Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

McDonald, Julie A. K.; Schroeter, Kathleen; Fuentes, Susana; Heikamp-deJong, Ineke; Khursigara, Cezar M.; Vos, Willem M. de; Allen‐Vercoe, Emma

doi:10.1016/j.mimet.2013.08.008

Cited by 155 publications

(176 citation statements)

References 42 publications

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“…The De-stat culture has not been applied for studies of complex microbial consortia earlier, while chemostat gut models have been used by several groups. It has been shown that major shifts in variability of fecal microbiota take place within the first 3–4 residential times while slight fluctuations occur even after 30 residential times [13,20,30] because of complex nature of the microbiota. Hence, the De-stat presented in the current paper is a promising approach for analyzing of the growth rate in microbial consortia with potential impact on health.…”

Section: Discussionmentioning

confidence: 99%

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Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

Adamberg

2018

Microbial Ecology in Health and Disease

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Background: Nutrient and energy metabolism in human colon depends on bacterial growth rate that is determined by the colonic transit rate.Objective: A novel approach, De-stat culture was used to distinguish the fast and slow growing sub-populations from fecal microbiota.Design: The enrichment and metabolism of bacteria from pooled fecal cultures of children was studied at dilution rates D = 0.2–0.0 1/h in mucin-supplemented media containing either arabinogalactan or apple pectin.Results: The study revealed clear differentiation of the fecal microbiota at higher (above 0.1 1/h) and lower (below 0.1 1/h) dilution rates, along with metabolic changes. Similarity of the fast and slow growing bacteria was observed in two different fecal pools and on both substrates, suggesting the dilution rate as the main triggering parameter for selection of bacteria. At high dilution rates, the species Collinsella aerofaciens, Dorea longicatena, Escherichia coli, Lachnoclostridium torques, and different Bacteroides (B. caccae, B. fragilis, B. ovatus, B. thetaiotaomicron, B. vulgatus) were dominant in both media variants. At low dilution rates, Akkermansia muciniphila, Eisenbergiella tayi, Negativicoccus succinivorans, and a group of Ruminococcaceae became dominant in both media and in both fecal pools. This change in bacterial population accompanied by the increased production of propionic and butyric acids as well as higher consumption of alanine and branched chain amino acids at low dilution rates.Conclusions: The study suggests that specific growth rate has important effect on the dynamics of colon microbiota. Manipulation of the proportions of fast and slow growing gut bacteria through modulation of the transit rate could be a target in human nutrition studies. The De-stat study would enable to predict changes in microbiota composition associated with the decrease or increase of the colonic transit rate.

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Section: Discussionmentioning

confidence: 99%

“…In vitro models facilitate frequent sampling and increased reproducibility [13]. Despite clear associations between the colonic transit time and microbiota, the effect of specific growth rate on the composition and metabolism of microbiota is not studied thoroughly in vitro .…”

Section: Introductionmentioning

confidence: 99%

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

Adamberg

2018

Microbial Ecology in Health and Disease

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“…In vitro systems allow for even more control of microbial communities but come with the downside that the contributions of the host to ecosystem parameters can only be measured superficially (e.g., by the addition of host proteins, such as mucins; Allen-Vercoe 2013;McDonald et al 2013). Culturing microbes from the mammalian gut can be challenging because many are fastidious in their nutritional needs and require cooperation with other species for optimal growth (Allen-Vercoe 2013).…”

Section: Experimental Tests Of Microbiome Invasibilitymentioning

confidence: 99%

Invasions of Host-Associated Microbiome Networks

Murall

Abbate

Touzel

et al. 2017

Networks of Invasion: Empirical Evidence and Case Studies

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International audienceThe study of biological invasions of ecological systems has much to offer research on within–host (WH) systems, particularly for understanding infections and developing therapies using biological agents. Thanks to the ground-work established in other fields, such as community ecology and evolutionary biology, and to modern methods of measurement and quantification, the study of microbiomes has quickly become a field at the forefront of modern systems biology. Investigations of host-associated microbiomes (e.g. for studying human health) are often centred on measuring and explaining the structure, functions and stability of these communities. This momentum promises to rapidly advance our understanding of ecological networks and their stability, resilience and resistance to invasions. However, intrinsic properties of host-associated microbiomes that differ from those of free-living systems present challenges to the development of a WH invasion ecology framework. The elucidation of principles underlying the invasibility of WH networks will ultimately help in the development of medical applications and help shape our understanding of human health and disease

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“…The vessel was run in batch with pH control for 1 day prior to running under flow conditions (media fed at a rate of 400 mL/day) to give a retention time of 24 hours. Steady-state, as assessed through the amplification of 16S rRNA gene sequences using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE-PCR) with moving window analysis [32,33], was attained by 7 days following chemostat operation. At steady-state, samples were aseptically removed from the vessel into a Ruskin anaerobic chamber (The Baker Co., USA) with a gas composition of 80% N 2 , 10% CO 2 , and 10% H 2 and used within ~3 h for further experiments.…”

Section: Human Gut Ecosystemmentioning

confidence: 99%

Interaction between a Broad-spectrum Antibiotic and Silver Nanoparticles in a Human Gut Ecosystem

Das¹,

Saulnier²,

Carlucci³

et al. 2016

J Nanomed Nanotechnol

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The antimicrobial properties of engineered silver nanoparticles (AgNPs) have led to their wide use in diverse consumer products. Ampicillin too, acts as a broad-spectrum antibiotic and thus is prescribed for the treatment of many common infections, but with the problematic emergence of ampicillin-resistant bacteria. As a consequence, there has been some interest in the combination of these two distinct chemistries prompted by the clinical challenge of resistance. Prior to trials of combination therapy, however, it is important to understand the impact on human microbiomes. Here we investigated the effect of ampicillin and AgNPs, both individually and in a combined therapy on a human intestinal ecosystem known as a defined experimental community (DEC-60). The DEC-60 consortia was co-treated with a concentration of AgNPs (50 mg/L) known to have a minimal impact, and a broad range of the antibiotic up to the clinical dose (6 mg/L). The addition of AgNPs to sub-clinical doses of ampicillin (0.06 and 0.6 mg/L) had a significantly impact (p<0.001-0.05) on gas production (%CO 2 and %N 2 ) and changed the composition of fatty acid methyl ester signatures so that they were distinct from each individual antimicrobial, as well as un-treated control cultures. DNA sequencing, supported by multidimensional scaling analysis, confirmed the community shift and showed distinct phylogenetic distributions at different concentrations of ampicillin, depending on the presence of AgNPs. Together, these results suggest that the antibacterial efficacy of sub-clinical doses of ampicillin was increased by AgNPs, possibly due to the synergistic effect of damage to the bacterial cell walls. Not only does this analysis provide insight into AgNP toxicity, it offers some promise that combined antimicrobial therapies may have value in a clinical setting.

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Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

Cited by 155 publications

References 42 publications

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

Invasions of Host-Associated Microbiome Networks

Interaction between a Broad-spectrum Antibiotic and Silver Nanoparticles in a Human Gut Ecosystem

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