Diversity and Abundance of Single-stranded DNA Viruses in Human Feces

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2011 Sep 28

PMID 21948823

Citations 131

Authors

Min-Soo Kim

Eun-Jin Park

Seong Woon Roh

Jin-Woo Bae

Affiliations

Soon will be listed here.

Abstract

In this study, we investigated the abundance and diversity of single-stranded DNA (ssDNA) viruses in fecal samples from five healthy individuals through a combination of serial filtration and CsCl gradient ultracentrifugation. Virus abundance ranged from 10⁸ to 10⁹ per gram of feces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments (5 to 10). Viral DNA was extracted and randomly amplified using phi29 polymerase and analyzed through high-throughput 454 pyrosequencing. Among 400,133 sequences, an average of 86.2% viromes were previously uncharacterized in public databases. Among previously known viruses, double-stranded DNA podophages (52 to 74%), siphophages (11 to 30%), myophages (1 to 4%), and ssDNA microphages (3 to 9%) were major constituents of human fecal viromes. A phylogenetic analysis of 24 large contigs of microphages based on conserved capsid protein sequences revealed five distinct newly discovered evolutionary microphage groups that were distantly related to previously known microphages. Moreover, putative capsid protein sequences of five contigs were closely related to prophage-like sequences in the genomes of three Bacteroides and three Prevotella strains, suggesting that Bacteroides and Prevotella are the sources of infecting microphages in their hosts.

Citing Articles

Dysbiosis of gut microbiota in COVID-19 is associated with intestinal DNA phage dynamics of lysogenic and lytic infection.

Ishizaka A, Tamura A, Koga M, Mizutani T, Yamayoshi S, Iwatsuki-Horimoto K Microbiol Spectr. 2024; 13(1):e0099824.

PMID: 39656008 PMC: 11705802. DOI: 10.1128/spectrum.00998-24.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.

Lopez J, McKeithen-Mead S, Shi H, Nguyen T, Huang K, Good B bioRxiv. 2024; .

PMID: 39386523 PMC: 11463441. DOI: 10.1101/2024.09.27.614587.

Stable coexistence between an archaeal virus and the dominant methanogen of the human gut.

Baquero D, Medvedeva S, Martin-Gallausiaux C, Pende N, Sartori-Rupp A, Tachon S Nat Commun. 2024; 15(1):7702.

PMID: 39231967 PMC: 11375127. DOI: 10.1038/s41467-024-51946-x.

Role of bacteriophages in shaping gut microbial community.

Mahmud M, Tamanna S, Akter S, Mazumder L, Akter S, Rakibul Hasan M Gut Microbes. 2024; 16(1):2390720.

PMID: 39167701 PMC: 11340752. DOI: 10.1080/19490976.2024.2390720.

Antimicrobial resistance: use of phage therapy in the management of resistant infections.

Ikpe F, Williams T, Orok E, Ikpe A Mol Biol Rep. 2024; 51(1):925.

PMID: 39167154 DOI: 10.1007/s11033-024-09870-2.

References

Gomez-Alvarez V, Teal T, Schmidt T . Systematic artifacts in metagenomes from complex microbial communities. ISME J. 2009; 3(11):1314-7. DOI: 10.1038/ismej.2009.72. View

Niu B, Fu L, Sun S, Li W . Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics. 2010; 11:187. PMC: 2874554. DOI: 10.1186/1471-2105-11-187. View

Turnbaugh P, Ley R, Mahowald M, Magrini V, Mardis E, Gordon J . An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006; 444(7122):1027-31. DOI: 10.1038/nature05414. View

Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet J . Towards the human intestinal microbiota phylogenetic core. Environ Microbiol. 2009; 11(10):2574-84. DOI: 10.1111/j.1462-2920.2009.01982.x. View

Kristensen D, Mushegian A, Dolja V, Koonin E . New dimensions of the virus world discovered through metagenomics. Trends Microbiol. 2009; 18(1):11-9. PMC: 3293453. DOI: 10.1016/j.tim.2009.11.003. View

Roberts A, Chandler M, Courvalin P, Guedon G, Mullany P, Pembroke T . Revised nomenclature for transposable genetic elements. Plasmid. 2008; 60(3):167-73. PMC: 3836210. DOI: 10.1016/j.plasmid.2008.08.001. View

Maslowski K, Vieira A, Ng A, Kranich J, Sierro F, Yu D . Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature. 2009; 461(7268):1282-6. PMC: 3256734. DOI: 10.1038/nature08530. View

Tamura K, Dudley J, Nei M, Kumar S . MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007; 24(8):1596-9. DOI: 10.1093/molbev/msm092. View

Larsen N, Vogensen F, van den Berg F, Nielsen D, Andreasen A, Pedersen B . Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One. 2010; 5(2):e9085. PMC: 2816710. DOI: 10.1371/journal.pone.0009085. View

10.

Breitbart M, Rohwer F . Here a virus, there a virus, everywhere the same virus?. Trends Microbiol. 2005; 13(6):278-84. DOI: 10.1016/j.tim.2005.04.003. View

11.

Zhang T, Breitbart M, Lee W, Run J, Wei C, Soh S . RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 2005; 4(1):e3. PMC: 1310650. DOI: 10.1371/journal.pbio.0040003. View

12.

Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C . Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res. 2010; 20(11):1605-12. PMC: 2963823. DOI: 10.1101/gr.108332.110. View

13.

Yooseph S, Sutton G, Rusch D, Halpern A, Williamson S, Remington K . The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007; 5(3):e16. PMC: 1821046. DOI: 10.1371/journal.pbio.0050016. View

14.

Yu Z, Morrison M . Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques. 2004; 36(5):808-12. DOI: 10.2144/04365ST04. View

15.

Schloss P, Westcott S, Ryabin T, Hall J, Hartmann M, Hollister E . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75(23):7537-41. PMC: 2786419. DOI: 10.1128/AEM.01541-09. View

16.

Danovaro R, Manini E, DellAnno A . Higher abundance of bacteria than of viruses in deep Mediterranean sediments. Appl Environ Microbiol. 2002; 68(3):1468-72. PMC: 123732. DOI: 10.1128/AEM.68.3.1468-1472.2002. View

17.

Polz M, Cavanaugh C . Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol. 1998; 64(10):3724-30. PMC: 106531. DOI: 10.1128/AEM.64.10.3724-3730.1998. View

18.

Danovaro R, Serresi M . Viral density and virus-to-bacterium ratio in deep-sea sediments of the Eastern Mediterranean. Appl Environ Microbiol. 2000; 66(5):1857-61. PMC: 101423. DOI: 10.1128/AEM.66.5.1857-1861.2000. View

19.

Wommack K, Colwell R . Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev. 2000; 64(1):69-114. PMC: 98987. DOI: 10.1128/MMBR.64.1.69-114.2000. View

20.

Roossinck M . The good viruses: viral mutualistic symbioses. Nat Rev Microbiol. 2011; 9(2):99-108. DOI: 10.1038/nrmicro2491. View