“Ancient” Bacteria With Patchwork Genomes Are Younger Than They Seem

A few groups of modern bacteria use anoxygenic photosynthesis (photosynthesis that does not produce oxygen) as an energy source, and the scientific community has assumed that these groups are ancient lineages that evolved when the Earth’s atmosphere was largely devoid of oxygen and oxygen species.

The green, non-sulfur bacteria called Chloroflexi, commonly found in microbial mat communities, is one of these groups of ancient anoxygenic phototrophs, but the authors of this study found that anoxygenic photosynthesis in Chloroflexi only evolved after the oxygenation of the Earth’s atmosphere. Moreover, several of the genes for both photosynthesis and Chloroflexi’s unique mechanism for fixing CO2 (called the 3-hydroxyproprionate bi-cycle) were acquired from other bacteria through horizontal transfer to make a “patchwork” genome. This study highlights how both the genomes and metabolism of bacteria are much more plastic than we thought.

The original article can be found here.

Author: Albatros4825 (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons
Caption: Microbial mat at Yellowstone National Park with growths of green Chloroflexus bacteria.


Citation: Shih, P. M., Ward, L. M., and Fischer, W. W. (2017). Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi. Proceedings of the National Academy of Sciences, U.S.A. published online before print. http://dx.doi.org/10.1073/pnas.1710798114


The Influence of C-sections, Formula Feeding, and Antibiotics on the Infant Gut Microbiome

Researchers at the University of Alberta in Canada have discovered that the gut microbiomes of formula-fed or Caesarian-born infants do not develop the in the same way or on the same schedule as vaginally born, breast-fed babies, and the bacterial colonies they develop are often linked to food allergies and rapid weight gain.

The team, led by Anita Kozyrskyj, used the Significance Analysis of Microarray method to study the gut microbiome composition of 166 infants through the first year of their lives.  Although previous research has established what bacteria are seen in growing infants, Kozyrskyj and her colleagues are the first to link the rates of colonization for each of these bacteria with infant age, creating a roadmap for microbial evolution in the developing gut.

The authors explained that over one thousand types of bacteria live in the intestines.  In infants, these bacteria not only help them digest food, they train the baby’s developing immune system.

“We hope this research will help clinicians and parents understand that Caesarean section increases the chance of antibiotic treatment or formula-feeding of newborns, which can affect the development of gut microbiota in later infancy [and affect the future health] of the child,” said Kozyrskyj.

For more information, go to Frontiers in Pediatrics; DOI: 10.3389/fped.2017.00200.

Soil Microbiome Influences Resistance to Climate Change

Microbes in soil decompose litter, recycle nutrients, and produce and regulate greenhouse gases that are important at the ecosystem level; but how will climate change impact all these functions?  Researchers tried to answer that question in a new study by exposing soils from arid regions across the world to disturbances such as warming, wetting-drying cycles, and nitrogen fertilization.  The composition of bacterial and fungal soil communities significantly affected how well soil samples functioned after being disturbed, but microbial diversity and abundance were not drivers of the soil microbiome and did not correlate to functional resistance – rather, specific taxa, including members of Ascomycota, Verrucomicrobia, Chloroflexi, and Acidobacteria, drove resistance. In turn, the abundances of these microbes were strongly correlated to pH, suggesting that this may be a way to control soil functionality. This study has implications for how soils affect ecosystem functioning, how arid ecosystems can survive global climate change, and  how microbial communities affect the functioning of other ecosystems.

Mean, Green, Microbe Machines

Algal ponds are an energy-efficient and cost-effective way to treat wastewater.  By converting the organics and nutrients in wastewater to algal biomass, not only can clean water be returned to the environment, but the algae can be used to produce fertilizer, biofuels, or other chemicals.  This study examines the diversity and reliability of microalgal pond communities used to treat wastewater over time and under different environmental conditions.  Despite some turnover in abundant species caused by zooplankton grazers and fluctuations in influent nitrogen levels, the performance of algal ponds remains remarkably stable.  If robust communities of algae can be maintained in the variable conditions present in wastewater treatment plants, we may be able to recover additional resources from our wastes.

Original article can be found here.

Forensic Human Identification Using Skin Microbiomes

Researchers from the University of North Texas may add a new tool to the detective’s field kit: microbiome identification.  To determine whether microbiomes are reliable indicators of individuality, the team collected DNA samples from a variety of different locations on the body from 12 subjects every year for three years.  They used metagenomics and supervised machine learning to characterize the samples and found that skin microbiome marker gene nucleotides could accurately identify each subject.  Although using skin microbiomes to identify crime suspects (and victims) may be a long way off, this study shows that, while many of our microbiomes are remarkably similar, our skin microbiomes may be as different as our fingerprints.

Original article can be found here.

Mum’s Gut Microbiome Protects Fetus

The authors have provided compelling evidence to support the hypothesis that maternal gut bacteria can protect or expose the fetus against insults associated with immune activation. It is well known that maternal immune activation (MIA), cause by, for instance, a viral infection, can result in behavioral abnormalities, in offspring, including autism-spectrum behaviors in humans.This effect is caused by T helper 17 (TH17) cells, which are involved in multiple inflammatory conditions, activating interleukin-17a (IL-17a),. The authors have demonstrated that mother requires a microbiome that activates TH17 cell differentiation to result in the IL17a activation, and aberrant fetal neurological development. This might suggest that the corollary is true, that a microbiome that does not activate TH17 differentiation could be protective against MIA, opening up new options for therapeutic avenues to prevent onset of Autism like behaviors in offspring.

Original article can be found here.

Music of the Microbiome

Have you ever wondered what your microbiome sounds like? Thanks to Biota Beats, now you can! Record-like Petri dishes were used to grow colonies of microbes found on the human body, and data from those colonies was used to make electronic music. The goal of this project is to capture the interest of people who normally don’t think about our microbiota. You can listen here.


Microbiome Changes Seasonally in Hunter-Gatherers

A study investigating changes in the gut microbiomes of members of the Hadza tribe, a small community in Tanzania with a primarily hunter-gatherer lifestyle, found big seasonal shifts that reflected the food available at different times of year, including meat, berries, tubers, baobab fruit, and honey.  No matter what time of year it was, the diversity of the Hadza’s gut microbiome was high and also highly functional.

Map of United Republic of Tanzania 

In contrast, the microbiomes of industrialized populations do not have strong seasonal shifts, are less diverse, and can perform fewer functions(Hadza gut microbiomes could degrade a wider array of carbohydates than American gut microbiomes).  It is unclear what the health impacts of these losses might be, but the study paves the way for more research in this area.

Giant gut bacteria helps its host digest food

Epulopiscium, one of the largest bacteria known, is a symbiont in the guts of coral-reef surgeonfishes of the Acanthuridae family. These fish feed on different kinds of marine algae.  David Kamanda Ngugi and his colleagues in Saudi Arabia, Singapore, Germany, and the U.S. sequenced the genomes and transcriptomes of Epulopiscium and closely-related bacteria from other species of surgeonfish and found that the bacteria were responsible for producing most of the hydrolytic enzymes that degrade polysaccharides in the algae the fish eat. These enzymes are specifically tailored to the algal diet of their hosts, which makes Epulopiscium crucial to the ecological success and diversification of coral-reef surgeonfish.

The original article can be found here.

Unidentifiable DNA Found in Circulating Blood

During its journey through the human body, blood collects free-floating bits of DNA.  Although clinicians use this cell-free DNA to detect human disease, analysis reveals that approximately 1% of it is not human.  In a new study, researchers sequenced and attempted to characterize cell-free DNA in the bloodstream and found more diversity, more unclassifiable sequences, and more sequences from the microbiome than they expected.  They also found several interesting viruses.

Their surprise might be due to the fact that microbiome studies tend to focus on just a few locations (such as the gut, the mouth, or the skin) and sequence those communities in depth, while blood reaches every part of the body and collects particles from areas that have not yet been explored.  The results also suggest that symbiont or pathogenic microorganisms could be detected in blood samples, which would be a big help in determining what organisms are necessary for human health and what is causing human disease.

Of course, science is all about peer review and confirming each other’s work. For a second opinion on this study, check out this blog post by A. Murat Eren (writer of the popular ‘omics analysis tool anvi’o). This second analysis of the same data largely confirms the results of the study, but adds that many of these unclassifiable sequences may come from the same microorganism.