State of the Art in the Culture of the Human Microbiota: New Interests and Strategies

Abstract

SUMMARY The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization–time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.

In vitro Study of Bifidobacterium lactis BL-99 With Fructooligosaccharide Synbiotics Effected on the Intestinal Microbiota

“…Specifically, 0.8 ± 0.02 g of the sample was placed in a HALO-F100 fecal processor (Suzhou Hailu Biotech, Jiangsu, China) to obtain a 10% fecal suspension. Subsequently, 0.5 mL of the clarified suspension was injected into the fermentation flasks containing YCFA medium ( 18 ). Samples were divided into the following 4 groups: blank control (no additional addition), BL-99 (5 × 10 9 cfu/mL), FOS (concentration of 4 g/L, purchased from Baolingbao Biology, Shandong, China), and BL-99_FOS (BL-99 concentration of 5 × 10 9 cfu/mL and FOS concentration of 4 g/L).…”

Biobanking of Oral-Derived Bioresources

“…현재의 기술로는 미생물 종류의 90% 이상을 연구실 환경에서 배양할 수 없어 배양 조건에 살아남는 미생물만 배 양할 수 있다 103) . 특히 혐기성 세균은 혐기성 환경을 생성할 수 있는 워크스테이션 장비 등을 이용해야 한다 104) . 오믹스 기술의 발전으로 단편적인 시간을 구성하는 마이크로바이옴 의 분석은 용이하나, 시간 및 공간에 따라 역동적으로 변하는 마이크로바이옴의 양상을 온전히 분석하는 것은 한계가 있다 105,106) .…”

Diplocloster agilis gen. nov., sp. nov. and Diplocloster modestus sp. nov., two novel anaerobic fermentative members of Lachnospiraceae isolated from human faeces

“…Recent progress in culture methods for isolation of fastidious, strictly anaerobic bacteria and advancements in the sequencing methods and mass spectrometric identification have significantly increased the number of cultured and phenotypically described bacterial taxa previously considered ‘unculturable’ [1, 2]. In human gut microbiota, especially among adults, the largest biodiversity was found in the phylum Firmicutes , represented mainly by the families Lachnospiraceae and Oscillospiraceae of class Clostridia [1, 3, 4].…”