Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode

Hanachi, Mariem; Maghrebi, Olfa; Bichiou, Haifa; Trabelsi, Ferdaous; Bouyahia, Najla Maha; Zhioua, Fethi; Belghith, Mériam; Harigua‐Souiai, Emna; Baouendi, Meriem; Guizani-Tabbane, Lamia; Benkahla, Alia; Souiai, Oussema

doi:10.3389/fmicb.2022.780568

Cited by 4 publications

(3 citation statements)

References 60 publications

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“…Given the necessity for ATP production, it is unsurprising that historically, studies have primarily relied on the methanogenic gene methyl-coenzyme M reductase A (mcrA) or 16S rRNA for identification of gut-associated methanogens 7,[24][25][26] . McrA has been identified in all methanogens to date, as the protein performs a critical role in the final methane production step of methanogenesis 26,27 .…”

Section: Methanococcales Methanomicrobiales Methanosarcinales Methano...mentioning

confidence: 99%

Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea

Feehan

Ran

Dorman

et al. 2022

Preprint

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Background: Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focussing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea detection and methanogenic functions while assessing global and host distribution of our novel archaeal metagenome assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, and MAG taxonomic assignment and functional annotation. Results: We generated 1,130 non-redundant MAGs with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in monogastric archaea which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further our understanding of microbiome development and functions.

show abstract

Section: Methanococcales Methanomicrobiales Methanosarcinales Methano...mentioning

confidence: 99%

Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea

Feehan

Ran

Dorman

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Several studies have described human GM development in African, , Asian, and Western cohorts. − Neonates and infants (NIs) in sub-Saharan African (SSA) countries such as Nigeria are frequently exposed to mycotoxins that may potentially influence early life GM . Still, to our knowledge, no study has so far assessed the development of early life GM in a mycotoxin-exposed NIs’ population.…”

Section: Introductionmentioning

confidence: 99%

“…Several studies have described human GM development in African, 19 , 20 Asian, 21 and Western cohorts. 22 − 26 Neonates and infants (NIs) in sub-Saharan African (SSA) countries such as Nigeria are frequently exposed to mycotoxins 4 that may potentially influence early life GM.…”

Section: Introductionmentioning

confidence: 99%

Biomonitoring of Dietary Mycotoxin Exposure and Associated Impact on the Gut Microbiome in Nigerian Infants

Ayeni,

Seki,

Pjevac

et al. 2024

Environ. Sci. Technol.

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Mycotoxins are toxic chemicals that adversely affect human health. Here, we assessed the influence of mycotoxin exposure on the longitudinal development of early life intestinal microbiota of Nigerian neonates and infants (NIs). Human biomonitoring assays based on liquid chromatography tandem mass spectrometry were applied to quantify mycotoxins in breast milk (n = 68) consumed by the NIs, their stool (n = 82), and urine samples (n = 15), which were collected longitudinally from month 1−18 postdelivery. Microbial community composition was characterized by 16S rRNA gene amplicon sequencing of stool samples and was correlated to mycotoxin exposure patterns. Fumonisin B 1 (FB 1 ), FB 2 , and alternariol monomethyl ether (AME) were frequently quantified in stool samples between months 6 and 18. Aflatoxin M 1 (AFM 1 ), AME, and citrinin were quantified in breast milk samples at low concentrations. AFM 1 , FB 1 , and ochratoxin A were quantified in urine samples at relatively high concentrations. Klebsiella and Escherichia/Shigella were dominant in very early life stool samples (month 1), whereas Bifidobacterium was dominant between months 3 and 6. The total mycotoxin levels in stool were significantly associated with NIs' gut microbiome composition (PERMANOVA, p < 0.05). However, no significant correlation was observed between specific microbiota and the detection of certain mycotoxins. Albeit a small cohort, this study demonstrates that mycotoxins may influence early life gut microbiome composition.

show abstract

Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea

et al. 2023

View full text Add to dashboard Cite

Background Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1–156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination. Results We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.

show abstract

Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode

Cited by 4 publications

References 60 publications

Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea

Novel Complete Methanogenic Pathways in Longitudinal Genomic Study of Monogastric Age-Associated Archaea

Biomonitoring of Dietary Mycotoxin Exposure and Associated Impact on the Gut Microbiome in Nigerian Infants

Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea

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