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      Microbial Dynamics in Mixed-Culture Biofilms of Salmonella Typhimurium and Escherichia coli O157:H7 and Bacteria Surviving Sanitation of Conveyor Belts of Meat Processing Plants

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      Microorganisms
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          Abstract

          Biofilm formation can lead to the persistence of Salmonella Typhimurium (ST) and E. coli O157:H7 (O157). This study investigated the impact of meat processing surface bacteria (MPB) on biofilm formation by O157 (non-biofilm former; NF) and ST (strong biofilm former; BF). MPB were recovered from the contacting surfaces (CS), non-contacting surfaces (NCS), and roller surfaces (RS) of a beef plant conveyor belt after sanitation. O157 and ST were co-inoculated with MPB (CO), or after a delay of 48 h (IS), into biofilm reactors containing stainless steel coupons and incubated at 15 °C for up to 144 h. Coupons were withdrawn at various intervals and analyzed by conventional plating and 16S rRNA gene amplicon sequencing. The total bacterial counts in biofilms reached approximately 6.5 log CFU/cm2, regardless of MPB type or development mode. The mean counts for O157 and ST under equivalent conditions mostly did not differ (p > 0.05), except for the IS set at 50 h, where no O157 was recovered. O157 and ST were 1.6 ± 2.1% and 4.7 ± 5.0% (CO) and 1.1 ± 2.2% and 2.0 ± 2.8% (IS) of the final population. Pseudomonas dominated the MPB inocula and biofilms, regardless of MPB type or development mode. Whether or not a pathogen is deemed BF or NF in monoculture, its successful integration into complex multi-species biofilms ultimately depends on the presence of certain other residents within the biofilm.

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          DADA2: High resolution sample inference from Illumina amplicon data

          We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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              The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

              SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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                Author and article information

                Contributors
                Journal
                MICRKN
                Microorganisms
                Microorganisms
                MDPI AG
                2076-2607
                February 2023
                February 07 2023
                : 11
                : 2
                : 421
                Article
                10.3390/microorganisms11020421
                9960345
                36838386
                fe5099f3-534e-4d4a-935b-7d7ba826d75d
                © 2023

                https://creativecommons.org/licenses/by/4.0/

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