Cause or effect? The spatial organization of pathogens and the gut microbiota in disease

Nguyen, Jen; Pepin, Deanna M.; Tropini, Carolina

doi:10.1016/j.micinf.2021.104815

Cited by 22 publications

(15 citation statements)

References 79 publications

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“…Unfortunately for the host, it’s the pathogens, which tend to have a wider arsenal of stress response pathways than commensal bacteria. Infectious agents can even reinforce the disrupted habitat, further hampering recovery of the microbiota and gut health (which we recently reviewed in the context of gut biogeography [ 11 ]). Diseased states can become stable and lead to chronic conditions where homeostasis is not retained by the host.…”

Section: Disease Reshapes the Gut Environmentmentioning

confidence: 99%

How the Physical Environment Shapes the Microbiota

Tropini

2021

mSystems

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Section: Disease Reshapes the Gut Environmentmentioning

confidence: 99%

How the Physical Environment Shapes the Microbiota

Tropini

2021

mSystems

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“…The calibration curve of the ZnO-PVA chemiresistor upon exposure to acetic acid at a frequency of 1000 Hz is represented in Figure 2d, showing a linear response, 𝑍 && = −2.303𝐶 && [𝑚𝑔/𝑚𝑙] + 178. 4, where 𝑍 && is the magnitude of impedance and 𝐶 && is the concentration of dissolved acetic acid in the electrolyte in mg/ml. The small error bars (standard deviation from the mean values) and high R 2 value (~0.97, 𝑝 − 𝑣𝑎𝑙𝑢𝑒 < 0.0001) demonstrate the reliability of the measurements.…”

Section: Impedance Spectroscopy Of Individual Scfasmentioning

confidence: 99%

“…Gut bacteria produce many bioactive metabolites which are absorbed by the gut lining and transported into the portal blood system [1,2]. Some of the most important bioactive compounds produced by the gut microbiota are short chain fatty acids (SCFAs), which are mainly produced through the bacterial fermentation of non-digestible carbohydrates in the diet (e.g., plant fiber) and exert significant effects on host metabolism and protection against invading pathogens [3,4]. The most abundant SCFAs in the gut are acetate, propionate, and butyrate, produced by a wide range of bacterial species [5].…”

Section: Introductionmentioning

confidence: 99%

An impedance-based chemiresistor for the real-time detection of gut microbiota-generated short-chain fatty acids

Yavarinasab

Flibotte²,

Liu

et al. 2022

Preprint

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Short chain fatty acids (SCFAs) are key molecules produced by gut bacteria in the intestine, that are absorbed into the bloodstream and strongly influence human health. SCFA disruption and imbalances have been linked to many diseases; however, they are seldom used diagnostically as their detection requires extensive sample preparation and expensive equipment. In this work, an electrochemical sensor was developed to enable real time, quantitative measurement of SCFAs from complex samples in liquid phase without the need for extraction, evaporation, or destruction. An impedance based sensor for in vitro detection of acetic acid, propionic acid, and butyric acid (accounting for more than 95% of SCFAs in the intestine) was fabricated by the deposition of a ZnO and polyvinyl alcohol (PVA) on the surface of a microfabricated interdigitated gold electrode. The sensor was first exposed to a broad, physiologically relevant range of concentrations of SCFAs in isolation (0.5 to 20 mg/ml) and unlike previously published SCFA sensors that could detect only in gas form with the aid of evaporation, it was able to detect them directly in the liquid phase at room temperature. Electrochemical impedance spectroscopy analysis was then applied to the mixture of SCFAs prepared at different ratios and in complex media at concentrations ranging from 0.5 to 10 mg/ml, which showed the capability of the sensor to measure SCFAs in experimentally relevant mixture. The recorded faradaic responses were then used to train a fit to data model to utilize the sensor to screen human bacterial isolates and detect which species secrete SCFAs in vitro. This work will allow for the rapid and non destructive determination of the levels of SCFAs in complex biological samples, providing a miniaturized, highly stable, and highly sensitive sensor for real time monitoring applications.

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“…The survival of specific taxa is driven by the function of genes and pathways that regulate metabolism and stress responses over short and chronic time scales. These genes and pathways play a key role in establishing the microbiota members that can grow in specific regions of the gut and host states (1)(2)(3). For example, the steep intraluminal oxygen gradient partitions strictly anaerobic bacteria such as Faecalibacterium away from the more oxygenated epithelium, while more aerotolerant bacteria such as Enterobacteriaceae can associate with the mucosa (12).…”

Section: Introductionmentioning

confidence: 99%

“…The animal digestive tract naturally consists of numerous distinct environments in which physical and chemical conditions such as oxygen concentration, acidity, mucosal stiffness, and temperature are tightly regulated by host-microbial interactions. Environmental gradients along the intestine create a continuum of habitats that the microbiota explores in its voyage along the intestinal tract (1)(2)(3). Alterations in pH and particle concentration (osmolality) commonly occur in gut disease or result from the ingestion of specific compounds.…”

Section: Introductionmentioning

confidence: 99%

Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota

Pannu

Liu

et al. 2022

Preprint

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Changes to gut environmental factors such as pH and osmolality due to disease or drugs correlate with major shifts in microbiome composition; however, we currently cannot predict which species can tolerate such changes or how the community will be affected. Here, we assessed the growth of 92 representative human gut bacterial strains spanning 28 families across multiple pH values and osmolalities in vitro. The ability to grow in extreme pH or osmolality conditions correlated with the availability of known stress response genes in many cases, but not all, indicating that novel pathways may participate in protecting against acid or osmotic stresses. Machine learning analysis uncovered genes or subsystems that are predictive of differential tolerance in either acid or osmotic stress. For osmotic stress, we corroborated the increased abundance of these genes in vivo during osmotic perturbation. The growth of specific taxa in limiting conditions in isolation in vitro correlated with survival in complex communities in vitro and in an in vivo mouse model of diet-induced intestinal acidification. Our data show that in vitro stress tolerance results are generalizable and that physical parameters may supersede interspecies interactions in determining the relative abundance of community members. Importantly, we provide an extensive resource for predicting shifts in microbial composition and gene abundance in complex perturbations. Furthermore, this work highlights the physical environment as a major driver of bacterial composition and the importance of performing physical measurements in animal and clinical studies to elucidate the drivers of shifts in microbiota abundance.

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Cause or effect? The spatial organization of pathogens and the gut microbiota in disease

Cited by 22 publications

References 79 publications

How the Physical Environment Shapes the Microbiota

How the Physical Environment Shapes the Microbiota

An impedance-based chemiresistor for the real-time detection of gut microbiota-generated short-chain fatty acids

Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota

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