The gut microbiota and metabolic disease: current understanding and future perspectives

Arora, Tulika; Bäckhed, Fredrik

doi:10.1111/joim.12508

Cited by 232 publications

(175 citation statements)

References 107 publications

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“…The gastrointestinal microbiota has an important role in human health with impact on nutrition, immune functions, and physiology [1]. The metabolic activity of the gut microbiota is equally important as its diversity, the suggested indicator of gut health [2].…”

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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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: 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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“…To date, the most widely studied system is the gut microbiome due to its critical role in food metabolism [26][27][28], profound influence on the immune system [29,30] and suspected role in a wide variety of diseases including gut infections [31], inflammatory bowel and Crohn's diseases [32,33], obesity [34], diabetes [35], cardiovascular disease [36], rheumatoid arthritis [37], colorectal cancer [38] and even depression [39]. The human gut microbiome is a highly complex multispecies system thought to consist of at approximately 1800 genera and 15,000-36,000 species of microbes [40].…”

Section: Introductionmentioning

confidence: 99%

Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut Microbiome

Henson

Phalak

2017

Processes

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Abstract:The gut microbiome is a highly complex microbial community that strongly impacts human health and disease. The two dominant phyla in healthy humans are Bacteroidetes and Firmicutes, with minor phyla such as Proteobacteria having elevated abundances in various disease states. While the gut microbiome has been widely studied, relatively little is known about the role of interspecies interactions in promoting microbiome stability and function. We developed a biofilm metabolic model of a very simple gut microbiome community consisting of a representative bacteroidete (Bacteroides thetaiotaomicron), firmicute (Faecalibacterium prausnitzii) and proteobacterium (Escherichia coli) to investigate the putative role of metabolic byproduct cross feeding between species on community stability, robustness and flexibility. The model predicted coexistence of the three species only if four essential cross-feeding relationships were present. We found that cross feeding allowed coexistence to be robustly maintained for large variations in biofilm thickness and nutrient levels. However, the model predicted that community composition and short chain fatty acid levels could be strongly affected only over small ranges of byproduct uptake rates, indicating a possible lack of flexibility in our cross-feeding mechanism. Our model predictions provide new insights into the impact of byproduct cross feeding and yield experimentally testable hypotheses about gut microbiome community stability.

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“…Bacteria are now considered key players in multiple aspects of the biology of multicellular organisms (1)(2)(3). The richness and importance of these interactions were so far neglected because laboratory biology had succeeded in simplifying and standardizing the environment of the model organisms, providing in most cases a single microbe as a food source, and not necessarily even a naturally encountered one.…”

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confidence: 99%

Caenorhabditis elegans responses to bacteria from its natural habitats

Samuel

Rowedder

Braendle

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

341

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Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacteria in C. elegans habitats, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria being most abundant. From laboratory assays using isolated natural bacteria, C. elegans is able to forage on most bacteria (robust growth on ∼80% of >550 isolates), although ∼20% also impaired growth and arrested and/or stressed animals. Bacterial community composition can predict wild C. elegans population states in both rotting apples and reconstructed microbiomes: alpha-Proteobacteria-rich communities promote proliferation, whereas Bacteroidetes or pathogens correlate with nonproliferating dauers. Combinatorial mixtures of detrimental and beneficial bacteria indicate that bacterial influence is not simply nutritional. Together, these studies provide a foundation for interrogating how bacteria naturally influence C. elegans physiology.Caenorhabditis elegans | host-microbe interactions | ecology B iological organisms constantly live in contact with other organisms in a complex web of ecological interactions, which include prey-predator, host-parasite, competitive, or positive symbiotic relationships. Bacteria are now considered key players in multiple aspects of the biology of multicellular organisms (1-3). The richness and importance of these interactions were so far neglected because laboratory biology had succeeded in simplifying and standardizing the environment of the model organisms, providing in most cases a single microbe as a food source, and not necessarily even a naturally encountered one. The many aspects of organismal biology that were shaped by evolution in natural environments are thus undetectable in the artificial laboratory environment and can only be revealed in the presence of other interacting species. Examples include feeding behavior, metabolism of diverse natural food sources, interactions with natural pathogens that have shaped the organism's immune system, behavioral traits, and regulation of development and reproduction. At the genomic level, many individual genes may not be required in a standard laboratory environment but their role may be revealed by using more diverse and relevant environments (4, 5).The nematode Caenorhabditis elegans is a typical example of a model organism that has been disconnected from its natural ecology: although the species has been studied intensively in the laboratory for half a century, its habitat and natural ecology-what it naturally feeds on, its natural predators and pathogens,

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The gut microbiota and metabolic disease: current understanding and future perspectives

Abstract: Abstract. Arora T and B€ ackhed

Cited by 232 publications

References 107 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

Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut Microbiome

Caenorhabditis elegans responses to bacteria from its natural habitats

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