[citation report] A microbial survey of the International Space Station (ISS)

Cited by 65 publications

(74 citation statements)

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“…The second most abundant Corynebacterium genus annotated OTU in Lang et al . (Lang et al ., ) was equivalent to ANCHOR OTU C. tuberculostearicum_1 at 100% similarity.…”

Section: Resultsmentioning

confidence: 93%

“…While challenging within unknown systems, the results are briefly interpreted in an attempt to establish whether they are biologically coherent and, if so, whether they can build upon the previous findings reported by Lang et al . (Lang et al ., ) and deepen our knowledge of this unique environment. A total of 1,132,141 amplicons were assembled from the ISS samples, 553,762 of which were unique.…”

Section: Resultsmentioning

confidence: 98%

“…Each of these genera included highly abundant OTUs, which could be annotated at species level when the data set was analyzed using ANCHOR, such as Finegoldia magna, Haemophilus parainfluenzae and Akkermansia muciniphila ; although some ANCHOR OTUs were highly ambiguous, such as the most abundant OTU Staphylococcus MS_3, where the sequence was conserved at 100% identity to nine species [Table ; Supplementary file 5; Staphylococcus was also the most abundant genera in Lang et al . (Lang et al ., )]. The additional resolution of ANCHOR analysis also yielded original bacterial species, such as Lawsonella clevelandensis (second most abundant OTU at 4.3% of all amplicons), as well as archaeal species, such as Methanobrevibacter smithii , Methanosphaera stadtmaniae and Nitrosopumilus maritimus .…”

Section: Resultsmentioning

confidence: 99%

“…The additional resolution of ANCHOR analysis also yielded original bacterial species, such as Lawsonella clevelandensis (second most abundant OTU at 4.3% of all amplicons), as well as archaeal species, such as Methanobrevibacter smithii , Methanosphaera stadtmaniae and Nitrosopumilus maritimus . By again comparing results generated by ANCHOR to the analysis of this data by Lang (Lang et al ., ) using Qiime1, it is possible to decipher that the Corynebacterium (genus) reported as dominating the ISS samples was actually constructed from: L. clevelandensis and Corynebacterium tuberculostearicum , two highly abundant species representing 4.3% and 2.2% of the sequences, and annotated by ANCHOR without ambiguity. The two major Qiime1 Corynebacterium sequences (OTU:495067 and OTU:1012948) corresponded to 4.25% and 2.11% of reads, respectively, and were indeed most similar to L. clevelandensis and C. tuberculostearicum (but at only 98% instead of 100% BLASTn identity NCBI nr/nt due to sequence modification).…”

Section: Resultsmentioning

confidence: 99%

“…The increasing data set complexity is used to assess the challenges of real‐world systems and test the method's potential for biological discovery. The ISS data set [surface swabs were taken on May 9, 2014 (Lang et al ., )] was deliberately selected as technically nonideal and biologically complex: sampling had no replicated biological comparison design. A design was applied a posteriori , predicated on sampling location with unbalanced replication (destiny module = 10n while harmony module = 4n).…”

Section: Methodsmentioning

confidence: 99%

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ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

González

Pitre

Brereton

2019

Environmental Microbiology

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SummaryAnalysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.

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“…The second most abundant Corynebacterium genus annotated OTU in Lang et al . (Lang et al ., ) was equivalent to ANCHOR OTU C. tuberculostearicum_1 at 100% similarity.…”

Section: Resultsmentioning

confidence: 93%

Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations