Classifications Of Bacteria Pdf Free
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Classifications Of Bacteria Pdf Free
Abstract:Several lactic acid bacteria (LAB) isolates from the Lactobacillus genera have been applied in food preservation, partly due to their antimicrobial properties. Their application in the control of human pathogens holds promise provided appropriate strains are scientifically chosen and a suitable mode of delivery is utilized. Urinary tract infection (UTI) is a global problem, affecting mainly diabetic patients and women. Many uropathogens are developing resistance to commonly used antibiotics. There is a need for more research on the ability of LAB to inhibit uropathogens, with a view to apply them in clinical settings, while adhering to strict selection guidelines in the choice of candidate LAB. While several studies have indicated the ability of LAB to elicit inhibitory activities against uropathogens in vitro, more in vivo and clinical trials are essential to validate the efficacy of LAB in the treatment and prevention of UTI. The emerging applications of LAB such as in adjuvant therapy, oral vaccine development, and as purveyors of bioprotective agents, are relevant in infection prevention and amelioration. Therefore, this review explores the potential of LAB isolates and their bacteriocins to control uropathogens, with a view to limit clinical use of antibiotics.Keywords: bacteriocins; lactic acid bacteria; uropathogens
Although Kraken-GB does have higher sensitivity than Kraken, it sometimes makes surprising errors, which we discovered were caused by contaminant and adapter sequences in the contigs of some draft genomes. These contaminant sequences come from other bacteria, viruses or even human genomes, and they result in incorrectly labelled k-mers in the database. We attempted to remove these from Kraken-GB (Materials and methods), but some contaminants may still slip through any filters. Thus for now, the default version of Kraken uses only complete RefSeq genomes.
We used Kraken to classify reads from three saliva samples collected as part of the Human Microbiome Project. Because these samples were obtained from humans, we created a Kraken database containing bacterial, viral and human genomes to classify these reads. Combining the three samples together, we report the taxonomic distribution of the classified reads (Figure 4). An analysis of the classified reads from the combined samples reveals that a majority of those reads were classified into one of three genera: Streptococcus (30%), Haemophilus (17%) and Prevotella (13%). Streptococcus mitis, Haemophilus parainfluenzae and Prevotella melaninogenica, the most abundant species (by read count) of each of these three genera, are all known to be associated with human saliva. We also performed the classification on each sample separately (Additional file 1: Figures S1,S2,S3).
The HiSeq and MiSeq metagenomes were built using 20 sets of bacterial whole-genome shotgun reads. These reads were found either as part of the GAGE-B project  or in the NCBI Sequence Read Archive. Each metagenome contains sequences from ten genomes (Additional file 1: Table S1). For both the 10,000 and 10 million read samples of each of these metagenomes, 10% of their sequences were selected from each of the ten component genome data sets (i.e., each genome had equal sequence abundance). All sequences were trimmed to remove low quality bases and adapter sequences.
The simBA-5 metagenome was created by simulating reads from the set of complete bacterial and archaeal genomes in RefSeq. Replicons from those genomes were used if they were associated with a taxon that had an entry associated with the genus rank, resulting in a set of replicons from 607 genera. We then used the Mason read simulator  with its Illumina model to produce 10 million 100-bp reads from these genomes. First we created simulated genomes for each species, using a SNP rate of 0.1% and an indel rate of 0.1% (both default parameters), from which we generated t