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Late lactation represents the main window for sow-to-piglet transmission of persistent gut strains

Maelle PomiesiD, Gabryelle Agoutin, Lucas AueriD, Adrien CastineliD, Olivier BoucheziD, Caroline Achard, Hélène Quesnel, Géraldine PascaliD, Sylvie CombesiD

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Abstract

The gut microbiota plays a key role in piglet health, and maternal microbial transmission may represent a promising lever to shape early-life microbiota and prevent post-weaning digestive disorders. This study aimed to better characterize sow-to-piglet microbiota transmission and persistence using a long-read metabarcoding approach targeting the 16S-ITS-23S region. Fecal samples (n = 204) were collected from 17 families, a family being as sow and three of her piglets, at multiple stages: late gestation (G110), early (L6) and late lactation (L28) for sows; early lactation (L6), late lactation (L28), and 5 days post-weaning for piglets. To approximate strain-level resolution, a putative strain (PS) approach was developed by clustering ASVs (n = 6064) affiliated with the same species based on abundance covariance (r > 0.9), resulting in 4857 PS. Piglet microbiota progressively diversified during lactation and converged toward that of sow. In sows, 27 {+/-} 6% of PS were persistent from late gestation to late lactation. In piglets, only 4.2 {+/-} 2.5% of PS persisted from d6 to 5 days post-weaning. Persistent PS in piglets were mainly affiliated with Limosilactobacillus reuteri and Lactobacillus amylovorus followed with Holdemanella porci and H. biformis, Lentihominibacter hominis and Dorea formicigenerans. Shared PS were significantly higher within families than between unrelated pairs (p < 0.05). Maternal transmission peaked at the end of lactation (35 {+/-} 7% at L28). Persistent transmitted PS represented 2.7 {+/-} 1.6% (d6-post-weaning) and 15.4 {+/-} 5.6% (d28-post-weaning). Early-transmitted persistent PS were mainly affiliated with Limosilactobacillus reuteri, Lactobacillus amylovorus, and Paraeggerthella hominis, whereas late-transmitted persistent PS were associated with Prevotella spp., Sphaerochaeta globosa, and Bariatricus comes. These findings highlight the significance of maternal transmission in shaping the post-weaning microbiota and identify late lactation as a critical window for microbiota transfer.

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Claude Opus 5.5 · xhigh effort · 8 Nov 2026 · from the full text of version 1 (24 Sept 2026) · CC BY 4.0

Long-read 16S-ITS-23S tracking in 17 sow-piglet families shows maternal putative-strain sharing peaks in late lactation, which supplies most maternally derived strains persisting post-weaning.

Post-weaning dysbiosis and diarrhoea in piglets drive antibiotic use, and earlier source-tracking work in pigs estimated the sow's share of piglet microbiota without resolving which species or strains are passed on, while metagenomic strain tracking scales poorly. Full-length 16S-ITS-23S operon amplicons with covariance-defined putative strains offer a higher-throughput way to time and identify maternally transmitted, persistent strains.

Key results

  1. ShownSharing of putative strains (PS) between sows and piglets was family-specific and depended on stage. It was lowest in early lactation and highest at weaning age (L28), then fell after weaning, which the authors attribute to the end of direct contact with the sow.

    Piglets shared more PS with their own sow than with unrelated sows (p < 0.05) at every stage pair except L28 piglets vs G110 sows. Maternal transmission peaked at L28 (35 ± 7%, reported in the abstract). n = 17 sows, 51 piglets; linear mixed models with Benjamini-Hochberg correction. · Abstract; Statistical analysis; Transmission of sow-derived gut putative strains…; Sow-to-piglet transmission: a stage-dependent…

  2. ShownMost maternally shared PS persisting after weaning were acquired in late lactation. Few persisted from day 6 to 5 days post-weaning; only 2 Limosilactobacillus PS (including L. reuteri) did so in at least one piglet per family, with L. amylovorus and P. hominis missing in one or two litters.

    Transmitted and persistent PS: 5.5 ± 3.4% (mean 43 PS per piglet) for L6-L28; 15.4 ± 5.6% (122 PS) for L28-W5; 2.7 ± 1.6% (21 PS) for L6-W5. The late-established set included Prevotella spp., Sphaerochaeta globosa (4 PS) and Bariatricus comes (2 PS), mostly assigned below 95% identity. · PS transmitted to piglets and persistent from…; PS transmitted to piglets and persistent from…; PS transmitted to piglets and persistent from…

  3. ShownPS were more stable in sows than in piglets. In piglets, persistence was highest across weaning. The small core that persisted from day 6 to post-weaning was led by Limosilactobacillus reuteri and Lactobacillus amylovorus.

    Sows: 27.2 ± 5.9% of L28 PS had persisted since G110, and 15 PS were present in all 17 sows. Piglets: 11.2 ± 7.8% persisted across lactation, 25.1 ± 8.3% from L28 to W5, and 4.1 ± 2.5% across all three stages; 34 PS persisted in all piglets of the 17 families. · Persistence of putative strain in sow and…

  4. SuggestedTransmission and core persistence appeared decoupled from abundance. The most frequently transmitted PS were not the most abundant in L28 sows, and the link between abundance and persistence lost significance within the core persistent set.

    Transmission score vs sow L28 abundance: R = 0.15, p = 0.3 (top 50 PS). Persistence vs abundance: R = 0.74, p < 0.001 across all PS, but R = 0.33, p = 0.053 for the 34 core PS. A single L. reuteri PS reached every piglet in all families. · Persistence of putative strain in sow and…; Transmission of sow-derived gut putative strains…

  5. ShownClustering full-operon ASVs of the same species by abundance covariance into putative strains reduced dataset complexity only modestly, because most ASVs remained unmerged.

    6064 ASVs were grouped into 4857 PS at r ≥ 0.9. 4,064 PS were singletons, leaving 67% of ASVs (55% of sequences) ungrouped. 65.3% of PS (75.6% of sequence count) were assigned to species at > 90% identity. Reads averaged 4200 ± 171 bp. · Bioinformatics analysis of long-read 16S-ITS-23S…; Construction of putative strain from 16S-ITS-23S…; Results

Methods, data and reproducibility

Fecal DNA from sows (G110, L6, L28) and three female piglets per litter (L6, L28, 5 days post-weaning) was sequenced for the full 16S-ITS-23S operon with PacBio HiFi. FROGS ASVs of the same species were merged into putative strains by abundance correlation (r ≥ 0.9), and set-intersection persistence and transmission were compared with linear mixed models.

  • Fecal 16S-ITS-23S HiFi amplicons from 17 families (sow plus three female piglets); sows at G110, L6, L28, piglets at L6, L28 and 5 days post-weaning · pig (Landrace x Large White sows; Piétrain-sired piglets) · n = 204 samples (51 sow, 153 piglet); 11,550,265 reads · ENA PRJEB113713
  • Parent trial of Landrace x Large White sows fed control or live-yeast (Levucell SB) diets; 33 families fully sampled, 17 retained (5 Control, 12 yeast-supplemented) · pig · n = 48 sows and litters in 4 batches; 33 complete; 17 retained · doi:10.57745/3ZJXTI (Table S1 animal metadata)
  • Fecal samples extracted and sequenced in duplicate to assess repeatability (Supplemental Figure S1) · pig · n = Five
  • 16S-ITS-23S-DB FROGS reference database used for taxonomic affiliation (below 90% identity flagged as weak affiliation) · doi:10.57745/IRLQI1
Methods & tools
PacBio Sequel II HiFi sequencing, 16S-27F / 23S-2241R operon PCR with BOA (Barcoded Overhang Adapters) protocol, ZR-96 Soil Microbe DNA Kit (Zymo Research), FROGS v5.1, 16S-ITS-23S-DB (FROGS database), FastQC v0.12.1, MultiQC v1.27.1, seqkit v2.9.0, R v4.2.1 (hclust, cutree), vegan, pairwiseAdonis (PERMANOVA), Linear mixed models with Benjamini-Hochberg correction
Code
https://forge.inrae.fr/geraldine.pascal/sow-to-piglet-data-article
Data & accessions
https://doi.org/10.57745/3ZJXTIhttps://doi.org/10.57745/IRLQI1
Software & environment
FROGS v5.1 (parameters in Table 1); R v4.2.1 with vegan and pairwiseAdonis; FastQC v0.12.1, MultiQC v1.27.1, seqkit v2.9.0
Reproducibility gaps
Versions of vegan and pairwiseAdonis and the R package used for the mixed models are not stated; no container or environment file is described.
Limitations (6)
  • Putative-strain clustering merged few ASVs. Over two-thirds stayed unmerged, either because they were too rare to estimate correlations reliably or because their operon copies had already collapsed during ASV inference, so most PS are single ASVs. · stated by the authors
  • Most of the late-established post-weaning taxa (Prevotella spp., Sphaerochaeta globosa, Bariatricus comes) were assigned below 95% sequence identity, so their species identities are uncertain. · stated by the authors
  • Persistence of core strains in suckling piglets may reflect repeated re-inoculation from the sow rather than stable colonization. · stated by the authors
  • These results conflict with Tancredi et al. (2025), who found the maternal contribution highest in early lactation. The authors note that inference method, cohort size, tracking resolution and husbandry (antibiotics, housing, hygiene) can all shift transmission estimates. · stated by the authors
  • Only 17 of 48 families were analyzed (5 Control, 12 live-yeast). Treatment was left out of the models even though unrelated sow-piglet pairs may span diets, and only female piglets were sampled. · noted in this summary
  • Sharing is inferred from co-detection after rarefaction to 10000 reads, with no environmental, milk or teat sampling, so direct sow-to-piglet transfer cannot be separated from a shared farrowing environment. The abstract and results also differ on piglet persistence (4.2 vs 4.1 ± 2.5%). · noted in this summary

Who should read:Read this if you study maternal microbiota transfer in livestock, want strain-like resolution from full-length rRNA operon amplicons, or design sow interventions against post-weaning gut disorders.

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