Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome
Open accessAbstract
Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such as Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae, which are frequently implicated in nosocomial infection and preterm infant gut colonization. Of the 15 K. pneumoniae strains detected in the study, four were detected in both infant gut and room samples. Time series experiments showed that nearly all strains associated with infant gut colonization can be detected in the room after, and often before, detection in the gut. Thus, we conclude that a component of premature infant gut colonization is the cycle of microbial exchange between the room and the occupant.
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Some authors set a cut-off of less than or equal to two SNV differences, while others set an ANI value of greater than 98% for isolates to be considered to come from the same natural strain.
“Some authors set a cut-off of less than or equal to two SNV differences [58], while others set an ANI value of greater than 98% [59] for isolates to be considered to come from the same natural strain.”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [59]
The Results section (“Organisms found in the infant gut have room reservoirs”) reports that a prior study treated two near-complete genome bins as the same strain when they shared >98% ANI across 95% of the bin. But this paper’s own strain-transfer analysis (“Evidence of strain transfer among infants and rooms”) uses 99.999% ANI, and the reported >98% criterion concerns genome bins rather than isolates. The ≤2-SNV criterion is attributed to a different citation, not this source. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe lower fraction of microbes shared in non-westernized microbiomes is not due to technical artifacts and may be partly explained by higher microbiome richness, possibly due to increased acquisition from other environmental or family sources.
“suggesting the lower fraction of microbes shared in non-westernized microbiomes is not due to technical artifacts and may be in part explained by a much higher microbiome richness, possibly due to increased acquisition of microbiome members from other environmental or family sources.42,43”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [42]
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- Authors
- Brooks, B., Olm, M. R., Firek, B. A., Baker, R., Thomas, B. C., Morowitz, M. J., & Banfield, J. F.
- Affiliations
- University of California, Berkeley (US)
- University of Pittsburgh (US)
- Magee-Womens Hospital (US)
- Corresponding author
- Banfield, Jillian F.
- ORCID
- Venue
- Nature Communications
- Published
- 2017-11-27
- Volume
- 8
- Issue
- 1
- Pages
- 1814-1814
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC5703836
- OpenAlex
- W2769228004
- Cited by
- 226
- References
- 30
- Citations by year
- 2026: 12 · 2025: 19 · 2024: 30 · 2023: 32 · 2022: 31 · 2021: 41 · 2020: 20 · 2019: 32 · 2018: 9
- FWCI
- 6.81
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- Funders
- National Science Foundation (S10 OD018174)
- Foundation for the National Institutes of Health
- Alfred P. Sloan Foundation (APSF-2012-10-05)
- University of California Berkeley
- National Institutes of Health (1s10od018174-01, 5r01ai092531-13, 5R01AI092531)
- National Institute of Allergy and Infectious Diseases (R01-AI092531)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Health Sciences › Medicine › Pediatrics, Perinatology and Child Health › Infant Development and Preterm Care
- Keywords
- infant gut microbiota, preterm infants, hospital room environment, nosocomial infections, Klebsiella pneumoniae, Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, neonatal intensive care unit, strain-resolved metagenomics
- MeSH terms
- Gastrointestinal Microbiome, Cross Infection, Environmental Exposure, Feces, Female, Humans, Infant, Infant, Newborn, Infant, Premature, Intensive Care Units, Neonatal, Gastrointestinal Tract, Metagenomics
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