ArticleISME communications2023
Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques.
Article in ISME communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 15 citations in OpenAlex.
- Article
- Human milk microbiome as a modulator of the early-life gut-brain axis: mechanisms and translational opportunities for neurodevelopment.Journal of translational medicine · 2026Review
- Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.Microbiology spectrum · 2026Article
- Article
- The human breast milk microbiome: a landscape review of its composition, origins, and impact on infant health.Archives of microbiology · 2026Review
- The triad of maternal gut-breast milk-infant gut microbial transmission in early life as a critical pathway for microbial inheritance.Gut microbes · 2025Article
- Microbiome Profiling of Pretreated Human Breast Milk Using Shotgun Metagenomic Sequencing.Journal of microbiology and biotechnology · 2025Article
- Microbiome in heritage: how maternal microbiome transmission impacts next generation health.Microbiome · 2025Review
- Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.bioRxiv : the preprint server for biology · 2025Article
- Examining the healthy human microbiome concept.Nature reviews. Microbiology · 2025Review
- Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.Scientific reports · 2025Article
- Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M.Frontiers in microbiology · 2025Article
- The influence of the maternal microbiome on offspring neurodevelopment: a critical review of associations, controversies, and challenges.Frontiers in neuroscience · 2025Review
- Comparing the effectiveness of different DNA extraction methods in MX-80 bentonite.Environmental microbiology reports · 2024Article
- The Influence of Maternal Lifestyle Factors on Human Breast Milk Microbial Composition: A Narrative Review.Biomedicines · 2024Review
- Article
- GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences.Microbial genomics · 2024Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human milk microbiome studies are currently hindered by low milk bacterial/human cell ratios and often rely on 16S rRNA gene sequencing, which limits downstream analyses. Here, we aimed to find a method to study milk bacteria and assess bacterial sharing between maternal and infant microbiota. We tested four DNA isolation methods, two bacterial enrichment methods and three sequencing methods on mock communities, milk samples and negative controls. Of the four DNA isolation kits, the DNeasy PowerSoil Pro (PS) and MagMAX Total Nucleic Acid Isolation (MX) kits provided consistent 16S rRNA gene sequencing results with low contamination. Neither enrichment method substantially decreased the human metagenomic sequencing read-depth. Long-read 16S-ITS-23S rRNA gene sequencing biased the mock community composition but provided consistent results for milk samples, with little contamination. In contrast to 16S rRNA gene sequencing, 16S-ITS-23S rRNA gene sequencing of milk, infant oral, infant faecal and maternal faecal DNA from 14 mother-infant pairs provided sufficient resolution to detect significantly more frequent sharing of bacteria between related pairs compared to unrelated pairs. In conclusion, PS or MX kit-DNA isolation followed by 16S rRNA gene sequencing reliably characterises human milk microbiota, and 16S-ITS-23S rRNA gene sequencing enables studies of bacterial transmission in low-biomass samples.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.