Dynamics and diversity of the ‘Atopobium cluster' in the human faecal microbiota, and phenotypic characterization of ‘Atopobium cluster' isolates

Thorasin, T.; Hoyles, Lesley; McCartney, Anne L.

doi:10.1099/mic.0.000016

Cited by 25 publications

(25 citation statements)

References 51 publications

(64 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Also the abundance of members of the Atopobium cluster of Actinobacteria (i.e., genera such as Collinsella and Atopobium ) was higher in South Asians. This group of bacteria are saccharolytic (i.e., they break down small sugars) [45] and have been seen to decrease in abundance in the microbiome of individuals with a diet rich in whole grains [46]. These genera have also been associated with higher levels of low-density lipoprotein in humans [47] and, along with other members of the Actinobacteria , have been associated with high hepatic levels of triglycerides and low hepatic levels of glycogen and glucose in mice [48].…”

Section: Discussionmentioning

confidence: 99%

Ethnic and diet-related differences in the healthy infant microbiome

et al. 2017

View full text Add to dashboard Cite

BackgroundThe infant gut is rapidly colonized by microorganisms soon after birth, and the composition of the microbiota is dynamic in the first year of life. Although a stable microbiome may not be established until 1 to 3 years after birth, the infant gut microbiota appears to be an important predictor of health outcomes in later life.MethodsWe obtained stool at one year of age from 173 white Caucasian and 182 South Asian infants from two Canadian birth cohorts to gain insight into how maternal and early infancy exposures influence the development of the gut microbiota. We investigated whether the infant gut microbiota differed by ethnicity (referring to groups of people who have certain racial, cultural, religious, or other traits in common) and by breastfeeding status, while accounting for variations in maternal and infant exposures (such as maternal antibiotic use, gestational diabetes, vegetarianism, infant milk diet, time of introduction of solid food, infant birth weight, and weight gain in the first year).ResultsWe demonstrate that ethnicity and infant feeding practices independently influence the infant gut microbiome at 1 year, and that ethnic differences can be mapped to alpha diversity as well as a higher abundance of lactic acid bacteria in South Asians and a higher abundance of genera within the order Clostridiales in white Caucasians.ConclusionsThe infant gut microbiome is influenced by ethnicity and breastfeeding in the first year of life. Ethnic differences in the gut microbiome may reflect maternal/infant dietary differences and whether these differences are associated with future cardiometabolic outcomes can only be determined after prospective follow-up.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-017-0421-5) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 99%

Ethnic and diet-related differences in the healthy infant microbiome

et al. 2017

View full text Add to dashboard Cite

show abstract

“…NATTS have already been reported (Tsuji et al, 2010; Sugiyama et al, 2014). 16S rRNA gene-based primers targeting Coriobacteriaceae species have also been developed (Harmsen et al, 2000; Thorasin et al, 2015; Cho et al, 2016). However, as the microbial typing of the human gut microbiota is not yet complete (Harmsen and de Goffau, 2016), the coverage of the current coriobacterial primers is uncertain.…”

Section: Discussionmentioning

confidence: 99%

“…Nearly all those isolated so far fall into the family Coriobacteriaceae (Clavel et al, 2014), which includes a series of newly described, nutritionally-fastidious species that are difficult to isolate from other intestinal microbes. Some qPCR methods for detecting and quantifying Coriobacteriaceae species in faecal samples have already been developed (Harmsen et al, 2000; Thorasin et al, 2015; Cho et al, 2016). However, as the amplification primers are based on 16S rRNA sequences, their coverage is currently uncertain in the highly diverse human gut ecosystem.…”

Section: Introductionmentioning

confidence: 99%

Development and Use of a Real-Time Quantitative PCR Method for Detecting and Quantifying Equol-Producing Bacteria in Human Faecal Samples and Slurry Cultures

et al. 2017

View full text Add to dashboard Cite

This work introduces a novel real-time quantitative PCR (qPCR) protocol for detecting and quantifying equol-producing bacteria. To this end, two sets of primers targeting the dihydrodaidzein reductase (ddr) and tetrahydrodaidzein reductase (tdr) genes, which are involved in the synthesis of equol, were designed. The primers showed high specificity and sensitivity when used to examine DNA from control bacteria, such as Slackia isoflavoniconvertens, Slackia equolifaciens, Asaccharobacter celatus, Adlercreutzia equolifaciens, and Enterorhabdus mucosicola. To demonstrate the validity and reliability of the protocol, it was used to detect and quantify equol-producing bacteria in human faecal samples and their derived slurry cultures. These samples were provided by 18 menopausal women under treatment of menopause symptoms with a soy isoflavone concentrate, among whom three were known to be equol-producers given the prior detection of the molecule in their urine. The tdr gene was detected in the faeces of all these equol-producing women at about 4–5 log10 copies per gram of faeces. In contrast, the ddr gene was only amplified in the faecal samples of two of these three women, suggesting the presence in the non-amplified sample of reductase genes unrelated to those known to be involved in equol formation and used for primer design in this study. When tdr and ddr were present in the same sample, similar copy numbers of the two genes were recorded. However, no significant increase in the copy number of equol-related genes along isoflavone treatment was observed. Surprisingly, positive amplification for both tdr and ddr genes was obtained in faecal samples and derived slurry cultures from two non-equol producing women, suggesting the genes could be non-functional or the daidzein metabolized to other compounds in samples from these two women. This novel qPCR tool provides a technique for monitoring gut microbes that produce equol in humans. Monitoring equol-producing bacteria in the human gut could provide a means of evaluating strategies aimed at increasing the endogenous formation of this bioactive compound.

show abstract

“…The immunoregulatory activities of short-chain fatty acids (SCFA) produced by gut bacteria via the fermentation of carbohydrates and proteins has been already studied and reviewed extensively (141, 142) and will be described only briefly in the next section. The gut microbiota can also metabolize dietary lipids, cholesterol, and host-derived cholesterol metabolites such as steroids and bile acids (143–145). Hence, gut bacteria have the potential to alter the bioavailability and bioactivities of these compounds and thereby alter corresponding signaling networks.…”

Section: Lipids and Their Impact On Immune Responsesmentioning

confidence: 99%

“…The gut microbiota can also metabolize dietary lipids, cholesterol, and host-derived cholesterol metabolites such as steroids and bile acids. [143][144][145] Hence, gut bacteria have the potential to alter the bioavailability and bioactivities of these compounds and thereby alter corresponding signaling networks. When investigating the effects of gut microbial metabolites, it is important to keep in mind that the primary function of the digestive system is efficient absorption of dietary components and that many absorptive processes, including those for lipids, take place in proximal parts of the small intestine, whereas the densest microbial communities are found in the colon.…”

Section: Lipids and Their Impact On Immune Responsesmentioning

confidence: 99%

Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes

Clavel

Gomes-Neto

Lagkouvardos

et al. 2017

Immunological Reviews

102

View full text Add to dashboard Cite

Summary The community of microorganisms in the mammalian gastrointestinal tract, referred to as the gut microbiota, influences host physiology and immunity. The last decade of microbiome research has provided significant advancements for the field and highlighted the importance of gut microbes to states of both health and disease. Novel molecular techniques have unraveled the tremendous diversity of intestinal symbionts that potentially influence the host, many proof-of-concept studies have demonstrated causative roles of gut microbial communities in various pathologies, and microbiome-based approaches are beginning to be implemented in the clinic for diagnostic purposes or for personalized treatments. However, several challenges for the field remain: purely descriptive reports outnumbering mechanistic studies and slow translation of experimental results obtained in animal models into the clinics. Moreover, there is a dearth of knowledge regarding how gut microbes, including novel species that have yet to be identified, impact host immune responses. The sheer complexity of the gut microbial ecosystem makes it difficult, in part, to fully understand the microbiota-host networks that regulate immunity. In the present manuscript, we review key findings on the interactions between gut microbiota members and the immune system. Because culturing microbes allows performing functional studies, we have emphasized the impact of specific taxa or communities thereof. We also highlight underlying molecular mechanisms and discuss opportunities to implement minimal microbiome-based strategies.

show abstract

Dynamics and diversity of the ‘Atopobium cluster' in the human faecal microbiota, and phenotypic characterization of ‘Atopobium cluster' isolates

Cited by 25 publications

References 51 publications

Ethnic and diet-related differences in the healthy infant microbiome

Ethnic and diet-related differences in the healthy infant microbiome

Development and Use of a Real-Time Quantitative PCR Method for Detecting and Quantifying Equol-Producing Bacteria in Human Faecal Samples and Slurry Cultures

Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes

Contact Info

Product

Resources

About