The Microbiology of Sourdough Starters

If you bake sourdough, starter cultures are a big deal.  This mix of live yeasts and bacteria is what gives sourdough its distinctive taste.  There are even heirloom starters that have supposedly been passaged for over 100 years!  A group of researchers have crowd-sourced samples of sourdough starters from all over the world to study the variations between starters and their impact on finished sourdough bread, and to study the principles of microbial ecology in a relatively simple microbiome.  Stay tuned for results from this ongoing project!

Original Articles can be found here:

It’s not easy having a disrupted microbiome

The link between microbiome diversity and resistance to disease is often talked about, but is difficult to research.  A new study investigated this topic by disrupting the exterior microbiomes of tadpoles and measuring their resistance to parasites later in life.  Tadpoles were reared in either regular pond water, sterilized pond water, or sterilized pond water with long- or short-acting antibiotics.  All the tadpoles were exposed to parasitic gut worms once they reached adulthood.

Tadpoles raised in sterile pond water with long-acting antibiotics took longer to reach adulthood and weighed less as adults. They also had the lowest diversity in their skin and gut microbiomes of all the experimental groups.  Tadpoles raised in regular pond water had the greatest skin and gut microbial diversity.

When the frogs were exposed to parasitic worms, the same number of worms penetrated the guts of individuals in every experimental group, but the frogs that were raised in sterile pondwater or sterile pondwater with antibiotics ended up with significantly higher parasitic gut infestations.  Frogs with higher gut microbiome diversity were more resistant to parasitic worms than frogs who had lower gut microbiome diversity.

Original article can be found here:

Getting used to a new job: endosymbiotic algae that ferment, not photosynthesize

Many invertebrate animals, like green freshwater hydras, have symbiotic algae that live inside their cells; but only one species of vertebrate has algal symbionts: the salamander Ambystoma maculatum. Burns et al., from the American Museum of Natural History, compared gene expression patterns in Oophila amblystomatis algae that were 1) inside the salamanders’ egg capsules but still extracellular and 2) inside the cells of salamander embryos. They found that algae that were inside embryo cells showed signs of stress and had converted from an oxidative metabolism to fermentation, and additionally used host glutamine as a source of nitrogen. In contrast, the salamander host cells did not exhibit a stress response. They also increased expression of some regulatory genes that are known to suppress immune responses, and the few immunity-related genes that were differentially expressed were mostly involved in innate immunity.

Image attribution: By Fredlyfish4 (Own work) CC BY-SA 3.0  via Wikimedia Commons

Original article can be found here.

Are Wastewater Treatment Plants a “Hot Bed” For Antibiotic Resistance?


A portion of the antibiotics we consume are flushed down the toilet, either directly (not a good idea…) or by way of the human gastrointestinal tract. The antibiotics we increasingly feed to our meat sources may also end up at our local wastewater treatment facility. A recent metagnomic analysis reveals that bacteria containing a large number of antibiotic resistance genes (ARGs) and mobile elements (MEs) accumulate in our wastewater treatment plants, both in the activated sludge and anaerobic digestion processes. The ability of anaeorbic digestion to deactivate antibiotic resistant bacteria prior to biosolids utilization has been debated, and this study shows mixed results: anaeorbic digestion both increased and changed the overall abundance of ARGs but the number of MEs decreased. We should continue to monitor ARGs at our wastewater plants as we rely more heavily on antibiotics to protect and feed an ever growing human population.

Original article can be found here:


Not Time Sensitive: the microbiome throughout earth’s history

When we talk about microbiomes, most people think of host-associated microbial communities. This makes sense because the term was first made popular by the Human Microbiome Project.  Now, however, it has a broader meaning and refers to microbial communities everywhere, from buildings to natural hot springs.  Microbial life can be found in the strangest places, and microbiome research is as diverse as the subjects it addresses.

Between June 17th and July 22nd, 2017, an international group of students will learn about the microbiome in yet another context: the earth’s history.  For most of the time our planet has been in existence, only microbial life could thrive.  How microbes survived and influenced the conditions of early earth is one of the key questions in the field of geobiology.

Caltech and USC’s Wrigley Institute are hosting the Agouron International Geobiology course, to give graduate students and postdocs the tools to reach beyond their own field and tackle this interdisciplinary problem.  To chart our world’s history accurately, we must examine rock records and the biomarkers we find in them.

Taking water chemistry and microbiome samples at Mono Lake, CA

Curious?  Check out more here or follow along with #GeoBio17 on twitter for ongoing updates!

Summary – The Impact of Gut Microbiota on Gender-Specific Differences in Immunity.

Gut microbiota are different in male and female mammals, but no one has determined whether these differences are produced by innate variations in the male and female immune systems or whether immune system variations were produced by the microbiota in the gut.  To find out, Fransen et al examined the immune systems of male and female germ-free (GF) mice and discovered that innate differences in immunity already existed, including higher levels of type 1 interferon signaling in GF females and much higher levels of the gut microbes Alistipes, Rikenella, and Porphyromonadaceae, that proliferate in the absence of innate immune defense mechanisms, in GF males.  The team then transferred gut microbiota from conventional male and female mice into GF mice of the same gender or the opposite gender.  The female GF mice developed gut inflammations that produced weight loss and DNA damage if they received microbiota from conventional males. The authors concluded that microbiota-independent differences in the immune systems of males and females exist and drive gut microbiome differences between the genders.  They warned that these differences should be considered when designing treatment strategies to normalize gut microbiota caused by disease.

Original ArticleFrontiers in Immunity 2017, Volume 8, Article 754.


Dragon Blood Inspires Novel Synthetic Antimicrobial Treatment

The rise of multidrug-resistant bacteria in recent decades has increased the need for alternative antimicrobial treatments. Antimicrobial peptides offer a promising solution because they can target both gram-positive and gram-negative bacterial strains, some viruses, and fungi. Bioprospecting in wild animals, which have been exposed to a wide array of microbial assaults throughout their evolutionary history, has proven very useful in the identification of such peptides. In a recent article published in NPJ Biofilms and Microbiomes, Chung et al. 2017 identified a potential antimicrobial peptide in plasma collected from Komodo dragons (Varanus komodoensis). The team named the molecule DRGN-1 and created a synthetic version of it that demonstrated antimicrobial activity against both gram-negative Pseudomonas aeruginosa and gram-positive Staphylococcus aureus. It also inhibited the growth of biofilms and promoted wound healing.

Photo Credit: Tatiana Morozova



Chung, EMC, Dean, SN, Propst, CN, Bishop, BM, van Hoek, ML. (2017) Komodo dragon-inspired sythetic peptide DRGN-1 promotes wound-healing of a mixed-biofilm infected wound. npj Biofilms and Microbiomes, 3:9 doi:10.1038/s41522-017-0017-2

Unlikely Allies in an Anammox Bioreactor

Anaerobic ammonium oxidation (anammox) is one of the most energy efficient biotechnologies for removing nitrogen from high-strength ammonium wastewaters.  The system works using a combination of heterotrophic and anammox bacteria, but the specific metabolite exchange reactions between them in the anammox microbiome are poorly understood.  The team used metagenomics and metatranscriptomics to explore these interactions and determined that the anammox bacteria provide amino acids and B-vitamins essential for anaerobic respiration and growth, and the protein-degrading heterotrophic bacteria liberate the amino acids and vitamins from the anammox matrix as well as scavenging and disposing of the cell debris and peptides anammox bacteria produce.  The anammox bacteria Brocadia and the heterotrophic bacteria Chlorobi were the most dominant organisms, followed by heterotrophic bacteria affiliated with Chloroflexi, Bacteroidetes, and Proteobacteria.

The original article can be found here.

Bacterial E-mail

Quorum sensing, the production and detection of chemical signals produced when a critical mass of  bacteria (a quorum) is present, allows bacterial cells to communicate with each other and coordinate their activities.  Quorum sensing can happen between cells of the same species or between different species.  One well-studied example of quorum sensing is bioluminescence in the bobtail squid using the bacteria Aliibivibrio fischeri.  Producing light is energy-expensive, so these bacteria only do so when there are enough individuals collected to make the light visible when they glow.

The signaling molecules bacteria use to determine how many cells are present are generally made in their cytoplasms and then secreted into their environment.  These molecules are different for each organism.  How the molecules reach other cells is not fully understood, particularly if they cannot dissolve in water.

One option is membrane vesicles, bubbles of cell membrane enclosing fluid.  We know that bacteria in some environments, such as the ocean, make a lot of these.  This paper demonstrates that quorum sensing can occur via membrane vesicles in Paracoccus denitrificans, a gram-negative bacteria that is part of nitrate reduction.  A strain of Paracoccus that was not able to produce a signaling molecule was able to produce a quorum sensing response when supplemented with membrane vesicles from the wild-type strain.  Although this study focused on only one microbe, the results suggest that membrane vesicles may be an important mechanism of communication in microbiomes!



Can the organisms in your gut affect your risk of colorectal cancer?

Colorectal cancer (CRC) is among the most common human cancers, and routine screening is recommended by the Department of Health and Human Services. There is now evidence of a relationship between gut bacteria and the development of these malignancies.  The first clue was the association between the chronic gastritis caused by Helicobacter pylori infections in the stomach and low-grade, B-cell gastric lymphoma of the mucosa-associated lymphoid tissue.  Clinicians also noted that patients who had Streptococcus bovis infections developed CRC, and research has proven that this is more than an anecdotal association.  Several other organisms are associated with human colorectal cancer as well, including Fusobacteria and E. coli.  There is a direct relationship between the abundance of these organisms and cancer, and also with the stage of disease and the presence of lymph node metastases.  In contrast, Roseburia and Lachnospiraceae levels are lower in people with CRC.

Although the small bowel is significantly longer than the colon, cancers of the small bowel are much less common.  Some researchers think the discrepancy occurs because there are almost one million times as many bacteria in the colon as in the small bowel, and this theory spurred more investigation into the role of gut microbiota in CRC development.

Studies in mice and rats have strengthened the case for a microbial contribution to colorectal cancer.  Mice with genetic mutations that predispose them to CRC had less tumor growth if they were kept germ free and/or received antibiotics.  A “dysbiotic” gut microbiome has also been found that induces colitis and CRC in mice and is transmissible, suggesting that gut bacteria induce inflammation and the resulting cell turnover leads to DNA damage and cancer.

It is still unclear whether any particular gut organism causes or prevents CRC.  In the human studies published to date, samples were collected from CRC patients at the time of their initial therapeutic surgery and compared to healthy control microbiota sampled at a single time point, so it was not possible to determine whether the microbiome seen at surgery was present before the malignancy developed or was due to mucosal disruption and inflammation caused by the cancer.

More studies that look at gut microbiota before cancer develops and follow participants over a number of years will be necessary to determine whether cancer causes dysbiosis or vice versa.  It will also be important to factor diet into the equation because there appears to be a strong link between the consumption of red meat, processed meat, and CRC.