Quantitative, longitudinal profiling of the primate fecal microbiota reveals idiosyncratic, dynamic communities

Microbial populations in the gastrointestinal tract contribute to host health and nutrition. Although gut microbial ecology is well studied in livestock and domestic animals, little is known of the endogenous populations inhabiting primates or carnivora. We characterized microbial populations in fecal cultures from gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong) to compare the microbiomes associated with different gastrointestinal morphologies and different omnivorous feeding strategies. Each species was fed a distinct standardized diet for 2 weeks prior to fecal collection. All diets were formulated to reflect the species' feeding strategies in situ. Fresh fecal samples were pooled within species and used to inoculate in vitro batch cultures. Acetate, propionate, butyrate and valerate were measured after 24 h of incubation. Eubacterial DNA was extracted from individual fecal samples, pooled, and the cpn60 gene region was amplified and then sequenced to identify the major eubacterial constituents associated with each host species. Short chain fatty acids (P < 0.001) and methane (P < 0.001) were significantly different across species. Eubacterial profiles were consistent with fermentation data and suggest an increase in diversity with dietary fiber.

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“…; Leser & Mølbak ) and consistent with other studies of primates (Wireman et al . ; Ley et al . ; Szekely et al .…”

Section: Resultsmentioning

confidence: 99%

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong)

McKenney

Ashwell

Lambert

et al. 2014

Integrative Zoology

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“…Furthermore, even though the Luminex assay MFI data are linear and the qPCR data are logarithmic, we observed positive correlations between these two types of quantitative data ( Table 3), indicating that changes in the amplitude of a Luminex assay result for a given organism over time may be indicative of trends in the abundance of that organism. An elegant mathematical model that is able to compute the number of copies of a given target DNA present in a mixed amplicon by a fluorescent bead-based approach has been described (38), and this method has been used to characterize the dynamics of individual gastrointestinal communities (45). Such a method might also be useful in the current context; however, as a technique based on the analysis of the PCR endpoint, the results of the analysis with the Luminex instrument can best be viewed as being semiquantitative and only when lower template copy numbers are used.…”

Section: Discussionmentioning

confidence: 99%

Multiplex Detection of Bacteria Associated with Normal Microbiota and with Bacterial Vaginosis in Vaginal Swabs by Use of Oligonucleotide-Coupled Fluorescent Microspheres

et al. 2009

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Bacterial vaginosis (BV) is a recurrent condition that is associated with a range of negative outcomes, including the acquisition of human immunodeficiency virus and other sexually transmitted diseases, preterm births, and pelvic inflammatory disease. In contrast to the Lactobacillus-dominated normal vaginal microbiota, BV is characterized by a lack of lactobacilli and an abundance of anaerobic and gram-negative organisms, including Gardnerella vaginalis and Atopobium vaginae. To date, the laboratory diagnosis of BV has relied upon the fulfillment of criteria determined by microscopic observation of Gram-stained vaginal swabs. We describe a molecular-based method for the easy determination of the species profile within the vaginal microbiota based on the amplification of the chaperonin-60 genes of all bacteria present in the swab and hybridization of the amplicon to species-specific oligonucleotide-coupled fluorescent beads that are identified by flow cytometry with a Luminex instrument. We designed a nineplex Luminex array for characterization of the vaginal microbiota and applied it to the analysis of vaginal swabs from individuals from Africa and North America. Using the presence of A. vaginae or G. vaginalis, or both, as the defining criterion for BV, we found that the method was highly specific and sensitive for the diagnosis of BV using microscopy as a gold standard.Bacterial vaginosis (BV), which is defined by a reduction in the vaginal Lactobacillus populations and an increase in the number of microbial species present, including Gardnerella spp., Atopobium spp., and others, is increasingly recognized as an important risk factor for adverse reproductive health outcomes, such as miscarriage and premature birth, and sexually transmitted diseases, including human immunodeficiency virus infection (25). Despite intense investigation, the etiology and clinical course of BV have not been well defined, probably because the normal variation of the vaginal microbial communities between individuals and their dynamics over time are complex and poorly understood. Consequently, the accurate diagnosis of BV, as well as the elaboration of effective prevention and treatment strategies, remains a major challenge (26, 44).The current "gold standard" for the diagnosis of BV in the laboratory setting relies on microscopic profiling of microbial types in Gram-stained vaginal swab smears by using the criteria of Nugent et al. (29) or Ison and Hay (20). These scoring systems are based on the relative abundance of Lactobacillus morphotypes (large gram-positive rods) compared to the abundance of the bacterial morphotypes suggestive of BV (gramnegative or gram-variable coccobacilli and curved rods and gram-positive cocci). Although this method provides reliable information and is particularly well suited for use in resourcepoor settings, it requires well-trained, highly experienced individuals to interpret the results and is simplistic in its reflection of the variety of organisms present in the microbial communities present in he...

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“…The background signal was then subtracted using the no-DNA control and a standard curve computed with the internal standards. The concentration of each bead (and therefore the level of each species in a sample) was calculated from the standard curves using linear regression (28). The FlowJo program (Tree Star, Ashland, OR) was used for data analysis.…”

Section: Methodsmentioning

confidence: 99%

“…Bead-based flow cytometry has recently been used to measure the abundance of target organisms in complex bacterial communities (24,28). This cultivation-independent approach is capable of simultaneously measuring the levels of several organisms, both cultivated and uncultivated.…”

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confidence: 99%

Response of Subgingival Bacteria to Smoking Cessation

et al. 2010

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It has been demonstrated that smoking cessation alters the subgingival microbial profile; however, the response of individual bacteria within this ecosystem has not been well studied. The aim of this investigation, therefore, was to longitudinally examine the effect of smoking cessation on the prevalence and levels of selected subgingival bacteria using molecular approaches for bacterial identification and enumeration. Subgingival plaque was collected from 22 smokers at the baseline and 12 months following periodontal nonsurgical management and smoking cessation counseling. The prevalence and abundance of selected organisms were examined using nested PCR and multiplexed bead-based flow cytometry. Eleven subjects successfully quit smoking over 12 months (quitters), while 11 continued to smoke throughout (smokers). Smoking cessation led to a decrease in the prevalence of Porphyromonas endodontalis and Dialister pneumosintes at 12 months and in the levels of Parvimonas micra, Filifactor alocis, and Treponema denticola. Smoking cessation also led to an increase in the levels of Veillonella parvula. Following nonsurgical periodontal therapy and smoking cessation, the subgingival microbiome is recolonized by a greater number of health-associated species and there are a significantly lower prevalence and abundance of putative periodontal pathogens. The results indicate a critical role for smoking cessation counseling in periodontal therapy for smokers in order to effectively alter the subgingival microbiome.It is established that bacterial consortia within the subgingival microbiome play a critical role in the etiology of chronic periodontitis. Although tobacco smoking has been shown to preferentially enrich this microbiome for pathogenic species (26, 29), it is not known if smoking cessation is capable of reversing this pathogenic colonization, since current evidence is based only on cross-sectional comparisons of former and current smokers (10,25). A longitudinal examination of subgingival bacteria following smoking cessation would allow us to determine how the individual bacteria within this ecosystem respond to smoking cessation.We have previously shown, using a cultivation-independent, open-ended approach, that smoking cessation results in a shift in the subgingival microbial profile during recolonization following periodontal therapy (7). In order to identify the individual organisms that contributed to this compositional shift, it is necessary to use a targeted, sensitive, and quantitative approach to measure the levels of these species.Bead-based flow cytometry has recently been used to measure the abundance of target organisms in complex bacterial communities (24,28). This cultivation-independent approach is capable of simultaneously measuring the levels of several organisms, both cultivated and uncultivated. It also has a wide dynamic range; that is, it is capable of quantifying both the less numerous and the numerically dominant members of a microbial community.The goals of the present investigation were to ...

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Quantitative, longitudinal profiling of the primate fecal microbiota reveals idiosyncratic, dynamic communities

Cited by 9 publications

References 47 publications

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong)

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong)

Multiplex Detection of Bacteria Associated with Normal Microbiota and with Bacterial Vaginosis in Vaginal Swabs by Use of Oligonucleotide-Coupled Fluorescent Microspheres

Response of Subgingival Bacteria to Smoking Cessation

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