Comparison of methods and animal models commonly used for investigation of fecal microbiota: Effects of time, host and gender

Bernbom, Nete; Nørrung, Birgit; Saadbye, Peter; Mølbak, Lars; Vogensen, Finn K.; Licht, Tine Rask

doi:10.1016/j.mimet.2005.10.014

Cited by 42 publications

(33 citation statements)

References 24 publications

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“…A study by Bernbom et al showed that the fecal microbiota of SPF rats and human microbiota-associated rats clustered according to the gender of the host animal (61). Our results are consistent also with the observations by Markle et al who suggested that sex hormones could influence microbial populations (62).…”

Section: Discussionmentioning

confidence: 99%

High purity galacto-oligosaccharides enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome

Monteagudo-Mera

Arthur

Jobin

et al. 2016

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Prebiotics are selectively fermented ingredients that result in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon the host health. The aim of this study was to evaluate the influence of a β (1–4) galacto-oligosaccharides formulation consisting of 90% pure GOS (GOS90), on the composition and activity of the mouse gut microbiota. Germ-free mice were colonized with microbiota from four pathogen-free wt 129 mice donors (SPF), and stools were collected during a feeding trial in which GOS90 was delivered orally for 14 days. Pyrosequencing of 16S rDNA amplicons showed that Bifidobacterium and specific Lactobacillus, Bacteroides and Clostridiales were more prevalent in GOS90-fed mice after 14 days, although the prebiotic impact on Bifidobacterium varied among individual mice. Prebiotic feeding also resulted in decreased abundance of Bacteroidales, Helicobacter and Clostridium. High-throughput quantitative PCR showed an increased abundance of Bifidobacterium adolescentis, B. pseudocatenulatum, B. lactis and B. gallicum in the prebiotic-fed mice. Control female mice showed a higher diversity (Phylogenetic Diversity PD = 15.1 ± 3.4 in stools and PD = 13.0 ± 0.6 in intestinal contents) than control males (PD = 7.8 ± 1.6 in stool samples and PD = 9.5 ± 1.0 in intestinal contents). GOS90 did not modify inflammatory biomarkers (IL-6, IL-12, IL-1β, IFN-γ and TNF-α). Decreased butyrate, acetate and lactate concentrations in stools of prebiotic fed mice suggested an increase in colonic absorption and reduced excretion. Overall, our results demonstrate that GOS90 is capable of modulating the intestinal microbiome resulting in expansion of the probiome (autochtonous commensal intestinal bacteria considered to have a beneficial influence on health).

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Section: Discussionmentioning

confidence: 99%

High purity galacto-oligosaccharides enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome

Monteagudo-Mera

Arthur

Jobin

et al. 2016

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“…However, the ruminant-specific 16S rRNA gene marker, CF128F, was detected more frequently than the non-16S rRNA gene markers in water and sediment samples in the stream directly impacted by cattle (Tables 4 and 7). Differences in the abundance, host distribution, and environmental survival rates of targeted populations may partially explain the different detection rates observed for the molecular markers tested with water samples (1,22). In addition, differences in copy number between targeted genes and amplification efficiency can also contribute to the differences in sensitivity among MST assays.…”

Section: Discussionmentioning

confidence: 99%

Temporal Assessment of the Impact of Exposure to Cow Feces in Two Watersheds by Multiple Host-Specific PCR Assays

Lee

Molina

Domingo

et al. 2008

Appl Environ Microbiol

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Exposure to feces in two watersheds with different management histories was assessed by tracking cattle feces bacterial populations using multiple host-specific PCR assays. In addition, environmental factors affecting the occurrence of these markers were identified. Each assay was performed using DNA extracts from water and sediment samples collected from a watershed directly impacted by cattle fecal pollution (WS1) and from a watershed impacted only through runoff (WS2). In WS1, the ruminant-specific Bacteroidales 16S rRNA gene marker CF128F was detected in 65% of the water samples, while the non-16S rRNA gene markers Bac1, Bac2, and Bac5 were found in 32 to 37% of the water samples. In contrast, all source-specific markers were detected in less than 6% of the water samples from WS2. Binary logistic regressions (BLRs) revealed that the occurrence of Bac32F and CF128F was significantly correlated with season as a temporal factor and watershed as a site factor. BLRs also indicated that the dynamics of fecal-source-tracking markers correlated with the density of a traditional fecal indicator (P < 0.001). Overall, our results suggest that a combination of 16S rRNA gene and non-16S rRNA gene markers provides a higher level of confidence for tracking unknown sources of fecal pollution in environmental samples. This study also provided practical insights for implementation of microbial source-tracking practices to determine sources of fecal pollution and the influence of environmental variables on the occurrence of source-specific markers.The fecal bacterial group is one of the top three contaminants impacting the quality of recreational waters and drinking water sources in the United States (30). Bodies of water with high levels of pollution are believed to be polluted primarily by nonpoint sources, such as wildlife, domesticated animals, and agricultural and urban runoff (30). While inadequately treated sewage and septic system failure can occasionally impact surface waters, animal fecal pollution is unquestionably the major source of pollution in developed countries (23). The annual production of animal feces in the United States is approximately 1 ϫ 10 9 tons (29), and this number will likely increase due to current trends in the American diet. Poultry, cattle, and swine are responsible for 44, 31, and 24% of the total annual production of animal feces, respectively (14).Detecting and ranking the sources of fecal pollution are challenging as conventional methods used to monitor pollution cannot discriminate among the various potential nonpoint sources impacting a body of water (30). As a consequence of the development and implementation of total maximum daily loads, several microbial source-tracking (MST) methods have been developed and tested in field applications (3,5,19,26,27). Among these methods, culture-independent host-specific PCR assays are gaining acceptance because of their potential for high throughput and quick turn-around times (22). In most MST studies using host-specific PCR assays, researchers hav...

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“…DGGE was carried out as previously described [9] using a DCode™ Universal Mutation Detection System instrument and gradient former model 475 according to the manufacturer's instructions (Bio-Rad Labs, Hercules, California). The denaturing gradient was formed with two 9% acrylamide (acrylamide-bis 37.5:1) stock solutions (Bio-Rad) in 1 × TAE (20 mM Tris, 10 mM acetate, 0.5 M EDTA, pH 7.4).…”

Section: Methodsmentioning

confidence: 99%

“…An example of such a fingerprinting method is Denaturing Gradient Gel Electrophoresis (DGGE) of PCR-amplified 16S rRNA genes, which have proved very useful for analysis of faecal bacteria [7-9]. While the DGGE profiles based on amplified rRNA genes (DNA-DGGE) provides a fingerprint of the composition of the investigated community, they do not necessarily reflect metabolic activities, and could even originate from dormant, lysed or dead cells.…”

Section: Introductionmentioning

confidence: 99%

Untitled

Licht¹,

Hansen²,

Poulsen³

et al. 2006

BMC Microbiol

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BackgroundA study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group), sucrose, potato starch, inulin (a long- chained fructan) or oligofructose (a short-chained fructan). Fructans are, opposite sucrose and starches, not digestible by mammalian gut enzymes, but are known to be fermentable by specific bacteria in the large intestine.ResultsAnimals fed with diets containing potato starch, or either of the fructans had a significantly (p < 0.05) higher caecal weight and lower caecal pH when compared to the reference group, indicating increased fermentation. Selective cultivation from faeces revealed a higher amount of lactic acid bacteria cultivable on Rogosa agar in these animals. Additionally, the fructan groups had a lower amount of coliform bacteria in faeces. In the inulin and oligofructose groups, higher levels of butyrate and propionate, respectively, were measured.Principal Component Analysis of profiles of the faecal microbiota obtained by Denaturing Gradient Gel Electrophoresis (DGGE) of PCR amplified bacterial 16S rRNA genes as well as of Reverse Transcriptase-PCR amplified bacterial 16S rRNA resulted in different phylogenetic profiles for each of the five animal groups as revealed by Principal Component Analysis (PCA) of band patterns.ConclusionEven though sucrose and cornstarch are both easily digestible and are not expected to reach the large intestine, the DGGE band patterns obtained indicated that these carbohydrates indeed affected the composition of bacteria in the large gut. Also the two fructans resulted in completely different molecular fingerprints of the faecal microbiota, indicating that even though they are chemically similar, different intestinal bacteria ferment them. Comparison of DNA-based and RNA-based profiles suggested that two species within the phylum Bacteroidetes were not abundant in numbers but had a particularly high ribosome content in the animals fed with inulin.

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Comparison of methods and animal models commonly used for investigation of fecal microbiota: Effects of time, host and gender

Cited by 42 publications

References 24 publications

High purity galacto-oligosaccharides enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome

High purity galacto-oligosaccharides enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome

Temporal Assessment of the Impact of Exposure to Cow Feces in Two Watersheds by Multiple Host-Specific PCR Assays

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