ArticleApplied and environmental microbiology2008
Relative abundance of Bacteroides spp. in stools and wastewaters as determined by hierarchical oligonucleotide primer extension.
Article in Applied and environmental microbiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 57 citations in OpenAlex.
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- A new Illumina MiSeq high-throughput sequencing-based method for evaluating the composition of the Bacteroides community in the intestine using the rpsD gene sequence.Microbial biotechnology · 2021Article
- Sialylation and fucosylation modulate inflammasome-activating eIF2 Signaling and microbial translocation during HIV infection.Mucosal immunology · 2020Article
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- Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods.Journal of medical microbiology · 2019Article
- ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples.Environmental microbiology · 2019Article
- Oral Nickel Changes of Intestinal Microflora in Mice.Current microbiology · 2019Article
- Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria.BMC microbiology · 2017Article
- Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water.MicrobiologyOpen · 2016Article
- Safety Assessment of Bacteroides uniformis CECT 7771 Isolated from Stools of Healthy Breast-Fed Infants.PloS one · 2016Article
- The microbiome of the built environment and mental health.Microbiome · 2015Review
- Assessing the Groundwater Quality at a Saudi Arabian Agricultural Site and the Occurrence of Opportunistic Pathogens on Irrigated Food Produce.International journal of environmental research and public health · 2015Article
- Associations among Human-Associated Fecal Contamination, Microcystis aeruginosa, and Microcystin at Lake Erie Beaches.International journal of environmental research and public health · 2015Article
- Use of a hierarchical oligonucleotide primer extension approach for multiplexed relative abundance analysis of methanogens in anaerobic digestion systems.Applied and environmental microbiology · 2013Article
- Distribution of genetic markers of fecal pollution on a freshwater sandy shoreline in proximity to wastewater effluent.Environmental science & technology · 2013Article
- Pathogenic potential of Campylobacter ureolyticus.Infection and immunity · 2012Article
- Preliminary safety evaluation of a new Bacteroides xylanisolvens isolate.Applied and environmental microbiology · 2012Article
- The development and stability of the genus Bacteriodes from human gut microbiota in HFA mice model.Current microbiology · 2011Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A molecular method, termed hierarchical oligonucleotide primer extension (HOPE), was used to determine the relative abundances of predominant Bacteroides spp. present in fecal microbiota and wastewaters. For this analysis, genomic DNA in feces of healthy human adults, bovines, and swine and in wastewaters was extracted and total bacterial 16S rRNA genes were PCR amplified and used as the DNA templates for HOPE. Nineteen oligonucleotide primers were designed to detect 14 Bacteroides spp. at different hierarchical levels (domain, order, cluster, and species) and were arranged into and used in six multiplex HOPE reaction mixtures. Results showed that species like B. vulgatus, B. thetaiotaomicron, B. caccae, B. uniformis, B. fragilis, B. eggerthii, and B. massiliensis could be individually detected in human feces at abundances corresponding to as little as 0.1% of PCR-amplified 16S rRNA genes. Minor species like B. pyogenes, B. salyersiae, and B. nordii were detected only collectively using a primer that targeted the B. fragilis subgroup (corresponding to approximately 0.2% of PCR-amplified 16S rRNA genes). Furthermore, Bac303-related targets (i.e., most Bacteroidales) were observed to account for 28 to 44% of PCR-amplified 16S rRNA genes from human fecal microbiota, and their abundances were higher than those detected in the bovine and swine fecal microbiota and in wastewaters by factors of five and two, respectively. These results were comparable to those obtained by quantitative PCR and to those reported previously from studies using whole-cell fluorescence hybridization and 16S rRNA clone library methods, supporting the conclusion that HOPE can be a sensitive, specific, and rapid method to determine the relative abundances of Bacteroides spp. predominant in fecal samples.
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