Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils

Felske, Andreas; Rheims, Holger; Wolterink, Arthur; Stackebrandt, Erko; Akkermans, A.D.L.

doi:10.1099/00221287-143-9-2983

Cited by 347 publications

(216 citation statements)

References 27 publications

(42 reference statements)

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“…The clone library was not used in this work for covariation analysis because of its qualitative nature and the uncertainty of its reproducibility (25)(26)(27). However, with the rapid development of high-throughput sequencing techniques (12,28), sequencing-based analysis will eventually become quantitative and cost-effective enough for this type of analysis.…”

Section: Discussionmentioning

confidence: 99%

Symbiotic gut microbes modulate human metabolic phenotypes

Wang

Zhang

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

1,005

739

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Humans have evolved intimate symbiotic relationships with a consortium of gut microbes (microbiome) and individual variations in the microbiome influence host health, may be implicated in disease etiology, and affect drug metabolism, toxicity, and efficacy. However, the molecular basis of these microbe-host interactions and the roles of individual bacterial species are obscure. We now demonstrate a''transgenomic'' approach to link gut microbiome and metabolic phenotype (metabotype) variation. We have used a combination of spectroscopic, microbiomic, and multivariate statistical tools to analyze fecal and urinary samples from seven Chinese individuals (sampled twice) and to model the microbialhost metabolic connectivities. At the species level, we found structural differences in the Chinese family gut microbiomes and those reported for American volunteers, which is consistent with population microbial cometabolic differences reported in epidemiological studies. We also introduce the concept of functional metagenomics, defined as ''the characterization of key functional members of the microbiome that most influence host metabolism and hence health.'' For example, Faecalibacterium prausnitzii population variation is associated with modulation of eight urinary metabolites of diverse structure, indicating that this species is a highly functionally active member of the microbiome, influencing numerous host pathways. Other species were identified showing different and varied metabolic interactions. Our approach for understanding the dynamic basis of host-microbiome symbiosis provides a foundation for the development of functional metagenomics as a probe of systemic effects of drugs and diet that are of relevance to personal and public health care solutions. covariation analysis ͉ gut microbiota ͉ metabonomics ͉ metabotype ͉ metagenomics

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Section: Discussionmentioning

confidence: 99%

Symbiotic gut microbes modulate human metabolic phenotypes

Wang

Zhang

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

1,005

739

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“…Universal bacterial primers: 8F (5 0 -CACGGATCCAGAC TTTGAT(C/T)(A/C)TGGCTCAG-3 0 ) and 1512R (5 0 -GTG AAGCTTACGG(C/T)TAGCTTGTTACGACTT-3 0 ), based on Escherichia coli positions, were used to amplify internal fragments of 16S rRNA gene (Felske et al, 1997). Eight microliters of a bacterial suspension was transferred to a sterile thin-walled PCR tube.…”

Section: Identification Of Egg Mass-degrading Bacteriamentioning

confidence: 99%

Vibrio cholerae and Aeromonas: do they share a mutual host?

et al. 2008

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Species of the genus Aeromonas are native inhabitants of aquatic environments and have recently been considered as an emergent human pathogen. It is estimated that aeromonads cause up to 13% of reported gastroenteritis cases in the United States. Although the autochthonous existence of Aeromonas in the aquatic environment has been established, its natural reservoir is as yet unknown. Chironomids are closely related to mosquitoes except they do not bite and they are the most widely distributed insects in freshwater. They infest drinking water systems in Israel and all over the world. Vibrio cholerae inhabit chironomids and are able to degrade their egg masses. The degradation of the egg masses is followed by failure of the eggs to hatch. In the current study, egg masses from a waste stabilization pond and a river in northern Israel were collected and cultured during a fivemonth period. Bacterial colonies were randomly chosen and checked for their egg mass degradation abilities. In addition to V. cholerae, most of the other isolates that had the ability to degrade the egg masses were identified as Aeromonas species, thus, demonstrating that Aeromonas species are natural inhabitants of chironomid egg masses. The following virulence-associated genes were detected in Aeromonas species that were isolated from chironomid egg masses: alt (78%); ahpB (76%); act/aerA/hlyA (65%); fla (59%); pla/lipH3/apl-1/lip (43%); and ast (2%). These findings indicate that the Aeromonas species inhabiting chironomid egg masses pose a potential health risk. Understanding the natural reservoir of Aeromonas will help to develop methods to monitor and control the bacteria in fresh and drinking water reservoirs and to better understand the relationships between chironomids, V. cholerae and Aeromonas populations.

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“…Universal bacterial primers 8f and 1512r (Felske et al, 1997) were used to amplify internal fragments of the 16S rRNA gene of strain MM2LB T . Purified PCR products were sequenced with primers 8f, 534r, 968f and 1512r as described in detail by Raats & Halpern (2007).…”

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confidence: 99%

Leucobacter chironomi sp. nov., a chromate-resistant bacterium isolated from a chironomid egg mass

Halpern

Shakéd

Pukall

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

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A Gram-positive, rod-shaped, aerobic, non-motile, yellow-pigmented bacterial strain, designated MM2LB T , was isolated from a chironomid egg mass that was sampled in a waste stabilization pond in northern Israel. 16S rRNA gene sequence analysis indicated that the isolate should be placed in the genus Leucobacter (family Microbacteriaceae). Levels of 16S rRNA gene sequence similarity between strain MM2LB T and the type strains of recognized Leucobacter species were 97.1 % or lower. The dominant cellular fatty acids of strain MM2LB T were anteiso-C 15 : 0 , iso-C 16 : 0 and anteiso-C 17 : 0 , which are typical of members of the genus Leucobacter. Strain MM2LB T grew at 17-37 6C, in the presence of 0-7.0 % NaCl and at pH 4.0-9.5. Cell-wall amino acids were alanine, glycine, threonine, 2,4-diaminobutyric acid, glutamic acid and caminobutyric acid in a B-type cross-linked peptidoglycan. The quinone system consisted of menaquinones MK-11, MK-10 and MK-12. The novel isolate was able to grow in medium containing 18 mM Cr(VI). On the basis of phenotypic properties and phylogenetic distinctiveness, strain MM2LB T is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chironomi sp. nov. is proposed. The type strain is MM2LB T (5LMG 24399 T 5DSM 19883 T ).The genus Leucobacter (family Microbacteriaceae) was erected by Takeuchi et al. (1996). All species of the genus are characterized by 2,4-diaminobutyric acid (DAB) as the diagnostic diamino acid in the peptidoglycan. However, there are differences in the amounts of other amino acids in the peptidoglycan. Among members of the genus, caminobutyric acid has been found only in Leucobacter albus and Leucobacter komagatae. At the time of writing, the genus comprises eight recognized species: L. komagatae (Takeuchi et al., 1996) Strains belonging to the genus Leucobacter occur in a variety of ecological niches such as activated sludge (from a treatment plant containing chromium-contaminated wastewater; Morais et al., 2004, 2006), soil (Lin et al., 2004, river sediment (Morais et al., 2006), nematodes (Somvanshi et al., 2007, Muir & Tan, 2007 and the phyllosphere of potato plants (Behrendt et al., 2008). In the present study, an obligately aerobic, non-motile, Gram-positive, rod-shaped bacterium (strain MM2LB T ), isolated from a freshwater insect egg mass, is proposed as representing a novel species of the genus Leucobacter.Strain MM2LB T was isolated during the course of studies aimed at identifying culturable bacteria from chironomid (non-biting midge, Chironomidae; Diptera) egg masses. Chironomid egg masses were sampled from Tivon waste stabilization pond in northern Israel, as previously described (Halpern et al., 2007a). To determine the diversity of culturable bacteria in chironomid egg masses, the masses were washed thoroughly with sterile saline (vortexing for 1 min with five changes of saline) and then their homogenates were diluted and cultured directly on Luria-Bertani (LB) agar (Himedia). More than 10 4 faecal coliforms ml ...

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Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils

Cited by 347 publications

References 27 publications

Symbiotic gut microbes modulate human metabolic phenotypes

Symbiotic gut microbes modulate human metabolic phenotypes

Vibrio cholerae and Aeromonas: do they share a mutual host?

Leucobacter chironomi sp. nov., a chromate-resistant bacterium isolated from a chironomid egg mass

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