Review Exploring Prokaryotic Diversity In The Genomic Era-Books Pdf

Review Exploring prokaryotic diversity in the genomic era
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2 Genome Biology Vol 3 No 2 Hugenholtz, 16S rRNA framework to classify prokaryotes 6 replacing Proteobacteria 82 isolates Firmicutes 61 Actinobacteria. the previous ad hoc scheme that was based on traditional 29 and Bacteroidetes 4 This cultivation bias towards. phenotypic characterization 7 The Manual proposes a four bacterial phyla the big four is also reflected in micro. standardized prokaryote nomenclature that has mostly been bial culture collections for example 97 of prokaryotes. fitted to a classical taxonomic hierarchy species genus deposited in the Australian Collection of Microorganisms. family order class phylum I will adhere to this system as 11 are members of the big four Figure 1a In fact it is a. far as possible in this article see the taxonomic outline challenge to obtain isolates that do not belong to the big. available at 8 The phylum is the highest level grouping in four and these four phyla therefore dominate our present. the bacterial and archaeal domains 9 and therefore is a understanding of microbiology A logical question to ask is. useful rank for overviewing prokaryotic diversity how many prokaryotic phyla there are altogether in order to. estimate how biased a sampling of four may be, The eight most intensively studied prokaryotic genera listed. in the introduction are members of only three bacterial. phyla Proteobacteria Escherichia Helicobacter Pseudo Prokaryotic diversity beyond the weeds. monas Salmonella Firmicutes Bacillus Streptococcus In the mid 1980s Norman Pace and colleagues outlined a. Staphylococcus and Actinobacteria Mycobacterium molecular approach that bypassed the need to cultivate a. Moreover the top 25 most studied genera are all members microorganism in order to determine the sequence of its 16S. of these three phyla with the exceptions of Chlamydia and rRNA gene 16S rDNA 12 Essentially bulk nucleic acids. Borrelia clinically important genera of the bacterial phyla are extracted directly from environmental samples 16S. Chlamydiae and Spirochaetes respectively 2 In a recent rDNA sequences are isolated from the bulk DNA typically. study 177 environmental veterinary and clinical isolates via PCR using primers broadly targeting 16S rDNAs and. that were not identifiable by traditional phenotypic charac cloning and these sequences are compared with known. terization were evaluated by comparative 16S rRNA analysis sequences Figure 2 Gene sequences obtained in this. 10 The isolates included a large number of different manner environmental clone sequences can then be. genera and species but at the phylum level all except one assigned a location in a phylogenetic tree and can thus act as. of the 177 were members of only four bacterial phyla a marker for the organism from which they were obtained. a Other phyla b, Bacteroidetes, Other phyla, Firmicutes 29. 14 Proteobacteria, Proteobacteria 43, Actinobacteria. 23 Firmicutes, Bacteroidetes 19, Actinobacteria, 3 767 cultures 267 genome sequences.
Pie charts showing the phylum level distribution of prokaryotic isolates a in the Australian Collection of Microorganisms 11 and b in the prokaryote. genome sequences completed or in progress as of 20 August 2001 29. http genomebiology com 2002 3 2 reviews 0003 3, Environmental. sample Extraction, Fluorescence, hybridization, Bulk RNA DNA. Nucleic acid, Nucleic acid hybridization, probes Community. Probe Cloning, deposited research, Comparative sequences Sequencing. analysis and database, Phylogenetic, refereed research.
Full cycle rRNA approach to characterizing microorganisms in their natural settings without the need for cultivation Access to whole genomes. of uncultivated organisms is also possible using the same basic approach but with large insert cloning vectors such as BACs which remove the. need for PCR, The approach can be brought full circle by applying 16S presents a recent conservative estimate of bacterial diversity. rRNA targeted nucleic acid probes specific for the organ at the phylum level it is conservative because it includes. interactions, isms of interest to visualize and quantify the target group in only phyla for which at least four near full length 16S rDNA. the environmental sample using techniques such as whole sequences over 1 300 nucleotides are known The total. cell fluorescence in situ hybridization FISH and membrane number of phylum level lineages in this tree is 35 22 63. hybridization 13 Figure 2 of which have one or more cultivated representatives and 13. 37 of which are known only from environmental, Many researchers have applied the rRNA approach to a wide sequences There are at least another ten phylum level lin. variety of environmental samples over the past decade and eages however that are present in the bacterial domain but. perhaps not surprisingly given the great plate count are not shown in Figure 3a because they are represented by. information, anomaly the number of recognized bacterial phyla has too few and or only partial sequences These lineages. exploded from the original estimate of 11 in 1987 5 to 36 in include cultivated bacteria such as Chrysiogenes and Dictyo. 1998 14 This increase is due not only to environmental glomus which are recognized as representing independent. sequences that have filled out the tree but also to a steady phyla in the taxonomic outline of Bergey s Manual of Sys. trickle of sequences from exotic cultured organisms partic tematic Bacteriology 8 The latest tally of bacterial phyla is. ularly thermophiles that highlight new lineages Figure 3a therefore probably nearer 45. 4 Genome Biology Vol 3 No 2 Hugenholtz, a Bacteria b Archaea.
Proteobacteria 122 Methanomicrobia 3, Thermoplasmata 3. Acidobacteria Halobacteria 3, Termite group I, Sediment Archaea 1. Nitrospira pMC2 Euryarchaeota, Bacteroidetes 4, Chlorobi 1. Fibrobacteres 1 pMC1, Marine group A, Thermococci 3. Gemmimonas Archaeoglobi 1, Firmicutes 52 Methanococcales 4.
Fusobacteria 2, Methanobacteria 1, Actinobacteria 22. Thermoprotei 7, Cyanobacteria 9 YNPFFA, Synergistes Crenarchaeota. Deferribacteres, NKB19 C1 1, Verrucomicrobia 1, Chlamydiae 11. OP3 Korarchaeota, Planctomycetes 2, Spirochaetes 5 FCG2. Chloroflexi 2, Deinococcus Thermus 3, Aquificae 1, Thermodesulfobacteria.
Thermotogae 2, Evolutionary distance dendrograms of a bacterial and b archaeal diversity derived from comparative analysis of 16S rRNA gene sequences The trees. were constructed using the ARB software package and a sequence database modified from the March 1997 ARB database release 39 using 50. consensus sequence filters for each domain and the Olsen correction and neighbor joining options This modified database will be available from the. Ribosomal Database Project 40 user submitted alignments download site 41 Major lineages phyla are shown as wedges with horizontal dimensions. reflecting the known degree of divergence within that lineage Phyla with cultivated representatives are in gray and where possible named according to. the taxonomic outline of Bergey s Manual 8 Phyla known only from environmental sequences are in white because they are not formally recognized as. taxonomic groups they are usually named after the first clones found from within the group 14 20 Note that environmental groups E2 and E3 defined. in 20 are part of the Thermoplasmata phylum in the archaeal tree in b The number of genome sequences completed or in progress for each phylum is. given in brackets after the phylum name with the exception of Methanopyrus kandleri which is not included in the tree because it is represented by a. single sequence The scale bar represents 0 1 changes per nucleotide. As more 16S rDNA sequences accumulate from both cul least four distinct phylum level lineages that include the. tured and uncultured prokaryotes the boundaries of existing Haloanaerobiales Thermoanerobacteriales and Sulfobacil. phyla are being challenged and need to be re evaluated For lus groups 9 Higher level associations between bacterial. example the bacterial phylum Firmicutes as currently phyla have not been resolved in 16S rDNA trees with. defined 8 may not be monophyletic and may comprise at the exceptions of the sister group affiliations of the. http genomebiology com 2002 3 2 reviews 0003 5, Bacteroidetes and Chlorobi and of the Chlamydiae and Ver notable exception is candidate phylum C1 Figure 3b which. rucomicrobia 14 This is presumably because such relation contains Cenarchaeum symbiosum an uncultured archaeon. ships are beyond the resolution that can be obtained from that has been amenable to detailed study including partial. the 16S rRNA molecule and or the current inference genome sequencing because it exists as a near monoculture. methods 9 14 Recently trees based on concatenated ribo in a marine sponge 21 Members of the C1 group are partic. somal proteins obtained from complete genome sequences ularly prevalent in marine habitats 22. have suggested higher order associations between Chlamy. diae and Spirochaetes between Thermotogae and Aquificae. and between Actinobacteria Deinococcus Thermus and The bumpy transition from gene phylogeny to. Cyanobacteria 15 The phylum Verrucomicrobia is also genome phylogeny. likely to be a member of the same group as Chlamydiae and The advent of large scale DNA sequencing has provided. Spirochaetes given that it is a sister group to Chlamydiae unprecedented access to molecular data for inferring the. this prediction can be tested when a completed genome tree of life Currently complete genome sequences of. sequence becomes available for the Verrucomicrobia prokaryotes have been obtained only from pure cultures. and hence at the phylum level microbial genomics reflects. Several candidate phyla 16 comprising only environmen the bias towards the big four phyla Figures 1b 3 This bias. tal clone sequences have developed into large groups with 71 from the big four is not as extreme as in culture col. sequence divergences similar to or greater than those within lections 97 Figure 1 because phyla containing human. the big four phyla examples include OP11 14 and WS6 pathogens such as Chlamydiae and Spirochaetes are. 16 and yet we know nothing about these lineages beyond better represented by genome sequences Figure 3a 23. a crude outline of their environmental distribution Most as are Archaea Figure 3b Increasing efforts are being. have not even been knowingly observed under the micro made to select phylogenetically diverse prokaryotes. scope In a preliminary investigation of one candidate Archaea for example for genome sequencing using the. phylum TM7 we determined that representatives of the 16S rRNA phylogeny as a guide 24. group had typical Gram positive cell envelopes and that they. deposited research, may have Archaea like streptomycin resistance 17 But is selection solely on the basis of an exotic location in a 16S. Detailed study of lineages like this one may yield insights rRNA tree justified The implicit assumption is that the evolu. into the evolutionary history of Gram positive bacteria tionary history of 16S rRNA represents the evolutionary. including perhaps a radical proposal that Gram positive history of the whole organism the whole genome but the. bacteria are related to Archaea 18 which so far appear to concept of a unified organismal phylogeny has been signifi. have a restricted phylum level distribution within the bacte cantly compromised by the finding of widespread lateral gene. rial domain Actinobacteria and Firmicutes TM7 bacteria transfer LGT between organisms 25 LGT appears to affect. have also been implicated in human subgingival gum the informational genes those involved in transcription and. disease which might promote their study 19 translation to a lesser extent than metabolic and other opera. refereed research, tional genes leading to the hypothesis that a core set of verti. The Archaea are formally divided into two phyla Crenar cally transmitted informational genes define organismal. chaeota and Euryarchaeota from 16S rRNA phylogeny 8 phylogeny 26 Recent evidence suggests that this may not be. but these groupings may be artifacts because analysis of con the case for the Euryarchaeota however here informational. catenated ribosomal protein sequences suggests that Eury genes are apparently no less subject to LGT than operational. archaeota at least is not a monophyletic group 15 genes 27 Reliable detection of LGT by comparison of gene. Figure 3b presents a current estimate of the major lineages trees is complicated by gene duplication and loss 23 and dif. in the archaeal 16S rDNA tree below the level of the Crenar ferent methods for detecting LGT are not particularly consis. interactions, chaeota and Euryarchaeota indicated to the right of the tent 28 The extent to which LGT blurs organismal.
tree using the same criteria and annotation used for the phylogenies is therefore unclear at this point At one extreme. bacterial tree Figure 3a The total number of phylum level if genomes are largely chimeric assemblages of genes with dif. lineages in the archaeal tree is 18 of which 8 44 have cul ferent histories then any random sampling of organisms. tivated representatives and 10 56 have none A higher should provide a representative window into genome space. tally of 23 phyla is arrived at if lineages not meeting the On the other hand if a core of vertically transmitted genes. selection criteria are included in the estimate These include which includes 16S. Review Exploring prokaryotic diversity in the genomic era Philip Hugenholtz Address ComBinE group Advanced Computational Modelling Centre The University of Queensland Brisbane 4072 Australia E mail philiph biosci uq edu au Current address Department of Environmental Science Policy and Management Hilgard Hall University of California Berkeley CA 94720 USA E mail philiph nature

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