Fecal Microbial Diversity in a Strict Vegetarian as Determined by Molecular Analysis and Cultivation

Abstract

Fecal microbial diversity in a strictly vegetarian woman was determined by the 16S rDNA library method, terminal restriction fragment length polymorphism (T‐RFLP) analysis and a culture‐based method. The 16S rDNA library was generated from extracted fecal DNA, using bacteria‐specific primers. Randomly selected clones were partially sequenced. T‐RFLP analysis was performed using amplified 16S rDNA. The lengths of T‐RF were analyzed after digestion by HhaI and MspI. The cultivated bacterial isolates were used for partial sequencing of 16S rDNA. Among 183 clones obtained, approximately 29% of the clones belonged to 13 known species. About 71% of the remaining clones were novel “phylotypes” (at least 98% similarity of clone sequence). A total of 55 species or phylotypes were identified among the 16S rDNA library, while the cultivated isolates included 22 species or phylotypes. In addition, many new phylotypes were detected from the 16S rDNA library. The 16S rDNA library and isolates commonly included the Bacteroides group, Bifidobacterium group, and Clostridium rRNA clusters IV, XIVa, XVI and XVIII. T‐RFLP analysis revealed the major composition of the vegetarian gut microbiota were Clostridium rRNA subcluster XIVa and Clostridium rRNA cluster XVIII. The dominant feature of this strictly vegetarian gut microbiota was the detection of many Clostridium rRNA subcluster XIVa and C. ramosum (Clostridium rRNA cluster XVIII).

Fecal microbiota of a dugong (Dugong dugong) in captivity at Toba Aquarium

“…There was a similar observation of the mirobiota in human vegetarian feces, which showed 90.7% of Fermicutes, 59.6% of Clostridium rRNA Subcluster XIVa, and 6.0% of CytophagaFlexibacter-Bacteroides (Hayashi et al, 2002b). However, no bacterial species contributing to the fiber degradation in the proximal colon was identified in this study, suggesting that the fiber-degrading bacteria, such as Ruminococcus albus, Ruminococcus flavefaciens, and Fibrobacter succinogenes, may be a minor species, at least less than detection levels.…”

Effect of Antibiotic Therapy on Human Fecal Microbiota and the Relation to the Development of Clostridium difficile

“…The non exhaustive data of the microbiota we found show species only from Clostridiales order, Clostridiaceae, Eubacterium and Lachnospiraceae family. This is not surprising since novel or yet uncultured species are most often identified upon characterization of fecal microbiota using cloned 16S rDNA genes librairies [11]. Recent culture-independent studies have shown that approximately 70% of the dominant human gut microorganisms have not been isolated and described [3].…”

Molecular analysis of human forearm superficial skin bacterial biota

“…Each previously uncharacterized phylotype was identified only in a single subject, consistent with the observed low level of interpersonal consensus. That 7.1% of clones and 17.8% of phylotypes were previously uncharacterized, based on a criterion of Ͻ97% similarity, is much lower than in other human niches, including the intestine (23), feces (39), tongue dorsum (40), and human subgingival crevice (20). The presence of a few dominant species in the skin, use of varying definitions in different studies (19,23,41), as well as the progressive recognition of human-associated species, may partially explain this difference.…”