Microbial Macroecology
Bacteria and archaea are the most abundant, widespread and functional important forms of life on Earth, yet many fundamental questions remain unanswered. How many bacterial species are there in one gram of soil? How are resources allocated among members of a microbial community? What fraction of a microbial community is dormant (persister cell) and therefore tolerant to antibiotics? Using publicly available big microbiome data, we are developing a unified theory of microbial ecology that can answer these types of questions at once. We are looking for people with a strong aptitude for math and modeling to join us in this exciting area of research.
Microbial Macroevolution
Does trait evolution proceed gradually or by jumps? Although animal studies using fossil records and phylogenetically comparative traits have largely supported the pulsed evolution theory, our understanding of the tempo and mode of evolution across the tree of life remains limited. This long-standing debate calls for a test in bacteria and archaea, the most ancient and diverse forms of life with their own unique population genetic properties (e.g., asexual reproduction, large population sizes, short generation times, high dispersal rates and extensive lateral gene transfers). Using a likelihood-based framework, we showed that pulsed evolution is not only present but also prevalent and predominant in microbial genomic trait evolution.
Gut microbiome in the Wild
We are interested in studying the host and environmental factors that shape the gut microbiome in nature. We show that in nature, environmental factors exert a much stronger influence on gut microbiome than host traits such as sex, age and genetics. For example, we have found a remarkable seasonal rhythm in the structure of gut flora in the North American red squirrels, most likely driven by the seasonal dietary shift.
Microbiome and Human Health
We are interested in the role of gut microbime in human health and disease. In collaboration with researchers at University of Virginia School of Medicine and around the country, we have investigated microbime changes associated with Clostridium difficile infection, middle ear infection, and depression. We are currently involved in a NIH funded project to study the role of gut microbiome in causing type II diabetes. We are developing a next generation sequencing based approach for real-time diagnosis of antibiotic resistance in Clostridium difficile infections. We are also interested in studying the potential role of tick microbiome in causing the red meat allergy.
Endosymbiosis and the Origin of Mitochondria
Overwhelming evidence supports the endosymbiosis theory that mitochondria originated once from within a specific group of bacteria called α-proteobacteria. However, it is still not clear which bacterial species are its “first cousins”. Placing mitochondria correctly within the bacterial branch of tree of life is of great importance for elucidating the origin and early evolution of mitochondria and eukaryotes. It would shed light on many fascinating questions: What was its genetic make-up of the mitochondrial ancestor? What was the driving the initial endosymbiosis? To gain more insights into these exciting questions and better pinpoint the origin of mitochondria, we sequenced 18 bacterial endosymbionts that are close to mitochondria. Using phylogenomic methods, we reconstructed the genetic make-up of the mitochondrial ancestor. Surprisingly, our analyses indicate that mitochondrial ancestor was most likely an energy parasite that stole ATP from the host cell, a far cry from modern mitochondria as the powerhouse of the eukaryotic cell.
Bacterial Tree of Life
A key prerequisite for studying microbial evolution and diversity is the accurate determination of the evolutionary relationships among the organisms of interest. The explosive growth of bacterial genomic sequences makes it possible to reconstruct the bacterial tree of life on the genome level. Such “genome trees” are fairly robust and offer an excellent alternative to the widely used 16s rRNA based phylogeny. We have developed a simple, fast and accurate method (AMPHORA) to automate the genome tree construction process. With the arriving of thousands of new genomes on the horizon, we’ll continually update the bacterial tree of life.
With the bacterial tree of life in hand, we tested the generation-time hypothesis in bacteria and showed that spore-forming bacteria evolve significantly slower than their close relatives that have lost the ability to sporulate.
With the bacterial tree of life in hand, we tested the generation-time hypothesis in bacteria and showed that spore-forming bacteria evolve significantly slower than their close relatives that have lost the ability to sporulate.
