Evaluation of an optimal preparation of human standardized fecal inocula for in vitro fermentation studies

Aguirre, Manuel A.; Eck, Anat; Koenen, M.; Savelkoul, Paul H. M.; Budding, Andries E.; Venema, Koen

doi:10.1016/j.mimet.2015.07.019

Cited by 59 publications

(41 citation statements)

References 49 publications

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“…Seven replicate plates were used per dilution, which were incubated at 28°C in dark for 7 days. Actinomycete colonies were counted, transferred onto oatmeal agar plates (ISP medium 3) supplemented with 0.1% yeast extract (OMYEA) (Küster, 1959) and stored in 20% glycerol (cryoprotectant) at -20°C (Wellington and Williams, 1978). All isolates were tentatively identified and grouped to the genus level on the basis of their standard morphological criteria and according to the absence or presence of aerial mycelium, distribution (aerial/substrate) and form of any spores present and stability or fragmentation of substrate mycelium (Cross, 1989).…”

Section: Methodsmentioning

confidence: 99%

Streptomyces globosus UAE1, a Potential Effective Biocontrol Agent for Black Scorch Disease in Date Palm Plantations

et al. 2017

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Many fungal diseases affect date palm causing considerable losses in date production worldwide. We found that the fungicide Cidely® Top inhibited the mycelial growth of the soil-borne pathogenic fungus Thielaviopsis punctulata, the causal agent of black scorch disease of date palm, both in vitro and in vivo. Because the use of biocontrol agents (BCAs) can minimize the impact of pathogen control on economic and environmental concerns related to chemical control, we aimed at testing local actinomycete strains isolated from the rhizosphere soil of healthy date palm cultivated in the United Arab Emirates (UAE) against T. punctulata. The selected isolate can thus be used as a potential agent for integrated disease management programs. In general, the BCA showed antagonism in vitro and in greenhouse experiments against this pathogen. The most promising actinomycete isolate screened showed the highest efficacy against the black scorch disease when applied before or at the same time of inoculation with T. punctulata, compared with BCA or fungicide application after inoculation. The nucleotide sequence and phylogenetic analyses using the 16S ribosomal RNA gene with other Streptomyces spp. in addition to morphological and cultural characteristics revealed that the isolated UAE strain belongs to Streptomyces globosus UAE1. The antagonistic activity of S. globosus against T. punctulata, was associated with the production by this strain of diffusible antifungal metabolites i.e., metabolites that can inhibit mycelial growth of the pathogen. This was evident in the responses of the vegetative growth of pure cultures of the pathogen when exposed to the culture filtrates of the BCA. Altogether, the pathogenicity tests, disease severity indices and mode of action tests confirmed that the BCA was not only capable of suppressing black scorch disease symptoms, but also could prevent the spread of the pathogen, as a potential practical method to improve disease management in the palm plantations. This is the first report of an actinomycete, naturally occurring in the UAE with the potential for use as a BCA in the management of the black scorch disease of date palms in the region.

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Section: Methodsmentioning

confidence: 99%

Streptomyces globosus UAE1, a Potential Effective Biocontrol Agent for Black Scorch Disease in Date Palm Plantations

et al. 2017

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“…Equal volumes of the seven fecal slurries were pooled together and aliquots were kept at −80 • C for repetitive cultivation experiments. Similar sample preparation (standardization by pooling) has also been used and approved by others for in vitro testing in the TIM-2 proximal colon model (Aguirre et al, 2015;Bussolo de Souza et al, 2019).…”

Section: Fecal Inoculummentioning

confidence: 99%

Use of Changestat for Growth Rate Studies of Gut Microbiota

Adamberg

Raba

Adamberg

2020

Front. Bioeng. Biotechnol.

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Human colon microbiota, composed of hundreds of different species, is closely associated with several health conditions. Controlled in vitro cultivation and up-todate analytical methods make possible the systematic evaluation of the underlying mechanisms of complex interactions between the members of microbial consortia. Information on reproducing fecal microbial consortia can be used for various clinical and biotechnological applications. In this study, chemostat and changestat cultures were used to elucidate the effects of the physiologically relevant range of dilution rates on the growth and metabolism of adult fecal microbiota. The dilution rate was kept either at D = 0.05 or D = 0.2 1/h in chemostat cultures, while gradually changing from 0.05 to 0.2 1/h in the A-stat and from 0.2 to 0.05 1/h in the De-stat. Apple pectin as a substrate was used in the chemostat experiments and apple pectin or birch xylan in the changestat experiments, in the presence of porcine mucin in all cases. The analyses were comprised of HPLC for organic acids, UPLC for amino acids, GC for gas composition, 16S-rDNA sequencing for microbial composition, and growth parameter calculations. It was shown that the abundance of most bacterial taxa was determined by the dilution rate on both substrates. Bacteroides ovatus, Bacteroides vulgatus, and Faecalibacterium were prevalent within the whole range of dilution rates. Akkermansia muciniphila and Ruminococcaceae UCG-013 were significantly enriched at D = 0.05 1/h, while Bacteroides caccae, Lachnospiraceae unclassified and Escherichia coli clearly preferred D = 0.2 1/h. In the chemostat cultures, the production of organic acids and gases from pectin was related to the dilution rate. The ratio of acetate, propionate and butyrate was 5:2:1 (D = 0.05 1/h) and 14:2:1 (D = 0.2 1/h). It was shown that the growth rate-related characteristics of the fecal microbiota were concise in both directions between D = 0.05 and 0.2 1/h. Reproducible adaptation of the fecal microbiota was shown in the continuous culture with a changing dilution rate: changestat. Consortia cultivation is a promising approach for research purposes and several biotechnological applications, including the production of multi-strain probiotics and fecal transplantation mixtures.

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“…In the past, several cryoprotective additives have been used (e.g. DMSO, glycerol) to store bacteria (34), and glycerol seems to be the most widely used cryoprotective agent for storing fecal bacteria (35,36). In an accompanying study, the use of glycerol and the resuscitation conditions for a human fecal…”

Section: Aspects Contributing To the In Vitro Ileal Fermentation Assaymentioning

confidence: 99%

Development of an In Vivo and In Vitro Ileal Fermentation Method in a Growing Pig Model

Montoya

Haas

Moughan

2018

The Journal of Nutrition

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Evaluation of an optimal preparation of human standardized fecal inocula for in vitro fermentation studies

Cited by 59 publications

References 49 publications

Streptomyces globosus UAE1, a Potential Effective Biocontrol Agent for Black Scorch Disease in Date Palm Plantations

Streptomyces globosus UAE1, a Potential Effective Biocontrol Agent for Black Scorch Disease in Date Palm Plantations

Use of Changestat for Growth Rate Studies of Gut Microbiota

Development of an In Vivo and In Vitro Ileal Fermentation Method in a Growing Pig Model

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