Most of that study has relied on the culture method— samples of microbes are taken in the field and then grown in agar medium in the laboratory. “But only some bacteria will grow in culture medium,” says Dr. Mark Welch. “Which means we’ve been studying a limited set of bacteria.” How limited? Only about one-tenth of 1% of microbes can be cultured using standard methods. In a soil sample that contained 1,000 different kinds of microbes, only one would grow in the lab. “This phenomenon is called the great plate count anomaly,” she says, “because we know there are more bacteria out there than we were able to count on our culture plates.” Dr. Dewhirst’s research these days is focused on how to cultivate the remaining 1/3 so we can have as complete a picture as possible of the oral microbiome.” The Mission Dr. Mark Welch’s research group works to understand the structure and function of bacterial communities in the mouth. They’re studying how different bacteria work together and how they impact human health. “It seems that certain bacteria consistently live next to other kinds of bacteria, that there is a necessary relationship between them, which may explain why some don’t grow in culture,” she says. “Oral bacteria’s natural habitat is in this enormous, complex biofilm, which is a collection of bacteria of all sorts growing together inside a matrix that they make. One kind of bacteria is probably leaking metabolites and chemicals. So, the bacteria next to it knows it can get metabolites from its neighbour, so doesn’t make them itself.” Between the 1970s and early 1990s, researchers began using gene sequencing to identify uncultivatable bacteria. “They used a gene that all organisms have, coding for ribosomal RNA (rRNA),” says Dr. Mark Welch. “Comparing these genes, researchers were able to identify bacteria that they’d never seen before.” Dr. Floyd Dewhirst, a colleague of Dr. Mark Welch at the ADA Forsyth Institute, did pioneering research into the diversity, genetic capability and pathogenic potential of organisms in the mouth. He used 16S rRNA gene sequence information for cultured and as-yet-uncultured oral microbes to identify oral bacteria and place them into a taxonomy, an organized biological classification system. Dr. Dewhirst became the first curator of the Human Oral Microbiome Database, which now includes approximately 700 species of human oral bacteria. “The database includes the rRNA sequence and a name for all the bacteria, so that when you see it, you can recognize it. Once a bacterium has a stable name, you can study it,” says Dr. Mark Welch, who now also curates the database. “About 2/3 of these bacteria are culturable. Oral bacteria’s natural habitat is in this enormous, complex biofilm, which is a collection of bacteria of all sorts growing together inside a matrix that they make. Antoni van Leeuwenhoek made these drawings in the 1670s of the tiny creatures he saw through his microscope when he observed plaque scrapings from teeth. 25 Issue 1 | 2024 | Issues and People
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