Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism

Vatanen, Tommi; Jabbar, Karolina S.; Ruohtula, Terhi; Honkanen, Jarno; Ávila-Pacheco, Julián; Siljander, Heli; Stražar, Martin; Oikarinen, Sami; Hyöty, Heikki; Ilonen, Jorma; Mitchell, Caroline; Yassour, Moran; Virtanen, Suvi Μ.; Clish, Clary B.; Plichta, Damian R.; Vlamakis, Hera; Knip, Mikael; Xavier, Ramnik J.

doi:10.1016/j.cell.2022.11.023

Cited by 73 publications

(36 citation statements)

References 87 publications

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“…To examine if priority effects play a role in pBI143 monoclonality, we aimed to determine how pBI143 is acquired. Given that one established route of microbial acquisition is the vertical transmission of microbes from mother to infant 87 , we used our ability to track pBI143 SNVs between environments to investigate if there is evidence for vertical transmission. We followed the inheritance of identical SNV patterns in pBI143 using 154 mother and infant gut metagenomes from four countries, Finland 57 , Italy 60 , Sweden 68 , and the USA 69 , where each study followed participants from birth to 3 to 12 months of age.…”

Section: Resultsmentioning

confidence: 99%

A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut

Fogarty

Schechter

Lolans

et al. 2023

Preprint

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Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo, can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.

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Section: Resultsmentioning

confidence: 99%

A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut

Fogarty

Schechter

Lolans

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…S2, S3). It is possible that requiring only 5% of marker alleles to be shared rather than a 99.999% ANI permits the detection of horizontal gene transfers between lineages residing in mothers and infants [ 39 , 40 ]. However, in FEAST, by using any SNV with an informative distribution across sources as determined by our signature scoring method, we are able to quantify the relative contribution of all the sampled environments and assign a proportion to these putative sources.…”

Section: Discussionmentioning

confidence: 99%

SNV-FEAST: microbial source tracking with single nucleotide variants

2023

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Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.

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“…The private marker allele tracking approach in Nayfach et al 2016 provides an improved estimate of true percentage of species that share some portion of their genome with putative sources compared to inStrain ( Figure S2, S3 ). It is possible that requiring only 5% of marker alleles to be shared rather than a 99.999% ANI permits detection of horizontal gene transfers between lineages residing in mothers and infants (D. W. Chen & Garud, 2022; Vatanen et al, 2022). However, in FEAST, by using any SNV with an informative distribution across sources as determined by our signature scoring method, we are able to quantify the relative contribution of all the sampled environments and assign a proportion to these putative sources.…”

Section: Discussionmentioning

confidence: 99%

SNV-FEAST: microbial source tracking with single nucleotide variants

Briscoe

Halperin

Garud

2022

Preprint

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Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. "Source tracking" approaches to date leverage species abundance information, however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. We show that signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.

show abstract

Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism

Cited by 73 publications

References 87 publications

A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut

A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut

SNV-FEAST: microbial source tracking with single nucleotide variants

SNV-FEAST: microbial source tracking with single nucleotide variants

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