Different Bacteroides Species Colonise Human and Chicken Intestinal Tract

Kollarcikova, Miloslava; Faldynová, Marcela; Matiasovicova, Jitka; Jahodářová, Eva; Kubasová, Tereza; Seidlerová, Zuzana; Babák, Vladimír; Vídeňská, Petra; Čížek, Alois; Rychlı́k, Ivan

doi:10.3390/microorganisms8101483

Cited by 27 publications

(15 citation statements)

References 38 publications

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“…Since no other amino acid-dependent acid tolerance mechanisms were present in all genomes, the high prevalence of the GAD-system denotes an essential function for Bacteroides, especially in human gut isolates. Indeed, most strains lacking the GAD-system were obtained from animals (i.e., mouse, chicken, cattle, and swine, among others), corroborating another study where the absence of gadB and gadC could help discriminating chicken Bacteroides strains from human gut isolates (Kollarcikova et al, 2020). This evidence suggests host-specific adaptation of Bacteroides under distinct ecological constrains (e.g., diet, host physiology, and natural microbial community), potentially resulting in a loss-offunction (Hottes et al, 2013) of the GAD-system in animal isolates.…”

Section: Discussionsupporting

confidence: 80%

GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance

et al. 2021

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The high neuroactive potential of metabolites produced by gut microbes has gained traction over the last few years, with metagenomic-based studies suggesting an important role of microbiota-derived γ-aminobutyric acid (GABA) in modulating mental health. Emerging evidence has revealed the presence of the glutamate decarboxylase (GAD)-encoding gene, a key enzyme to produce GABA, in the prominent human intestinal genus Bacteroides. Here, we investigated GABA production by Bacteroides in culture and metabolic assays combined with comparative genomics and phylogenetics. A total of 961 Bacteroides genomes were analyzed in silico and 17 metabolically and genetically diverse human intestinal isolates representing 11 species were screened in vitro. Using the model organism Bacteroides thetaiotaomicron DSM 2079, we determined GABA production kinetics, its impact on milieu pH, and we assessed its role in mitigating acid-induced cellular damage. We showed that the GAD-system consists of at least four highly conserved genes encoding a GAD, a glutaminase, a glutamate/GABA antiporter, and a potassium channel. We demonstrated a high prevalence of the GAD-system among Bacteroides with 90% of all Bacteroides genomes (96% in human gut isolates only) harboring all genes of the GAD-system and 16 intestinal Bacteroides strains producing GABA in vitro (ranging from 0.09 to 60.84 mM). We identified glutamate and glutamine as precursors of GABA production, showed that the production is regulated by pH, and that the GAD-system acts as a protective mechanism against acid stress in Bacteroides, mitigating cell death and preserving metabolic activity. Our data also indicate that the GAD-system might represent the only amino acid-dependent acid tolerance system in Bacteroides. Altogether, our results suggest an important contribution of Bacteroides in the regulation of the GABAergic system in the human gut.

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Section: Discussionsupporting

confidence: 80%

GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance

et al. 2021

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“…All these bacteria do not express any specific form of adaptation to an aerobic environment, which influences their ecology. Non-spore-forming gut anaerobes are less likely to be found across multiple individuals than those capable of spore formation [ 48 ], and in agreement, host-dependent adaption of different species within genus Bacteroides has been described [ 67 ]. Bacteria no longer capable of sporulation are usually less prevalent but more abundant compared to spore-formers, suggesting an increase in colonization capacity [ 68 ].…”

Section: Novel Types Of Probiotics From Gut Microbiotamentioning

confidence: 80%

“…These bacteria are efficiently transferred by fecal transplantation in humans [ 69 ], and if administered to newly hatched chicks, they efficiently colonize the caecum after a single dose administration [ 32 , 70 ]. Interestingly, despite host adaptation, chicks can be equally colonized by both chicken- and human-adapted species [ 32 ], although only the chicken-adapted species will remain present until adulthood [ 67 ]. Their inability to extend environmental survival is therefore compensated for by their efficient colonization at the first opportunity and the slightly higher oxygen resistance of their vegetative cells than vegetative cells of spore-forming Clostridiales [ 35 ].…”

Section: Novel Types Of Probiotics From Gut Microbiotamentioning

confidence: 99%

Ecological Adaptations of Gut Microbiota Members and Their Consequences for Use as a New Generation of Probiotics

Kubasová

Seidlerová

Rychlı́k

2021

IJMS

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In this review, we link ecological adaptations of different gut microbiota members with their potential for use as a new generation of probiotics. Gut microbiota members differ in their adaptations to survival in aerobic environments. Interestingly, there is an inverse relationship between aerobic survival and abundance or potential for prolonged colonization of the intestinal tract. Facultative anaerobes, aerotolerant Lactobacilli and endospore-forming Firmicutes exhibit high fluctuation, and if such bacteria are to be used as probiotics, they must be continuously administered to mimic their permanent supply from the environment. On the other hand, species not expressing any form of aerobic resistance, such as those from phylum Bacteroidetes, commonly represent host-adapted microbiota members characterized by vertical transmission from mothers to offspring, capable of long-term colonization following a single dose administration. To achieve maximal probiotic efficacy, the mode of their administration should thus reflect their natural ecology.

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“…Strain-specific primers ( Table 1 ) were designed as described previously [ 13 ]. Real-time PCR was performed in 3 µL volumes in 384-well microplates using QuantiTect SYBR Green PCR Master Mix (Qiagen, Hilden, Germany) and a Nanodrop pipetting station (Innovadyne, Santa Rosa, CA, USA) for dispensing PCR mixtures, as reported elsewhere [ 13 ].…”

Section: Methodsmentioning

confidence: 99%

Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production

et al. 2021

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In this study, we addressed the origin of chicken gut microbiota in commercial production by a comparison of eggshell and feed microbiota with caecal microbiota of 7-day-old chickens, using microbiota analysis by 16S rRNA sequencing. In addition, we tested at which timepoint during prenatal or neonatal development it is possible to successfully administer probiotics. We found that eggshell microbiota was a combination of environmental and adult hen gut microbiota but was completely different from caecal microbiota of 7-day-old chicks. Similarly, we observed that the composition of feed microbiota was different from caecal microbiota. Neither eggshell nor feed acted as an important source of gut microbiota for the chickens in commercial production. Following the experimental administration of potential probiotics, we found that chickens can be colonised only when already hatched and active. Spraying of eggs with gut anaerobes during egg incubation or hatching itself did not result in effective chicken colonisation. Such conclusions should be considered when selecting and administering probiotics to chickens in hatcheries. Eggshells, feed or drinking water do not act as major sources of gut microbiota. Newly hatched chickens must be colonised from additional sources, such as air dust with spores of Clostridiales. The natural colonisation starts only when chickens are already hatched, as spraying of eggs or even chickens at the very beginning of the hatching process did not result in efficient colonisation.

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Different Bacteroides Species Colonise Human and Chicken Intestinal Tract

Cited by 27 publications

References 38 publications

GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance

GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance

Ecological Adaptations of Gut Microbiota Members and Their Consequences for Use as a New Generation of Probiotics

Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production

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