10% to 5% to 1% - (Jun/28/2008 )
To old-time microbiologist such as myself, the continuing perspective that we can culture an ever tinier part of the world's microorganisms is quite a culture change (no pun intended).
Some more context/Ref for this comment?
Sure -throughout mot of the last century, there was a tacit belief that all bacteria could be cultured in the lab. For the obvious and most notorious outliers T. pallidum and M. leprea, folks considered that it was just a matter of finding the right conditions. At the very end lf the century, molecular biology revealed an ever-increasing number of uncultured bacteria. Initially, these were phenomenal, then common, then predominant - to the current situation where the percentage of species that can be cultured is minimal - mayb 1%.
Heard some time ago a similar opinion. We just don't know them as they didn't grow on all the common media and now molecular techniques find seem. But as non-microbiologist I glad that there are even more divers fields compared to huge arthropods species numbers.
Thanks J.
I think while Treponma and leprea had the trouble, they constituted only a minor part of the known bacteria.
With shotgun sequencing of environmental DNA (soil, ocean etc.), we are identifying many more bacteria, but that is just checking en masse the diversity. There is no reason to conclude that if we wanted to culture them, and make a concerted effort, we can not culture them. Is there?
I guess, what I am trying to say is, that we have not cultured even 1% of bacteria, not that we can not culture 1% of bacteria. The effort perhaps has not been made yet.
Culture those? Doubt it. The fact that they were a surprise doesn't mean the environments were not cultured in any number of ways and, for those 2, I'd not presume to be so much better than folks who invested years worth of effort in just that endeavor. A personal anecdote that will age me - when i was finishing my PhD (a bit full of myself) and looking for a post doc , I tried to convince the Leprasorium at Carville La that I was the guy who could finally culture their bug. We went back and forth for a bit but in the end they couldn't dig up the money. Of course, success of sulfones put them out of business some decades later but I think they would have tolerated my ego if i would have done something more productive as well.
Not exactly what you were talking about, but what do you think about species divergence based on molecular data?
Like described in FEMS Microbiology reviews: Species divergence and the measurement of microbial diversity (p 557-578)
Catherine A. Lozupone, Rob Knight
Published Online: Apr 24 2008 12:00AM
DOI: 10.1111/j.1574-6976.2008.00111.x
thanks gerb, what a fascinating article. They make a good point that many of us see as the major question in (esp. microbial) taxonomy - that "species" are bumps in a continuum rather than distinct points .
I saw another article by these guys that speaks to what is being discussed in the Malassezia spp. of fungi that are part of our normal flora. What were formerly 2 or 3 poorly distinguished spp. were driven by molecular biology to as many as 14 almost very closely related spp. We figure these fungi evolved with mammals so much so that growing them in culture is very difficult.
Science. 2008 Jun 20;320(5883):1647-51. Epub 2008 May 22. Links
Evolution of mammals and their gut microbes.
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI.
Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108, USA.
Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.
Make that << 1%
Unexpectedly high bacterial diversity in decaying wood of a conifer as revealed by a molecular method
Han-Bo Zhanga, b, c, , , Ming-Xia Yangc and Ran Tuc
aLaboratory of Conservation and Utilization for Bio-resources, Yunnan University, Kunming 650091, PR China bKey Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, PR China cDepartment of Biology, Yunnan University, Kunming, Yunnan Province 650091, PR China
Received 17 March 2008; revised 10 June 2008; accepted 11 June 2008. Available online 8 August 2008.
Abstract
Bacterial communities in decaying sapwood and heartwood of Keteleeria evelyniana were demonstrated through constructing rRNA gene libraries. At 3% of sequence difference, 81 operational taxonomic units (OTUs) were identified from 91 partial 16S rRNA gene fragments. These clones belonged to Proteobacteria (63.7%), Actinobacteria (13.2%), Acidobacteria (8.8%), Firmicutes (3.3%), Chlamydiae (5.5%), Chloiroflexi (3.3%), Verrucomicrobia (1.1%) and Cyanobacteria (1.1%). The heartwood displayed higher species richness than the sapwood. No OTU overlapped between these two parts. Most α- and β-, and all δ-proteobacterial clones occurred in the heartwood, whereas γ-proteobacteria mainly occurred in the sapwood. Chlamydiae and Verrucomicrobia exclusively appeared in the heartwood, but Chloroflexi, Cyanobacteria, and Firmicutes, distributed in the sapwood. Clones belonging to Acidobacteria and Actinobacteria were also divided into distinct subgroups between in the sapwood and in the heartwood. Based on the present species definition, we estimated the wood-inhibiting bacteria of K. evelyniana achieved up 1056 species (ranging from 452 to 2647). Only small number of sequences (13/91) can be found the nearest neighbor previously cultured and named; thereby, the majority of wood-inhabiting bacteria still remains to be uncovered.
probably less....
....as I have been told by people working with bacteria that if you cultivate your bacteria and take them to new agar plates 4 - 5 times you will have bacteria that are completly different (in their physiological behaviour) than the primary culture. I do not know if a change in the 16S seq occurs so fast, but if you keep in mind that bacteria need to adapt to changing environmential conditions very quickly, maybe not only the species richness offered by 16S rDNA data but also the physiological condition of the different organism counts???????? But I do not know much about bacteria (fungi are enough
), so maybe you can help me out of my confusion?????But I think this would take us to this: 1
2