Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

Rettedal, Elizabeth A.; Gumpert, Heidi; Sommer, Morten Otto Alexander

doi:10.1038/ncomms5714

Cited by 138 publications

(144 citation statements)

References 60 publications

Supporting

Mentioning

135

Contrasting

Order By: Relevance

“…Recently, there has been a renewed interest in culturing methods for the detection of species (Goodman et al 2011;Ma et al 2014;Rettedal et al 2014). Lagier et al introduced the concept of culturomics by combining the mass spectrometry approach with existing sequencing (Lagier et al 2012).…”

Section: Future Directions To Shift From Description Of Diversity Ontmentioning

confidence: 99%

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Chaudhary

Gaci

Borrel

et al. 2015

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

Until recently, human gut microbiota was believed to be colonized by few methanogenic archaeal species. Much higher microbial diversity within the human gut was revealed by the use of molecular approaches as compared to routine microbiological techniques, but still, a lot remains unknown. Molecular techniques has the advantage of being rapid, reproducible, and can be highly discriminative as compared to conventional culturing methods. Some of them provide both qualitative and quantitative information. However, the choice of method should be taken with care to avoid biases. The advent of next-generation sequencing gives much deeper information from which functional and ecological hypotheses can be drawn. In this review, molecular techniques that are currently used together with their possible future developments to study gut methanogenic communities are indicated along with their limitations and difficulties that are encountered during their implementation. Moreover, the high amount of metagenomics data from the human gut microbiome indicate that this environment could be a paradigm for new directions in methanogen diversity studies and help to develop new approaches for other environments as well. Concerning humans, this should help us to better understand the possible association of methanogens with some of the diseased conditions and their peculiar distribution among age groups in human.

show abstract

Section: Future Directions To Shift From Description Of Diversity Ontmentioning

confidence: 99%

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Chaudhary

Gaci

Borrel

et al. 2015

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

show abstract

“…For these and other reasons, it is often desirable to simplify and define the members of a community in order to combine them in customizable ways depending on the specific goals of a study. High-throughput anaerobic culturing is a method that creates arrayed libraries of individual species from a given donor 13,14,16,138 . Combining this technique with gnotobiotics opens the door to identifying specific commensals that cause or exacerbate disease phenotypes or are responsible for specific host or microbiota traits.…”

Section: Figurementioning

confidence: 99%

An insider's perspective: Bacteroides as a window into the microbiome

2017

View full text Add to dashboard Cite

Over the last decade, our appreciation for the contribution of resident gut microorganisms—the gut microbiota—to human health has surged. However, progress is limited by the sheer diversity and complexity of these microbial communities. Compounding the challenge, the majority of our commensal microorganisms are not close relatives of Escherichia coli or other model organisms and have eluded culturing and manipulation in the laboratory. In this Review, we discuss how over a century of study of the readily cultured, genetically tractable human gut Bacteroides has revealed important insights into the biochemistry, genomics and ecology that make a gut bacterium a gut bacterium. While genome and metagenome sequences are being produced at breakneck speed, the Bacteroides provide a significant ‘jump-start’ on uncovering the guiding principles that govern microbiota–host and inter-bacterial associations in the gut that will probably extend to many other members of this ecosystem.

show abstract

“…Venn diagram showed that OMG and MSP shared 24 OTUs, but more OTUs were uniquely in either MSP pool or OMG sample (Figure ). This is one more example representing that the microbial diversities was differentially reflected with culture‐dependent and ‐independent methods, which is generally acknowledged for that none of the current tools is able to disclose the whole picture of microbial diversity in environments (Lagier et al., ; Rettedal, Gumpert, & Sommer, ; Sommer, ).…”

Section: Resultsmentioning

confidence: 99%

“…Later on, Rettedal et al. () demonstrated that the recovery rate and representativeness of culture‐dependent approaches in gut microbiota could be further improved by careful design of culture conditions. It is believed that, by optimization of the culture conditions, MSP method would have better performance in microbiome recovery.…”

Section: Discussionmentioning

confidence: 99%

Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis

et al. 2018

View full text Add to dashboard Cite

The termite gut microbiome is a model system to investigate microbial interactions and their associations with host. For decades, extensive research with molecular tools and conventional cultivation method has been carried out to define the microbial diversity in termite gut. Yet, many bacterial groups of the termite gut microbiome have not been successfully cultivated in laboratory. In this study, we adapted the recently developed microfluidic streak plate (MSP) technique for cultivation of termite gut microbial communities at both aerobic and anaerobic conditions. We found that 99 operational taxonomic units (OTUs) were cultivable by MSP approach and 18 OTUs were documented first time for termite gut microbiota. Further analysis of the bacterial diversities derived by culture-dependent MSP approach and culture-independent 16S rRNA gene typing revealed that both methods have bias in recovery of gut microbiota. In total 396 strains were isolated with MSP technique, and potential new taxa at species and/or genus levels were obtained that were phylogenetically related to Burkholderia, Micrococcus, and Dysgonomonas. Results from this study indicate that MSP technique is applicable for cultivating previously unknown and new microbial groups of termite gut microbiota.

show abstract

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

Cited by 138 publications

References 60 publications

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

An insider's perspective: Bacteroides as a window into the microbiome

Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis

Contact Info

Product

Resources

About