Halmos College of Natural Sciences and Oceanography Professor Participates in Global Microbiome Study

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The scientific paper “Diversity, Structure and Convergent Evolution of the Global Sponge Microbiome” by T. Thomas, et.al., was published in Nature Communications this past June. This research culminates a large collaborative effort between at least 20 different laboratories around the world, including Nova Southeastern University’s Halmos College of Natural Sciences and Oceanography. More than 81 different sponge species were studied from 20 countries bordering the Atlantic, Pacific and Indian oceans as well as the Mediterranean and Red seas.

NSU professor Jose Lopez, Ph.D. participated in this study. Lopez’s laboratory provided unique Caribbean sponge samples, consultation and coordination as a central “processing” hub for North American samples that eventually were sent to Rob Knight’s laboratory at the University of Colorado for high throughput DNA sequencing.

So what is a “microbiome”?

“Well, microbiomes are basically communities of different strains or species of microbes – mostly bacteria, but also include fungi and protozoans – that live in a specific habitat,” Lopez said. “Actually, microbiomes are virtually everywhere – in the soil, mangroves, seawater and freshwater, shower curtains, and even living on our own human skin and within our digestive tract.”

According to Lopez, when living with animals, mostly in a beneficial sense (some bacteria help us digest certain foods), we consider the microbiomes to be “symbiotic.” In the same vein, sponges live very closely with symbiotic bacteria, as some microbiomes can compose less than 50% of sponge’s total body mass (so that its less sponge than a large mass of microbes).

“Microbiomes vary considerably and researchers are still trying to fully understand what the bacteria do for the host and the factors that structure the communities,” said Lopez.

Lopez is also the founder of the Global Invertebrate Genomics Alliance (GIGA) an international organization of diverse scientists who will promote comparative genomics and bioinformatics research on non-insect/non-nematode invertebrates including sponges of course.

The sponge study also exemplifies a dataset that fits right into the current “Big Data” meme, since billions of DNA sequences were generated from the samples (on a state of the art Illumina HiSeq DNA sequencer) and then analysed with modern bioinformatics and statistical methods. The results show that patterns of symbiosis between the resident bacteria and each sponge host can be diverse and complex.

One of the sponges, Cliona delitrix, analysed hits close to home, since this species attacks weakened or recently dead coral substrate, unfortunately all too common in the Caribbean. This sponge was a subject of Dr. Lopez’s former NSU doctoral student, Andia Chaves Fonnegra. Overall host sponge phylogeny can exert a major influence in some cases, or the environment may be more dominant.

Collaborators Rob Knight and Jack Gilbert are founders of the Earthmicrobiome.org project, as well as other large scale microbiome projects, such as the Human Microbiome Project and the American Gut (http://americangut.org/). The sponge microbial symbiosis community conceived this project more than two years ago. With its large sample size and global distribution, this publication will set a new baseline for sponge microbiome research.