# Food-borne bacteria undercover: MAG reconstruction can reveal the biases in cultured food bacterial isolates and help identifying new species and strains

Sybille Tabuteau, Stéphane Chaillou

► To cite this version:

Sybille Tabuteau, Stéphane Chaillou. Food-borne bacteria undercover: MAG reconstruction can reveal the biases in cultured food bacterial isolates and help identifying new species and strains. ISME18 - 18th International Symposium on Microbial Ecology, Aug 2022, Lausanne (CH), Switzerland. . hal-04283313

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Submitted on 13 Nov 2023

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# Food-Borne Bacteria Undercover

MAGs (metagenome-assembled genomes) can reveal biases in cultured food bacterial isolates and help identifying new species and strains.

Sibylle Tabuteau¹ and Stéphane Chaillou¹

## HYPOTHESIS

Food-borne bacteria are considered non-recalcitrant to isolation on culture medium. However, recent studies on food microbiota using 16S amplicon sequencing has revealed that this paradigm deserves to be re-evaluated scientifically. The most obvious bias concerns the search for subdominant species (or even strains), the most part of which pass under the detection filter of isolation practices (requirement for non-canonical growth conditions, or less competitive than dominant strains), although these taxa may represent an important functional role, or participate in certain processes in a transient manner (dynamic succession of populations).

## MODELS & DATASET

The dataset is composed of ~80 food meta-genomes of raw sausagesA and fermented vegetablesB. To verify the hypothesis, 3 Target species were studied as models:

1. *Latilactobacillus sakei* (60 genomes available, high diversity of strains)

2. *Brochothrix thermopshacta* (25 genomes available, low diversity of strains)

3. *Dellaglioa algida* (4 genomes available, hard to cultivate)

## RESULTS

### 1. Latilactobacillus sakei

Phylogenomic trees of core genomes for the three target species. Isolates are shown in colored background whereas MAGs are shown in lighter colored background. Colors indicate main phylogenetic clades. New clades can clearly be detected for each species (yellow for *L. sakei* and purple for *B. thermosphacta*). For *D. aligida* (tree N°2), average Nucleotide index revealed that some MAGs (i.e; MAGDSP in yellow background) are representing a new candidate *Dellaglioa* species.

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### 2. Dellaglioa algida

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### 3. Brochothrix thermosphacta

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## METHODS

### 1. Assembly and binning of MAGs from metagenomic data

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Taxonomic assignment and reclustering of MAGs

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Blastn, Platon & Scripts ad hoc.

Prokka, Roary, Scarap
fasttree & R scripts

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ISOLATES

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Accessory genome

## CONCLUSIONS

➤ With only few metagenomes and few target species, our results clearly demonstrate the existence of strong biases in the diversity of cultured food-borne bacterial isolates.

➤ The potential of identifying new strains, clades or even species in food metagenomes is very high.

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➤ ¹ MICALIS INSTITUTE, INRAe Jouy-en-Josas, AgroParisTech, Université Paris-Saclay. France
stephane.chaillou@inrae.fr

➤ References
A Poirier et al., Data Brief. 2020 Mar 20;30:105453. doi: 10.1016/j.dib.2020.105453.
B Leech et al., mSystems. 2020 Nov 10;5(6):e00522-20. doi: 10.1128/mSystems.00522-20.