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190
Counting the uncountable: statistical approaches to estimating microbial diversity
- Appl. Environ
, 2001
"... This article cites 52 articles, 16 of which can be accessed free ..."
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Cited by 110 (0 self)
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This article cites 52 articles, 16 of which can be accessed free
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
- Genome Res
, 2009
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Cited by 97 (4 self)
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This article cites 109 articles, 59 of which can be accessed free at: service Email alerting click heretop right corner of the article or Receive free email alerts when new articles cite this article- sign up in the box at the
Phylogenetic approaches for describing and comparing the diversity of microbial communities
- Appl. Environ. Microbiol. 68:3673
"... Diversity is the hard currency of ecologists. Various statistics have been developed for summarizing the diversity of an eco-logical community. A commonly adopted summary statistic is the Shannon-Weiner index: H " #!pilnpi, where pi is the frequency of the ith species. In addition, species rich ..."
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Cited by 91 (3 self)
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Diversity is the hard currency of ecologists. Various statistics have been developed for summarizing the diversity of an eco-logical community. A commonly adopted summary statistic is the Shannon-Weiner index: H " #!pilnpi, where pi is the frequency of the ith species. In addition, species richness (the number of different species) often is reported, and recent work emphasizes the importance of accurate estimates of species richness when ecological communities and processes that affect the composition of communities and the function of ecosys-tems are described (5). The significance of diversity is often inferred by comparing communities characterized from differ-ent environments. Typically, such comparisons rely on stan-dard measures of overlap, including the percentage of species shared by two communities or similarity indices. One of the indices used is Sorensen’s index: S " S12/[0.5(S1! S2)], where
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
- PLoS Biol
, 2008
"... The human intestinal microbiota is essential to the health of the host and plays a role in nutrition, development, metabolism, pathogen resistance, and regulation of immune responses. Antibiotics may disrupt these coevolved interactions, leading to acute or chronic disease in some individuals. Our u ..."
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Cited by 65 (2 self)
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The human intestinal microbiota is essential to the health of the host and plays a role in nutrition, development, metabolism, pathogen resistance, and regulation of immune responses. Antibiotics may disrupt these coevolved interactions, leading to acute or chronic disease in some individuals. Our understanding of antibiotic-associated disturbance of the microbiota has been limited by the poor sensitivity, inadequate resolution, and significant cost of current research methods. The use of pyrosequencing technology to generate large numbers of 16S rDNA sequence tags circumvents these limitations and has been shown to reveal previously unexplored aspects of the ‘‘rare biosphere.’ ’ We investigated the distal gut bacterial communities of three healthy humans before and after treatment with ciprofloxacin, obtaining more than 7,000 full-length rRNA sequences and over 900,000 pyrosequencing reads from two hypervariable regions of the rRNA gene. A companion paper in PLoS Genetics (see Huse et al., doi: 10.1371/ journal.pgen.1000255) shows that the taxonomic information obtained with these methods is concordant. Pyrosequencing of the V6 and V3 variable regions identified 3,300–5,700 taxa that collectively accounted for over 99 % of the variable region sequence tags that could be obtained from these samples. Ciprofloxacin treatment influenced the abundance of about a third of the bacterial taxa in the gut, decreasing the taxonomic richness, diversity, and evenness of the community. However, the magnitude of this effect varied among individuals, and some taxa showed interindividual variation in the response to ciprofloxacin. While differences of community composition
Molecular monitoring of succession of bacterial communities in human neonates
- Appl. Environ. Microbiol
, 2002
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Cited by 39 (3 self)
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These include: This article cites 37 articles, 19 of which can be accessed free at:
and discovery strategies for biotechnology: The paradigm shift
- Microbiol. Mol. Biol. Rev. 2000
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16S rRNA-based analysis of microbiota from the cecum of broiler chickens
- Supplementary Information
"... The microbiota of the intestinal tract of chickens plays an important role in inhibiting the establishment of intestinal pathogens. Earlier culturing and microscopic examinations indicated that only a fraction of the bacteria in the cecum of chickens could be grown in the laboratory. Therefore, a su ..."
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The microbiota of the intestinal tract of chickens plays an important role in inhibiting the establishment of intestinal pathogens. Earlier culturing and microscopic examinations indicated that only a fraction of the bacteria in the cecum of chickens could be grown in the laboratory. Therefore, a survey of cecal bacteria was done by retrieval of 16S rRNA gene sequences from DNA isolated from the cecal content and the cecal mucosa. The ribosomal gene sequences were amplified with universal primers and cloned or subjected to temporal temperature gradient gel electrophoresis (TTGE). Partial 16S rRNA gene sequences were determined from the clones and from the major bands in TTGE gels. A total of 1,656 partial 16S rRNA gene sequences were obtained and compared to sequences in the GenBank. The comparison indicated that 243 different sequences were present in the samples. Overall, sequences representing 50 phylogenetic groups or subgroups of bacteria were found, but approximately 89 % of the sequences represented just four phylogenetic groups (Clostridium leptum, Sporomusa sp., Clostridium coccoides, and enterics). Sequences of members of the Bacteroides group, the Bifidobacterium infantis subgroup, and of Pseudomonas sp. each accounted for less than 2 % of the total. Sequences related to those from the Escherichia sp. subgroup and from Lactobacillus, Pseudomonas, and Bifidobacterium spp. were generally between 98 and 100 % identical to sequences already deposited in the GenBank. Sequences most closely related to those of the other bacteria were generally 97 % or less identical to
Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces
- Appl. Environ. Microbiol
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Bifidobacterial diversity in human feces detected by genusspecific PCR and denaturing gradient gel electrophoresis
- Appl. Environ
, 2001
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Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods.
- Microbiology
, 2004
"... Summary 20 The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the etiology of these diseases. Common wisdom is that ..."
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Cited by 28 (3 self)
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Summary 20 The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the etiology of these diseases. Common wisdom is that lactobacilli dominate the normal vaginal microflora of post-pubertal women. However, this conclusion is based on methods that require cultivation of microbial populations; an approach that 25 is known to yield a biased and incomplete assessment of microbial community structure. We The diversity and kinds of organisms that comprise the vaginal microbial community varied among women. Species of Lactobacillus dominated the communities in 4 of the 5 women. However, the community of one woman was dominated by Atopobium sp., whereas a second woman had 35 appreciable numbers of Megasphaera sp., Atopobium sp., and Leptotrichia sp.; none of which have previously been shown to be common members of the vaginal ecosystem. Of the women whose communities were dominated by lactobacilli, there were two distinct clusters, each of which consisted of a single species. One class consisted of two women with genetically divergent clones that were related to L. crispatus, whereas the second group of two women had clones of L. 40 iners that were highly related to a single phylotype. These surprising results suggest that cultureindependent methods can provide new insights to the diversity of bacterial species found in the human vagina, and this information could prove to be pivotal in understanding risk factors for various infectious diseases.
