Chapter 2 : Taxonomy, Phylogeny, and Physiology of Fecal Indicator Bacteria

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In studies of environmental quality, there are several different groups of bacteria frequently used as fecal indicators. The most widely applied approach is to use the group represented by the family (coliforms and fecal coliforms). Fecal indicators other than , include members of the genus (formally fecal ) and the anaerobic bacteria , , and some members of the genus . Due to their widespread use as indictors of the quality of water and other environments, this chapter covers the phylogeny, taxonomy, and physiology of the key fecal indicator bacteria. and are specifically classified as fecal coliforms. The major set of phenotypic characteristics defining the family include the following: small gram-negative rods, facultative but preferring aerobic metabolism, oxidase negative, catalase positive, can reduce nitrates to nitrites, do not require Na for growth, can ferment D-glucose, and contain enterobacterial common antigens. Originally, classification of coliform bacteria was based on fermentation of sucrose and dulcitol, production of indole and acetylmethylcarbinol, and gelatin liquefaction. Functionally, enterococci are divided into five groups based on their ability to produce acid from mannitol and sorbose, and hydrolyze arginine. spp. are present in much greater numbers than , and can account for up to 30% of the total fecal isolates, with the most common species being , , and .

Citation: Carrero-Colón M, Wickham G, Turco R. 2011. Taxonomy, Phylogeny, and Physiology of Fecal Indicator Bacteria, p 23-38. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch2

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Gram-Positive Bacteria
Clostridium perfringens
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Evolutionary relationships of fecal bacteria. The small-subunit, or 16S, rRNA-based evolutionary relationships of representative fecal bacteria are shown. A total of 36 (35 fecal bacteria sequences and 1 outgroup sequence) nearly full-length 16S rRNA sequences from the Ribosomal Database Project ( ) and/or the SILVA database ( ) were aligned in ARB ( ). A modified version of the Lane mask ( ) was used to define 1344 unambiguously aligned nucleotide positions for comparative analysis by quartet puzzling (Strimmer and ). Each sequence is denoted as an indicator (I), pathogen (P), or both (P/I). R1 was used to root the tree. The scale bar represents 0.4 fixed mutations per nucleotide position. Whenever available, sequences from type strains were used. In instances where sequences from non-type strains were not available, non-type strain sequences were chosen based on their length and quality. The accession identifier for each sequence is shown in parentheses below. Type strains: (X60408), (X83935), (M58729), (M38018), (D86183), (L14630), (AJ233408), A (L37585), (M59103), (AB004750), (AJ251469), (AF133535), (AJ420801), (AJ276355), (X80725), (Y17656), (X56153), subsp. serovar Typhi (Z47544), (AB002482), (X58318), (X74677), and (M59157). Non-type strains: (X74684), (AF025372), (AJ301831), (AF039898), (AY292868), (AJ131120), (EU118104), subsp. serovar Gallinarum (EU073018), (X96966), (EU009199), (D83357), (M59292), and (AF366383).

Citation: Carrero-Colón M, Wickham G, Turco R. 2011. Taxonomy, Phylogeny, and Physiology of Fecal Indicator Bacteria, p 23-38. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch2
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Table 1

Key fecal indicator bacteria used in determining fecal contamination in different environments

Citation: Carrero-Colón M, Wickham G, Turco R. 2011. Taxonomy, Phylogeny, and Physiology of Fecal Indicator Bacteria, p 23-38. In Sadowsky M, Whitman R (ed), The Fecal Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555816865.ch2

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