Metagenomic Analyses of an Uncultured Viral Community from Human Feces

Breitbart, Mya; Hewson, Ian; Felts, Ben; Mahaffy, Joseph M.; Nulton, James; Salamon, Peter; Rohwer, Forest

doi:10.1128/jb.185.20.6220-6223.2003

Cited by 694 publications

(647 citation statements)

References 33 publications

(16 reference statements)

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“…The largest fraction of C. watsonii WH8501 transcript sequences obtained from the bloom station in the day (30%) and night (18%) was conserved hypothetical proteins or proteins of unknown function, which is in line with C. watsonii WH8501 transcripts recovered from other stations in the southwest Pacific and equatorial Atlantic oceans (30.7%), and previous metagenomic studies of microorganisms (Tyson et al, 2004;Venter et al, 2004;Rusch et al, 2007) and viruses (Angly et al, 2006;Breitbart et al, 2002Breitbart et al, , 2003. The most highly expressed C. watsonii hypothetical protein (Cwat_DRAFT_0061; ZP_00519306.1) was present in the bloom day (15% of transcripts) and night (5% of transcripts) metatranscriptomes.…”

Section: Resultssupporting

confidence: 53%

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

et al. 2009

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The diazotrophic cyanobacterium Crocosphaera watsonii supplies fixed nitrogen (N) to N-depleted surface waters of the tropical oceans, but the factors that determine its distribution and contribution to global N 2 fixation are not well constrained for natural populations. Despite the heterogeneity of the marine environment, the genome of C. watsonii is highly conserved in nucleotide sequence in contrast to sympatric planktonic cyanobacteria. We applied a whole assemblage shotgun transcript sequencing approach to samples collected from a bloom of C. watsonii observed in the South Pacific to understand the genomic mechanisms that may lead to high population densities. We obtained 999 C. watsonii transcript reads from two metatranscriptomes prepared from mixed assemblage RNA collected in the day and at night. The C. watsonii population had unexpectedly high transcription of hypothetical protein genes (31% of protein-encoding genes) and transposases (12%). Furthermore, genes were expressed that are necessary for living in the oligotrophic ocean, including the nitrogenase cluster and the iron-stress-induced protein A (isiA) that functions to protect photosystem I from high-light-induced damage. C. watsonii transcripts retrieved from metatranscriptomes at other locations in the southwest Pacific Ocean, station ALOHA and the equatorial Atlantic Ocean were similar in composition to those recovered in the enriched population. Quantitative PCR and quantitative reverse transcriptase PCR were used to confirm the high expression of these genes within the bloom, but transcription patterns varied at shallower and deeper horizons. These data represent the first transcript study of a rare individual microorganism in situ and provide insight into the mechanisms of genome diversification and the ecophysiology of natural populations of keystone organisms that are important in global nitrogen cycling.

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Section: Resultssupporting

confidence: 53%

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

et al. 2009

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“…9,11,12,19,[20][21][22] Phages are also naturally present in many, if not all, commercial pet foods. 12 Thus, their general safety profile is excellent, and several phage preparations have been granted GRAS (Generally Recognized As Safe) status by the FDA for human food applications.…”

Section: Discussionmentioning

confidence: 99%

Bacteriophages safely reduceSalmonellacontamination in pet food and raw pet food ingredients

et al. 2016

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Contamination of pet food with Salmonella is a serious public health concern, and several disease outbreaks have recently occurred due to human exposure to Salmonella tainted pet food. The problem is especially challenging for raw pet foods (which include raw meats, seafood, fruits, and vegetables). These foods are becoming increasingly popular because of their nutritional qualities, but they are also more difficult to maintain Salmonella-free because they lack heat-treatment. Among various methods examined to improve the safety of pet foods (including raw pet food), one intriguing approach is to use bacteriophages to specifically kill Salmonella serotypes. At least 2 phage preparations (SalmoFresh Ò and Salmonelex TM ) targeting Salmonella are already FDA cleared for commercial applications to improve the safety of human foods. However, similar preparations are not yet available for pet food applications. Here, we report the results of evaluating one such preparation (SalmoLyse Ò ) in reducing Salmonella levels in various raw pet food ingredients (chicken, tuna, turkey, cantaloupe, and lettuce). Application of SalmoLyse Ò in low (ca. 2-4£10 6 PFU/g) and standard (ca. 9£10 6 PFU/g) concentrations significantly (P < 0.01) reduced (by 60-92%) Salmonella contamination in all raw foods examined compared to control treatments. When SalmoLyse Ò -treated (ca. 2£10 7 PFU/g) dry pet food was fed to cats and dogs, it did not trigger any deleterious side effects in the pets. Our data suggest that the bacteriophage cocktail lytic for Salmonella can significantly and safely reduce Salmonella contamination in various raw pet food ingredients.

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“…Exploration of such questions had been previously hindered by the nonculturability of the majority of viruses and microbes combined with the difficulties in identifying them at the level of both species and strain. Metagenomics now provides a culture-independent method for characterizing the viral and microbial communities present in an ecosystem, including the metabolic capabilities encoded in their genomes and the halo of variation within each species (Breitbart et al, 2002(Breitbart et al, , 2003(Breitbart et al, , 2004Tyson et al, 2004;Venter et al, 2004;Breitbart and Rohwer, 2005;Tringe et al, 2005;Angly et al, 2006;Edwards et al, 2006;Legault et al, 2006;Cuadros-Orellana et al, 2007;Desnues et al, 2008;Dinsdale et al, 2008a, b).…”

Section: Introductionmentioning

confidence: 99%

Viral and microbial community dynamics in four aquatic environments

et al. 2010

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The species composition and metabolic potential of microbial and viral communities are predictable and stable for most ecosystems. This apparent stability contradicts theoretical models as well as the viral-microbial dynamics observed in simple ecosystems, both of which show Kill-the-Winner behavior causing cycling of the dominant taxa. Microbial and viral metagenomes were obtained from four human-controlled aquatic environments at various time points separated by one day to 41 year. These environments were maintained within narrow geochemical bounds and had characteristic species composition and metabolic potentials at all time points. However, underlying this stability were rapid changes at the fine-grained level of viral genotypes and microbial strains. These results suggest a model wherein functionally redundant microbial and viral taxa are cycling at the level of viral genotypes and virus-sensitive microbial strains. Microbial taxa, viral taxa, and metabolic function persist over time in stable ecosystems and both communities fluctuate in a Kill-the-Winner manner at the level of viral genotypes and microbial strains.

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Metagenomic Analyses of an Uncultured Viral Community from Human Feces

Cited by 694 publications

References 33 publications

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

Bacteriophages safely reduceSalmonellacontamination in pet food and raw pet food ingredients

Viral and microbial community dynamics in four aquatic environments

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