogenesis of chronic wounds – R. Wolcott – Journal of Wound Care

Animal and in vitro models

Transient and Prolonged Response of Chicken Cecum Mucosa to Colonization with Different Gut Microbiota – Jiri Volf – PLOS ONE

Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel – Jonas Cremer – PNAS

Animal microbiome

Cutaneous Bacterial Communities of a Poisonous Salamander: a Perspective from Life Stages, Body Parts and Environmental Conditions – Eugenia Sanchez – Microbial Ecology

Characterization of the Cutaneous Bacterial Communities of Two Giant Salamander Subspecies – Obed Hernández-Gómez – Microbial Ecology

Host-specific functional significance of Caenorhabditis gut commensals – Maureen Berg – Frontiers in Microbiology

Sexual variation of bacterial microbiota of Dendroctonus valens guts and frass in relation to verbenone production – Letian Xu – Journal of Insect Physiology

Plant, root, and soil microbiome

Comparative Metagenomics Reveal Phylum Level Temporal and Spatial Changes in Mycobiome of Belowground Parts of Crocus sativus – Sheetal Ambardar – PLOS ONE

Community composition and abundance of nitrifiers and total bacterial and archaeal populations in savanna soils on contrasting bedrock material in Kruger National Park, South Africa – Saskia Rughoeft – Frontiers in Microbiology

Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance – Eva C. Preisner – Frontiers in Microbiology

Plant Drought Tolerance Enhancement by Trehalose Production of Desiccation-Tolerant Microorganisms – Juan I. Vílchez – Frontiers in Microbiology

Associations between an Invasive Plant (Taeniatherum caput-medusae, Medusahead) and Soil Microbial Communities – Elise S. Gornish – PLOS ONE

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input – Alacia Armstrong – Scientific Reports

Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming – Kai Xue – mBio

Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure – Suzanne L. Ishaq – Microbial Ecology


Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes – María-Eugenia DeCastro – Frontiers in Microbiology

Food microbiology

Kimchi and Other Widely Consumed Traditional Fermented Foods of Korea: A Review – Jayanta Kumar Patra – Frontiers in Microbiology


Fungal Super Glue: The Biofilm Matrix and Its Composition, Assembly, and Functions – Kaitlin F. Mitchell – PLOS Pathogens

Microbes in the news

Dr. Rob Knight, co-founder of American Gut, Discusses the Microbiota and Microbiota testing – Dr Ruscio

Flesh-Eating Bacteria Like It Hot – Hannah Gavin – Discover Magazine

Poll: display full posts or not?

Recently, I started to use the “Continue Reading” button here, which will only display the top part of a post, so that posts won’t show at full length at the home page. If you click on the post link, or the button, it will display the full post. A reader commented, however, that it was less easy to search for keywords from the home page. I’m very open for changing it back to the full-post display, but let’s do a poll first. My first poll here!


Update July 14: Alright, the audience has spoken! The majority of voters so far does not like the Continue Reading feature, so I have removed it from the recent blog posts, and I will go back to showing full-length posts on the home page.