Chicken- and duck-associated Bacteroides–Prevotella genetic markers for detecting fecal contamination in environmental water

Bacteroides–Prevotella group is one of the most promising targets for detecting fecal contamination in water environments, principally due to its host-specific distributions and high concentrations in feces of warm-blooded animals. We developed real-time PCR assays for quantifying chicken/duck-, chicken-, and duck-associated Bacteroides–Prevotella 16S rRNA genetic markers (Chicken/Duck-Bac, Chicken-Bac, and Duck-Bac). A reference collection of DNA extracts from 143 individual fecal samples and wastewater treatment plant influent was tested by the newly established markers. The quantification limits of Chicken/Duck-Bac, Chicken-Bac, and Duck-Bac markers in environmental water were 54, 57, and 12 copies/reaction, respectively. It was possible to detect possible fecal contaminations from wild ducks in environmental water with the constructed genetic marker assays, even though the density of total coliforms in the identical water samples was below the detection limit. Chicken/Duck-Bac marker was amplified from feces of wild duck and chicken with the positive ratio of 96 and 61 %, respectively, and no cross-reaction was observed for the other animal feces. Chicken-Bac marker was detected from 70 % of chicken feces, while detected from 39 % of cow feces, 8.3 % of pig feces, and 12 % of swan feces. Duck-Bac marker was detected from 85 % of wild duck feces and cross-reacted with 31 % of cow feces. These levels of detection specificity are common in avian-associated genetic markers previously proposed, which implies that there is a practical limitation in the independent application of avian-associated Bacteroides–Prevotella 16S rRNA genetic markers and a combination with other fecal contamination markers is preferable for detecting fecal contamination in water environments.     

Spatial succession and metabolic properties of functional microbial communities in an anaerobic baffled reactor

The spatial successions of bacterial and archaeal communities in anaerobic digestion were investigated in a glucose-degrading five-compartment anaerobic baffled reactor (ABR). The distributions of H₂-producing acetogens, H₂-utilizing acetogens and methanogens in different anaerobic-digestion stages were quantitatively analyzed using functional probes. The results show that the acidogenesis stage and acetogenesis stage were located in the first two compartments, while the methanogenesis were located in the last two compartments. In acidogenesis/acetogenesis stage of anaerobic digestion, H₂-producing acetogens (19.7%) and H₂-utilizing acetogens (8.3%) were the dominant bacterial community. While in methanogenesis stage, methanogens became the dominant (40.2%) with H₂-producing acetogens and H₂-utilizing acetogens only accounting for 6.6% and 4.8%, respectively. With the bacterial population decreasing from 7.2 ± 0.5 × 10¹² cells mL⁻¹ to 0.6 ± 0.3 × 10¹² cells mL⁻¹ along water flowing direction, their diversity increased from 2.79 to 299. The acidogenic bacteria, such as Lactococcus sp., Uncultured Firmicutes bacterium, and Uncultured Clostridium sp., etc., dominated in the acidogenesis/acetogenesis stage, while Uncultured Desulfobacterales bacterium became dominant in the methanogenesis stage. A two-stage anaerobic process may be suitable for easily degradable organic matters removal.     

Quantitative Determination of H2-Utilizing Acetogenic and Sulfate-Reducing Bacteria and Methanogenic Archaea from Digestive Tract of Different Mammals

Total number of bacteria, cellulolytic bacteria, and H₂-utilizing microbial populations (methanogenic archaea, acetogenic and sulfate-reducing bacteria) were enumerated in fresh rumen samples from sheep, cattle, buffaloes, deer, llamas, and caecal samples from horses. Methanogens and sulfate reducers were found in all samples, whereas acetogens were not detected in some samples of each animal. Archaea methanogens were the largest H₂-utilizing populations in all animals, and a correlation was observed between the numbers of methanogens and those of cellulolytic microorganisms. Higher counts of acetogens were found in horses and llamas (1 × 10⁴ and 4 × 10⁴ cells ml⁻¹ respectively).     

Detection and source identification of airborne extended-spectrum beta-lactamase-producing Escherichia coli isolates in a chicken house

To identify airborne dissemination of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) in a chicken house, airborne E. coli was collected from indoor air of a chicken house using six-stage Anderson sampler, and E. coli from chicken fecal samples were also isolated simultaneously. ESBL-producing E. coli isolates from indoor air and fecal samples were screened by a phenotypic confirmatory test according to CLSI recommendations. And then, the enterobacterial repetitive intergenic consensus polymerase chain reaction was performed to analyze the source of airborne ESBL-producing E. coli. The results showed that the ESBL-positive rates of E. coli isolates from feces and the indoor air were 56 % (18/32) and 40 % (6/15), respectively. Furthermore, airborne ESBL-producing E. coli isolates in the chicken house had 100 % genetic similarities with the strains from chicken feces, indicating that ESBL-producing E. coli from chicken feces could be aerosolized and spread to the air.     

Comparative studies of water permeability of red blood cells from humans and over 30 animal species: an overview of 20 years of collaboration with Philip Kuchel

NMR measurements of the diffusional permeability of the human adult red blood cell (RBC) membrane to water (P _d) and of the activation energy (E _a,d) of the process furnished values of P _d ~ 4 × 10^?3 cm/s at 25 °C and ~6.1 × 10^?3 cm/s at 37 °C, and E _a,d ~ 26 kJ/mol. Comparative NMR measurements for other species showed: (1) monotremes (echidna and platypus), chicken, little penguin, and saltwater crocodile have the lowest P _d values; (2) sheep, cow, and elephant have P _d values lower than human P _d values; (3) cat, horse, alpaca, and camel have P _d values close to those of humans; (4) guinea pig, dog, dingo, agile wallaby, red-necked wallaby, Eastern grey kangaroo, and red kangaroo have P _d values higher than those of humans; (5) mouse, rat, rabbit, and “small and medium size” marsupials have the highest values of P _d (>8.0 × 10^?3 cm/s at 25 °C and >10.0 × 10^?3 cm/s at 37 °C). There are peculiarities of E _a,d values for the RBCs from different species. The maximum inhibition of diffusional permeability of RBCs induced by incubation with p-chloromercuribenzene sulfonate varied between 0 % (for the chicken and little penguin) to ~50 % (for human, mouse, cat, sheep, horse, camel, and Indian elephant), and ~60–75 % (for rat, guinea pig, rabbit, dog, alpaca, and all marsupials). These results indicate that no water channel proteins (WCPs) or aquaporins are present in the membrane of RBCs from monotremes (echidna, platypus), chicken, little penguin and saltwater crocodile whereas WCPs from the membranes of RBCs from marsupials have peculiarities.     

Microbial community structure in a biofilm anode fed with a fermentable substrate: The significance of hydrogen scavengers

We compared the microbial community structures that developed in the biofilm anode of two microbial electrolysis cells fed with ethanol, a fermentable substrate—one where methanogenesis was allowed and another in which it was completely inhibited with 2‐bromoethane sulfonate. We observed a three‐way syntrophy among ethanol fermenters, acetate‐oxidizing anode‐respiring bacteria (ARB), and a H₂ scavenger. When methanogenesis was allowed, H₂‐oxidizing methanogens were the H₂ scavengers, but when methanogenesis was inhibited, homo‐acetogens became a channel for electron flow from H₂ to current through acetate. We established the presence of homo‐acetogens by two independent molecular techniques: 16S rRNA gene based pyrosequencing and a clone library from a highly conserved region in the functional gene encoding formyltetrahydrofolate synthetase in homo‐acetogens. Both methods documented the presence of the homo‐acetogenic genus, Acetobacterium, only with methanogenic inhibition. Pyrosequencing also showed a predominance of ethanol‐fermenting bacteria, primarily represented by the genus Pelobacter. The next most abundant group was a diverse community of ARB, and they were followed by H₂‐scavenging syntrophic partners that were either H₂‐oxidizing methanogens or homo‐acetogens when methanogenesis was suppressed. Thus, the community structure in the biofilm anode and suspension reflected the electron‐flow distribution and H₂‐scavenging mechanism. Biotechnol. Bioeng. 2010;105: 69–78. © 2009 Wiley Periodicals, Inc.     

Development of a Murine Model with Optimal Routes for Bacterial Infection and Treatment, as Determined with Bioluminescent Imaging in C57BL/6 Mice

Mice intragastrically infected with Listeria monocytogenes EGDe and Staphylococcus aureus Xen 36 showed no visible signs of infection over 48 h. However, high numbers (6.2 × 10⁵ cfu/mg feces) of S. aureus Xen 36 were detected 4 h, and 3.3 × 10⁵ cfu/mg feces of L. monocytogenes EGDe 8 h, after administration. Mice intraperitoneally infected with S. aureus Xen 36 (1 × 10⁷ cfu) developed infection immediately after administration and for at least the following 48 h. Injection with higher cell numbers of S. aureus Xen 36 (2 × 10⁸ cfu) resulted in more intense bioluminescence (infection) of the peritoneal cavity. Injection of S. aureus Xen 36 in the tail and penile veins resulted in localized tissue infection for the first 120 h. Injection of S. aureus Xen 36 into the thigh produced a faint bioluminescent signal for 15 min. Nisin F injected into the peritoneal cavity at the same area of infection led to an immediate statistically significant decrease in infection (from 2 × 10⁶ p/s/cm²/sr to 3 × 10⁵ p/s/cm²/sr) within 2 h. Similar results were recorded when nisin F was injected subcutaneously. Intraperitoneal administration is an optimal administration route for bacterial infection and treatment with antimicrobial peptides.     

Development of a Swine-Specific Fecal Pollution Marker Based on Host Differences in Methanogen mcrA Genes

The goal of this study was to evaluate methanogen diversity in animal hosts to develop a swine-specific archaeal molecular marker for fecal source tracking in surface waters. Phylogenetic analysis of swine mcrA sequences compared to mcrA sequences from the feces of five animals (cow, deer, sheep, horse, and chicken) and sewage showed four distinct swine clusters, with three swine-specific clades. From this analysis, six sequences were chosen for molecular marker development and initial testing. Only one mcrA sequence (P23-2) showed specificity for swine and therefore was used for environmental testing. PCR primers for the P23-2 clone mcrA sequence were developed and evaluated for swine specificity. The P23-2 primers amplified products in P23-2 plasmid DNA (100%), pig feces (84%), and swine waste lagoon surface water samples (100%) but did not amplify a product in 47 bacterial and archaeal stock cultures and 477 environmental bacterial isolates and sewage and water samples from a bovine waste lagoon and a polluted creek. Amplification was observed in only one sheep sample out of 260 human and nonswine animal fecal samples. Sequencing of PCR products from pig feces demonstrated 100% similarity to pig mcrA sequence from clone P23-2. The minimal amount of DNA required for the detection was 1 pg for P23-2 plasmid, 1 ng for pig feces, 50 ng for swine waste lagoon surface water, 1 ng for sow waste influent, and 10 ng for lagoon sludge samples. Lower detection limits of 10⁻⁶ g of wet pig feces in 500 ml of phosphate-buffered saline and 10⁻⁴ g of lagoon waste in estuarine water were established for the P23-2 marker. This study was the first to utilize methanogens for the development of a swine-specific fecal contamination marker.     

Noninvasive Genotyping of the Red-Legged Partridge (Alectoris rufa, Phasianidae): Semi-Nested PCR of Mitochondrial DNA from Feces

DNA-based studies using avian feces are scarce and deal only with large-sized species. The red-legged partridge, Alectoris rufa, is a medium-sized member of the order Galliformes. Our goal was to set up a fast, noninvasive procedure for mitochondrial DNA (mtDNA) genotyping of A. rufa fecal samples. We focused on the protected population from Elba Island (Tuscan Archipelago National Park, Italy). Dry A. rufa fecal samples (n = 30) were collected in winter. Both the cytochrome b gene (1,092 bp) and the control region (ca. 1,155 bp) were amplified by means of semi-nested PCRs. Twenty-five samples were successfully sequenced for both genes: 8 showed A. rufa mtDNA lineage and 17 chukar partridge (A. chukar), an exotic species. Mixed maternal ancestry suggests A. rufa × A. chukar hybridization. Our protocol allows noninvasive mtDNA genotyping of any Alectoris species and appears suitable to investigate protected populations as well as those existing either at very low density or inhabiting poorly accessible regions.     

Method for Detection and Enumeration of Cryptosporidium parvum Oocysts in Feces, Manures, and Soils

Eight concentration and purification methods were evaluated to determine percentages of recovery of Cryptosporidium parvum oocysts from calf feces. The NaCl flotation method generally resulted in the highest percentages of recovery. Based on the percentages of recovery, the amounts of fecal debris in the final oocyst preparations, the relatively short processing time (<3 h), and the low expense, the NaCl flotation method was chosen for further evaluation. Extraction efficiency was evaluated by using oocyst concentrations of 25, 50, 10², 10³, 10⁴, and 10⁵ oocysts g of bovine feces⁻¹. The percentages of recovery ranged from 10.8% (25 oocysts g⁻¹) to 17.0% (10⁴ oocysts g⁻¹) (r² = 0.996). A conservative estimate of the detection limit for bovine feces is ca. 30 oocysts g of feces⁻¹. Percentages of recovery were determined for six different types of animal feces (cow, horse, pig, sheep, deer, and chicken feces) at a single oocyst concentration (10⁴ oocysts g⁻¹). The percentages of recovery were highest for bovine feces (17.0%) and lowest for chicken feces (3.2%). Percentages of recovery were determined for bovine manure after 3 to 7 days of storage. The percentages of recovery ranged from 1.9 to 3.5% depending on the oocyst concentration, the time of storage, and the dispersing solution. The percentages of oocyst recovery from soils were evaluated by using different flotation solutions (NaCl, cold sucrose, ZnSO₄), different dispersing solutions (Triton X-100, Tween 80, Tris plus Tween 80), different dispersion techniques (magnetic stirring, sonication, blending), and different dispersion times (5, 15, and 30 min). Twenty-five-gram soil samples were used to reduce the spatial variability. The highest percentages of recovery were obtained when we used 50 mM Tris–0.5% Tween 80 as the dispersing solution, dispersion for 15 min by stirring, and saturated NaCl as the flotation solution. The percentages of oocyst recovery from freshly spiked sandy loam, silty clay loam, and clay loam soils were ca. 12 to 18, 8, and 6%, respectively. The theoretical detection limits were ca. 1 to 2 oocysts g of soil⁻¹ depending on the soil type. The percentages of recovery without dispersant (distilled H₂O or phosphate-buffered saline) were less than 0.1%, which indicated that oocysts adhere to soil particles. The percentages of recovery decreased with storage time, although the addition of dispersant (Tris-Tween 80) before storage appeared to partially prevent adhesion. These data indicate that the NaCl flotation method is suitable for routine detection and enumeration of oocysts from feces, manures, soils, or soil-manure mixtures.     

Aflatoxin B1 and zearalenone in dairy feeds in Portugal, 2009–2011

This paper presents 3 years of data (2009–2011) on the occurrence of two mycotoxins, aflatoxin B₁ (AFB₁) and zearalenone (ZEA), in samples of feedstuff for dairy cows (n?=?963), ewes (n?=?42), and goats (n?=?131) produced in Portugal. AFB₁ was found in 15 samples of cow feed (1.6 %), 3 samples of ewe feed (2.3 %) and in 2 samples of goat feed (4.8 %). All but two samples contained AFB₁ at levels below the European Union maximum level (5 μg/kg). Nearly half (45 %) of the samples were contaminated with ZEA, but its levels were relatively low, at 5–136.9 μg/kg, well below the European Union guidance value (500 μg/kg).     

Quantification of host-specific <Emphasis Type="Italic">Bacteroides–Prevotella</Emphasis> 16S rRNA genetic markers for assessment of fecal pollution in freshwater

Based on the comparative 16S rRNA gene sequence analysis of fecal DNAs, we identified one human-, three cow-, and two pig-specific Bacteroides–Prevotella 16S rRNA genetic markers, designed host-specific real-time polymerase chain reaction (real-time PCR) primer sets, and successfully developed real-time PCR assay to quantify the fecal contamination derived from human, cow, and pig in natural river samples. The specificity of each newly designed host-specific primer pair was evaluated on fecal DNAs extracted from these host feces. All three cow-specific and two pig-specific primer sets amplified only target fecal DNAs (in the orders of 9–11 log₁₀ copies per gram of wet feces), showing high host specificity. This real-time PCR assay was then applied to the river water samples with different fecal contamination sources and levels. It was confirmed that this assay could sufficiently discriminate and quantify human, cow, and pig fecal contamination. There was a moderate level of correlation between the Bacteroides–Prevotella group-specific 16S rRNA gene markers with fecal coliforms (r ² = 0.49), whereas no significant correlation was found between the human-specific Bacteroides 16S rRNA gene with total and fecal coliforms. Using a simple filtration method, the minimum detection limits of this assay were in the range of 50–800 copies/100 ml. With a combined sample processing and analysis time of less than 8 h, this real-time PCR assay is useful for monitoring or identifying spatial and temporal distributions of host-specific fecal contaminations in natural water environments.     

Spectroscopic Studies on the Interaction of Fluorine Containing Triazole with Bovine Serum Albumin

The binding of one fluorine including triazole (C₁₀H₉FN₄S, FTZ) to bovine serum albumin (BSA) was studied by spectroscopic techniques including fluorescence spectroscopy, UV–Vis absorption, and circular dichroism (CD) spectroscopy under simulative physiological conditions. Fluorescence data revealed that the fluorescence quenching of BSA by FTZ was the result of forming a complex of BSA–FTZ, and the binding constants (K _a) at three different temperatures (298, 304, and 310 K) were 1.516?×?10⁴, 1.627?×?10⁴, and 1.711?×?10⁴?mol L^?1, respectively, according to the modified Stern–Volmer equation. The thermodynamic parameters ΔH and ΔS were estimated to be 7.752 kJ mol^?1 and 125.217 J?mol^?1?K^?1, respectively, indicating that hydrophobic interaction played a major role in stabilizing the BSA–FTZ complex. It was observed that site I was the main binding site for FTZ to BSA from the competitive experiments. The distance r between donor (BSA) and acceptor (FTZ) was calculated to be 7.42 nm based on the Förster theory of non-radioactive energy transfer. Furthermore, the analysis of fluorescence data and CD data revealed that the conformation of BSA changed upon the interaction with FTZ.     

Development of a DNA macroarray for simultaneous detection of multiple foodborne pathogenic bacteria in fresh chicken meat

A DNA macroarray was developed to provide the ability to detect multiple foodborne pathogens in fresh chicken meat. Probes targeted to the 16S rRNA and genus- and species-specific genes, including fimY, ipaH, prfA, and uspA, were selected for the specific detection of Salmonella spp., Shigella spp., Listeria monocytogenes, and Escherichia coli, respectively. The combination of target gene amplification by PCR and a DNA macroarray in our system was able to distinguish all target bacteria from pure cultures with a detection sensitivity of 10⁵ c.f.u. ml^?1. The DNA macroarray was also applied to 10 fresh chicken meat samples. The assay validation demonstrated that by combining the enrichment steps for the target bacteria and the DNA macroarray, all 4 target bacteria could be detected simultaneously from the fresh chicken samples. The sensitivity of L. monocytogenes and Shigella boydii detection in the fresh chicken samples was at least 10 and 3 c.f.u. of the initial contamination in 25 g samples, respectively. The advantages of our developed protocol are high accuracy and time reduction when compared to conventional culture. The macroarray developed in our investigation was cost effective compared to modern oligonucleotide microarray techniques because there was no expensive equipment required for the detection of multiple foodborne pathogens.     

General medium for the autotrophic cultivation of acetogens

Syngas fermentation, a microbial process in which synthesis gas serves as a substrate for acetogens, has attracted increasing interest in the last few years. For the purposeful selection of acetogens for various applications, it would be useful to characterize and compare the process performances of as many autotrophic strains as possible under identical process conditions. Unfortunately, all the media compositions so far recommended for syngas fermentation differ considerably with respect to each individual strain. Therefore, a general medium for syngas fermentation was designed. The suitability of this new general-acetogen medium (GA-medium) was proven based on the autotrophic batch cultivation of Acetobacterium fimetarium, Acetobacterium wieringae, Blautia hydrogenotrophica, Clostridium magnum, Eubacterium aggregans, Sporomusa acidovorans, Sporomusa ovata and Terrisporobacter mayombei in anaerobic flasks with an initial gas phase of H₂:CO₂ (66:34) (P = 200 kPa). A comparison of the autotrophic batch processes with this medium revealed T. mayombei as the bacterium with the highest maximum growth rate of 5.77 day^?1 which was more than 10 times higher than the lowest identified maximum growth rate of A. fimetarium. The maximum growth rates of A. wieringae, C. magnum and S. acidovorans were all in the same order of magnitude around 1.7 day^?1. The newly designed GA-medium offers the possibility to compare autotrophic process performances of different acetogens under similar conditions absent the effects of various media compositions.     

Vancomycin-Resistant Enterococcus spp. Isolated from Wastewater and Chicken Feces in the United States

Vancomycin-resistant Enterococcus spp. (VRE) were isolated from sewage and chicken feces but not from other animal fecal sources (dog, cow, and pig) or from surface waters tested. VRE from hospital wastewater were resistant to ≥20 μg of vancomycin/ml and possessed the vanA gene. VRE from residential wastewater and chicken feces were resistant to 3 to 5 μg of vancomycin/ml and possessed the vanC gene.     

The effects of external electric field: creating non-zero first hyperpolarizability for centrosymmetric benzene and strongly enhancing first hyperpolarizability for non-centrosymmetric edge-modified graphene ribbon H2N-(3,3)ZGNR-NO2

How to generate a non-zero first hyperpolarizability for a centrosymmetric molecule is a challenging question. In this paper, an external (pump) electric field is used to make a centrosymmetric benzene molecule generate a non-zero value of the electric field induced first hyperpolarizability (β ^F ). This comes from the centrosymmetry breaking of electron cloud. Two interesting rules are exhibited. (1) β ^F is anisotropic for different directional fields (F _i, i?=?X, Y, Z). (2) The field dependence of β ^F is a non-monotonic function, and an optimum external electric field causes the maximum value of β ^F . The largest first hyperpolarizability β ^F reaches the considerable level of 3.9?×?10⁵ a.u. under F _Y?=?330?×?10^?4 a.u. for benzene. The external electric field effects on non-centrosymmetric edge-modified graphene ribbon H₂N-(3,3)ZGNR-NO₂ was also studied in this work. The first hyperpolarizability reaches as much as 2.1?×?10⁷ a.u. under F _X?=?600?×?10^?4 a.u. for H₂N-(3,3)ZGNR-NO₂. We show that the external electric field can not only create a non-zero first hyperpolarizability for centrosymmetric molecule, but also remarkably enhance the first hyperpolarizability for a non-centrosymmetric molecule.     

Characterization of the <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> Isolates Virulent Against Rice Leaf Folder, <Emphasis Type="Italic">Cnaphalocrocis medinalis</Emphasis> (Guenee)

Soil samples were collected from different rice fields of Singur, Hooghly, West Bengal, India. Spore forming bacteria were isolated from the soil samples and among them, two isolates (BUSNC25 and BUSNC26) were larvicidal against third, fourth and fifth instar larvae of rice leaf folder, Cnaphalocrocis medinalis. The phenotypic, biochemical characterization and 16S rDNA analysis of the two isolates were done. On the basis of phenotypic, biochemical and phylogenetic analysis, the selected bacterial isolates (BUSNC25 and BUSNC26) were identified as Bacillus thuringiensis. The antibiotic sensitivity tests of these two isolates against selected doses of some standard antibiotics were done. Against the 3rd, 4th and 5th instar larvae of C. medinalis, the LC₅₀ values of BUSNC25 were 2.45 × 10⁴, 1.325 × 10⁴ and 2.35 × 10⁴ cfu/ml and of BUSNC26 were 3.375 × 10⁴, 1.9 × 10⁴ and 3.325 × 10⁴ cfu/ml, respectively.     

Identification of Nonpoint Sources of Fecal Pollution in Coastal Waters by Using Host-Specific 16S Ribosomal DNA Genetic Markers from Fecal Anaerobes

We describe a new PCR-based method for distinguishing human and cow fecal contamination in coastal waters without culturing indicator organisms, and we show that the method can be used to track bacterial marker sequences in complex environments. We identified two human-specific genetic markers and five cow-specific genetic markers in fecal samples by amplifying 16S ribosomal DNA (rDNA) fragments from members of the genus Bifidobacterium and the Bacteroides-Prevotella group and performing length heterogeneity PCR and terminal restriction fragment length polymorphism analyses. Host-specific patterns suggested that there are species composition differences in the Bifidobacterium and Bacteroides-Prevotella populations of human and cow feces. The patterns were highly reproducible among different hosts belonging to the same species. Additionally, all host-specific genetic markers were detected in water samples collected from areas frequently contaminated with fecal pollution. Ease of detection and longer survival in water made Bacteroides-Prevotella indicators better than Bifidobacterium indicators. Fecal 16S rDNA sequences corresponding to our Bacteroides-Prevotella markers comprised closely related gene clusters, none of which exactly matched previously published Bacteroides or Prevotella sequences. Our method detected host-specific markers in water at pollutant concentrations of 2.8 × 10⁻⁵ to 2.8 × 10⁻⁷ g (dry weight) of feces/liter and 6.8 × 10⁻⁷ g (dry weight) of sewage/liter. Although our aim was to identify nonpoint sources of fecal contamination, the method described here should be widely applicable for monitoring spatial and temporal fluctuations in specific bacterial groups in natural environments.