Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ = 41.336, P < 0.001. The species similar in 16 rDNA were discriminative from the mass spectra, such as A. baumannii & A. junii, A. pittii & A. calcoaceticus, and A. nosocomialis & A. seifertii. Therefore, using MALDI-TOF MS to identify Acinetobacter strains isolated from clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. Graphical Abstract ᅟ.
Pickles are a kind of traditional Chinese fermented vegetable product. To detect microorganism differences, we investigated bacterial and fungal communities in pickled radishes with different qualities and from different regions (Chongqing, Sichuan) using an Illumina MiSeq sequencing method. The results showed that bacterial communities in good‐quality Chongqing pickled radishes (sample A1) contained Pediococcus (40.77%), Lactobacillus (38.46%), Marinospirillum (5.46%), Idiomarina (3.10%), Bacillus (2.17%), Halanaerobium (2.05%), and Halomonas (1.25%), and the fungal communities contained Kazachstania (86.9%), Pichia (6.99%), Candida (3.97%), and Millerozyma (1.23%). In the Sichuan pickled radish (sample A2), the bacterial communities included Bacillus (55.35%), Lactococcus (12.10%), Pediococcus (9.02%), Lactobacillus (3.93%), Streptococcus (2.01%), Pseudomonas (1.98%), Bifidobacterium (1.92%), Arcobacter (1.62%), and Geobacillus (1.05%); Kazachstania (98.64%) was the dominant fungal genus. A microbial community analysis established that Marinobacter and Marinilabilia were associated with texture‐softening of the pickled radishes. The discolored pickled radishes that contained the Suttonella genus was not fit to be eaten.
Practical applications
To meet the large demand of the market, industrialized pickle companies use large fermentation tank to ferment vegetables. During the fermentation process, the pickles will be deteriorated if the fermentation conditions are not managed well. It will cause food safety problems and great economic losses. The microbial communities of different qualities of pickled radishes were investigated to determine differences among communities using an Illumina MiSeq sequencing method. This study will help improve the quality of pickled radishes and reduce economic losses in pickle manufacturing.
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