Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain
            <i>Bacteria</i>
            with No Known Pure-Culture Representatives

Hugenholtz, Philip; Tyson, Gene W.; Webb, Richard I.; Wagner, Ankia M.; Blackall, Linda L.

doi:10.1128/aem.67.1.411-419.2001

Cited by 303 publications

(299 citation statements)

References 28 publications

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“…The FISH probes Succ654 (targeting S. dextrinosolvens and S. dextrinosolvens-like clones) and Ana1141 (targeting A. lipolyticus and similar clones) were designed using previously published methods (Hugenholtz et al, 2001. All probes (Table 2) were synthesized and labelled at the 5 0 end with the sulfoindocyanine dyes Cy3, Cy5 or fluorescein isothiocyanate (FITC; Thermo Electron Corporation, Ulm, Germany).…”

Section: Oligonucleotide Probe Design and Optimizationmentioning

confidence: 99%

Microbial ecology of the equine hindgut during oligofructose-induced laminitis

et al. 2008

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Alimentary carbohydrate overload is a significant cause of laminitis in horses and is correlated with drastic shifts in the composition of hindgut microbiota. Equine hindgut streptococcal species (EHSS), predominantly Streptococcus lutetiensis, have been shown to be the most common microorganisms culturable from the equine caecum prior to the onset of laminitis. However, the inherent biases of culture-based methods are estimated to preclude up to 70% of the normal caecal microbiota. The objective of this study was to evaluate bacterial population shifts occurring in the equine caecum throughout the course of oligofructose-induced laminitis using several cultureindependent techniques and to correlate these with caecal lactate, volatile fatty acid and degrees of polymerization 3-7 fructo-oligosaccharide concentrations. Our data conclusively show that of the total microbiota present in the equine hindgut, the EHSS S. lutetiensis is the predominant microorganism that proliferates prior to the onset of laminitis, utilizing oligofructose to produce large quantities of lactate. Population shifts in lactobacilli and Escherichia coli subpopulations occur secondarily to the EHSS population shifts, thus confirming that lactobacilli and coliforms have no role in laminitis. A large, curved, Gram-negative rod previously observed during the early phases of laminitis induction was most closely related to the Anaerovibrio genus and most likely represents a new, yet to be cultured, genus and species. Correlation of fluorescence in situ hybridization and quantitative real-time PCR results provide evidence supporting the hypothesis that laminitis is associated with the death en masse and rapid cell lysis of EHSS. If EHSS are lysed, liberated cellular components may initiate laminitis.

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Section: Oligonucleotide Probe Design and Optimizationmentioning

confidence: 99%

Microbial ecology of the equine hindgut during oligofructose-induced laminitis

et al. 2008

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“…LGCmix [equimolar concentrations of LGC354A, LGC354B and LGC354C (Meier et al, 1999)], TM7905 (Hugenholtz et al, 2001), Ntspa1413 (Maixner et al, 2006), HoAc1402 (Juretschko et al, 2002), CFX1223 and GNSB-941 (Bjornsson et al, 2002), Actino-221, Actino-651 (Kong et al, 2005), and PAOmix [equimolar concentrations of PAO651, PAO462 and PAO846 (Crocetti et al, 2000)], GB_G1 (GAOQ989) (Crocetti et al, 2002) and GB_G2, GB_1&2, GB_3, GB_4, GB_5, GB_7 (Kong et al, 2002), GB_6 [Gam1019 (Nielsen et al, 1999)], Cluster 6a-192 (Adamczyk et al, 2003), ZRA23a (Rossello-Mora et al, 1995), Azo644 (Hess et al, 1997), Thau-646 (Lajoie et al, 2000), Aqs997 (Thomsen et al, 2004), Sap309 (Schauer & Hahn, 2005), CF319a and CF319b (Manz et al, 1996) were used for FISH. All the probes, except the EUBmix, which was labelled with FLUOS, were labelled with either Cy3 or Cy5 (only for specificity check).…”

Section: Methodsmentioning

confidence: 99%

Structure and function of the microbial community in a full-scale enhanced biological phosphorus removal plant

et al. 2007

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The structure and function of the microbial community in a full-scale enhanced biological phosphorus removal wastewater treatment plant (WWTP; Skagen) were investigated using the full-cycle rRNA approach, combined with ecophysiological studies. A total of 87 16S rRNA gene sequences were retrieved, and 78 operational taxonomic units were identified. Novel oligonucleotide probes were designed, and quantitative fluorescence in situ hybridization revealed that six hitherto undescribed probe-defined groups within the phylum Bacteroidetes (two groups), and classes Betaproteobacteria (two groups) and Gammaproteobacteria (two groups), were relatively abundant (.1 % of total biovolume) in the Skagen WWTP and 10 other full-scale WWTPs with biological P removal. The most abundant was a group of rod-shaped Bacteroidetes attached to filamentous bacteria, which is distantly related to the genus Haliscomenobacter of the family Saprospiraceae, and comprised 9-19 % of the bacterial biovolume in all the WWTPs investigated. The other five probe-defined groups were found in all WWTPs, but they were less abundant (1-6 %). Two groups had a glycogen-accumulating phenotype and one Dechloromonas-related group had a polyphosphate-accumulating phenotype, and they were potentially all involved in denitrification. In total, about 81 % of all bacteria hybridizing with the general eubacterial probe were detected in the Skagen WWTP by using clone-or group-specific probes, indicating that most members of the microbial community had been identified. INTRODUCTIONAn increasing number of wastewater treatment plants (WWTPs) are designed, or have been upgraded, to remove C, N and P by using microbial activity in the process known as enhanced biological phosphorus removal (EBPR). This process is popular mainly because it is more environmentally friendly, due to reduced use of chemicals and low sludge production, compared to P removal by chemical precipitation (Seviour et al., 2003). The general understanding of design and operation of activated-sludge WWTPs has increased significantly in the last two decades, but occasionally EBPR WWTPs still suffer from suboptimal operation and breakdown of the P-removal process. These problems are believed to be due to poor understanding of the structure of the microbial community in EBPR WWTPs and insufficient knowledge of the ecophysiology of the key microbial populations.Our understanding of the microbiology of EBPR WWTPs is to a large extent obtained from culture-independent studies using enriched cultures in well-controlled laboratory-scale reactors by using the full-cycle rRNA approach (Amann, 1995), as reviewed in detail by Mino et al. (1998) and Seviour et al. (2003). Some potentially important micro-organisms involved in the EBPR process have been identified in such laboratory-scale reactors, but only a few of them have been shown to be important in full-scale WWTPs. These are all uncultured organisms and can thus only be detected and quantified by using molecular methods such as fluorescence in situ hybrid...

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“…In addition, the analysis confirmed our previously inferred cladal relationships with the other phyla, including Actinobacteria, Deinococcus-Thermus and Cyanobacteria. Interestingly, the closest phylogenetic neighbour of T49 T was the partial genome sequence of an uncultivated representative of TM7 (Podar et al, 2007), a broadly distributed candidate division that has been detected in activated sludge, human oral cavities, soils and plant rhizospheres (Hugenholtz et al, 2001). Similarly to the three formally described Armatimonadetes, the recently sequenced TM7 metagenome had a saccharolyticbased metabolism (Albertsen et al, 2013).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

et al. 2014

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Most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. Until the recent characterisation of several strains, the phylum Armatimonadetes (formerly known as 'candidate division OP10') was a dominant and globally-distributed lineage within this 'uncultured majority'. Here we report the first Armatimonadetes genome from the thermophile Chthonomonas calidirosea T49 T and its role as a saccharide scavenger in a geothermal steam-affected soil environment. Phylogenomic analysis indicates T49 T to be related closely to the phylum Chloroflexi. The predicted genes encoding for carbohydrate transporters (27 carbohydrate ATP-binding cassette transporter-related genes) and carbohydrate-metabolising enzymes (including at least 55 putative enzymes with glycosyl hydrolase domains) within the 3.43 Mb genome help explain its ability to utilise a wide range of carbohydrates as well as its inability to break down extracellular cellulose. The presence of only a single class of branched amino acid transporter appears to be the causative step for the requirement of isoleucine for growth. The genome lacks many commonly conserved operons (for example, lac and trp). Potential causes for this, such as dispersion of functionally related genes via horizontal gene transfer from distant taxa or recent genome recombination, were rejected. Evidence suggests T49 T relies on the relatively abundant r-factors, instead of operonic organisation, as the primary means of transcriptional regulation. Examination of the genome with physiological data and environmental dynamics (including interspecific interactions) reveals ecological factors behind the apparent elusiveness of T49 T to cultivation and, by extension, the remaining 'uncultured majority' that have so far evaded conventional microbiological techniques.

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Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives

Cited by 303 publications

References 28 publications

Microbial ecology of the equine hindgut during oligofructose-induced laminitis

Microbial ecology of the equine hindgut during oligofructose-induced laminitis

Structure and function of the microbial community in a full-scale enhanced biological phosphorus removal plant

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

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