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Illumina sequencing platforms have been widely used for amplicon-based environmental microbiome research. Analyses of amplicon data of environmental samples, generated from Illumina MiSeq platform illustrate the reverse (R2) reads in the PE datasets to have low quality towards the 3’ end of the reads which affect the sequencing depth of samples and ultimately impact the sample size which may possibly lead to an altered outcome. This study evaluates the usefulness of single-end (SE) sequencing data in microbiome research when the Illumina MiSeq PE dataset shows significantly high number of low-quality reverse reads. In this study, the amplicon data (V1V3, V3V4, V4V5 and V6V8) from 128 environmental (soil) samples, downloaded from SRA, demonstrate the efficiency of single-end (SE) sequencing data analyses in microbiome research. The SE datasets were found to infer the core microbiome structure as comparable to the PE dataset. Conspicuously, the forward (R1) datasets inferred a higher number of taxa as compared to PE datasets for most of the amplicon regions, except V3V4. Thus, analyses of SE sequencing data, especially R1 reads, in environmental microbiome studies could ameliorate the problems arising on sample size of the study due to low quality reverse reads in the dataset. However, care must be taken while interpreting the microbiome structure as few taxa observed in the PE datasets were absent in the SE datasets. In conclusion, this study demonstrates the availability of choices in analyzing the amplicon data without having the need to remove samples with low quality reverse reads.

Endophytic bacteria represent microorganisms that live during the whole life cycle within the tissues of healthy plants without causing any obvious signs of disease. In this study, the ability of 128 endophyte bacterial isolates from some cultivated and wild grain plants (Poaceae family) in Van, Turkey, were investigated in terms of producing several extracellular hydrolytic enzymes. It was demonstrated that lipases, proteases, amylases, cellulases, pectinases, and xylanases were produced by the bacteria with relative frequencies of 74.2%, 65.6%, 55.4%, 32%, 21.8%, and 7.8%, respectively. In addition, molecular identification of a certain number of isolates selected according to their enzyme-producing capabilities was performed by 16S rRNA gene sequencing using a next-generation sequencing platform. As a result of the analysis, the isolates yielded certain strains belonging toPseudomonas, Micrococcus, Paenibacillus, Streptococcus, Curtobacterium, Chryseobacterium, andBacillusgenera. Also, the strain G117Y1T was evaluated as a member of potential novel species based on 16S rRNA sequencing results.

Applications of massively parallel sequencing (MPS) in forensic genetics have allowed to exploit the true variation in core forensic STR loci, discover previously unknown STR alleles, aid mixture interpretation and will increase the statistical weight of the evidences. The worldwide populations database is exceedingly important in order to perform statistical calculations. In this study, we firstly present the population data for 27 autosomal STR loci of 148 Kinh ethnic individual living in Vietnam by using a MPS based on Illumina MiSeq platform. By using the largest number of markers for now, we indicated an increase in number of detected alleles as well. The combined match probability and power of exclusion reached 4.02E-30 and 0.999999999955384, respectively. The used markers are also demonstrated valuable in ancestry tracking of different human origins.

Objective The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with antimicrobial resistance (AMR) phenotypes. This study used a multidrug-resistant A. baumannii (strain ATCC BAA1605) as a model to study the genomic features of this pathogen. Results One circular chromosome and one circular plasmid were discovered in the complete genome of A. baumannii ATCC BAA1605 using whole-genome sequencing. The chromosome is 4,039,171 bp long with a GC content of 39.24%. Many AMR genes, which confer resistance to major classes of antibiotics (beta-lactams, aminoglycosides, tetracycline, sulphonamides), were found on the chromosome. Two genomic islands were predicted on the chromosome, one of which (Genomic Island 1) contains a cluster of AMR genes and mobile elements, suggesting the possibility of horizontal gene transfer. A subtype I-F CRISPR-Cas system was also identified on the chromosome of A. baumannii ATCC BAA1605. This study provides valuable genome data that can be used as a reference for future studies on A. baumannii. The genome of A. baumannii ATCC BAA1605 has been deposited at GenBank under accession no. CP058625 and CP058626.

The full mitogenome of an ethanol-preserved museum specimen of Ceramaster japonicus was determined using the NGS Illumina MiSeq platform. The specimen was collected from Tosa Bay, Japan, facing the Pacific Ocean (33.0781 N 134.0601 E), at 700 m depth in 2011. The mitogenome shows a typical metazoan genomic structure, with all of the 37 genes included in its 16,370 base-long mitogenome. We conducted phylogenetic analyses using a data set including 18 publicly available asteroids rooted against five ophiuroids as outgroups. The result confirms the position of C. japonicus in the order Valvatida. The complete mitogenome of C. japonicus reported here is the first reported for the family Goniasteridae Forbes, 1841.

β-Thalassemia (β-thal) is a common monogenic disease with ethnic-specific mutations on the HBB gene throughout the world. The reported mutations either reduce the expression or completely inactivate the HBB gene. In Pakistan, the prevalence of β-thal is high due to consanguineous marriages. Accurate identification of mutations in carriers is imperative for prevention of β-thal in subsequent generations. To overcome the limitations of traditional testing methods for β-thal, a next-generation sequencing (NGS)-based diagnostic test was designed and validated by sequencing the entire HBB gene. The primer set covering the entire HBB gene was designed and validated in a Pashtun β-thalassemic family. The polymerase chain reaction (PCR) product was sequenced using an Illumina MiSeq platform. A homozygous pathogenic insertion of A>AC/AC (rs35699606) was detected in an affected member of the family, while unaffected members were heterozygous for it. In addition, all family members were homozygous for the synonymous variant, A>G/G (rs713040), except the father who was heterozygous for it. We sequenced the entire HBB gene using the NGS-based test, which is highly sensitive, robust and specific for the diagnosis and screening of β-thal in Pakistan, especially for families practicing consanguineous marriages.

The varicella-zoster virus (VZV) genome, as with all other human herpesviruses, comprises both unique and repeated regions. In addition, the genome includes six sequences of tandemly repeating short elements termed reiteration regions, designated R1 to R5. The R4 element is duplicated, with one copy each in the terminal repeat short (TRs) and the internal repeat short (IRs) regions. The reiteration regions (R) are an understudied feature of the VZV genome even though three of them (R1, R2 and R3) reside inside the coding regions of important viral genes. R1 is located in ORF11, a tegument protein and the homoolog to herpes simplex virus UL47. R2 is located in ORF 14, which encodes glycoprotein C. R3 is located in ORF22, a component of the viral tegument and the largest gene product encoded by the virus. It is the homolog to herpes simplex virus UL36. R4A is located in the IRs and is duplicated, usually in inverted orientation, as R4B in the TRs. R5 is located in a non-coding region between ORF60 and 61. We developed primers to amplify and Sanger sequence all six reiteration regions, including primers that independently amplify the two copies of R4. We sequenced the reiteration regions from more than 80 genomes for viruses selected from the Kaiser Permanente Herpes Zoster Study, each of which was sampled from patients with well-characterized cases of herpes zoster. Samples were selected to provide a broad representation of VZV clades. The remainder of these genomes were sequenced using the Illumina MiSeq platform.

Understanding the microbial community of cheese is important in the dairy industry, as the microbiota contributes to the safety, quality, and physicochemical and sensory properties of cheese. In this study, the microbial compositions of different cheeses (Cheddar, provolone, and Swiss cheese) and cheese locations (core, rind, and mixed) collected from the Arbuthnot Dairy Center at Oregon State University were analyzed using 16S rRNA gene amplicon sequencing with the Illumina MiSeq platform (Illumina, San Diego, CA). A total of 225 operational taxonomic units were identified from the 4,675,187 sequencing reads generated. Streptococcus was observed to be the most abundant organism in provolone (72 to 85%) and Swiss (60 to 67%), whereas Lactococcus spp. were found to dominate Cheddar cheese (27 to 76%). Species richness varied significantly by cheese. According to alpha diversity analysis, porter-soaked Cheddar cheese exhibited the highest microbial richness, whereas smoked provolone cheese showed the lowest. Rind regions of each cheese changed color through smoking and soaking for the beverage process. In addition, the microbial diversity of the rind region was higher than the core region because smoking and soaking processes directly contacted the rind region of each cheese. The microbial communities of the samples clustered by cheese, indicated that, within a given type of cheese, microbial compositions were very similar. Moreover, 34 operational taxonomic units were identified as biomarkers for different types of cheese through the linear discriminant analysis effect size method. Last, both carbohydrate and AA metabolites comprised more than 40% of the total functional annotated genes from 9 varieties of cheese samples. This study provides insight into the microbial composition of different types of cheese, as well as various locations within a cheese, which is applicable to its safety and sensory quality.

Arbuscular mycorrhiza fungi (AMF) form one of the most common symbiosis with the majority of land plants. AMF supply the plant with various mineral elements, primarily phosphorus, and improve the water supply. The search for the most effective AMF strains for symbiosis and the creation of microbial preparations on that basis is an important task for modern biology. Owing to the difficulties of cultivation without a host plant and their high genetic polymorphism, identifying AMF is very difficult. A high number of cryptic species often makes morphological identification unreliable. Recent years have seen a growth in the number of AMF biodiversity studies performed by modern NGS-based methods, Illumina MiSeq in particular. Currently, there are still many questions that remain for the identification of AМF. The most important are whether conservative or variable sequences should be used to select a marker for barcoding and whether universal primers or those specific to AMF should be used. In our work, we have successfully used universal primers ITS3 and ITS4 for the sequencing in Illumina MiSeq of the 5.8S rDNA - ITS2 region of the 35S rRNA genes, which contain both a conservative and variable regions. The molecular genetic approach for AMF identification was quite effective and allowed us to reliably identify eight of nine isolates to the species level: five isolates of Rhizophagus irregularis, and one isolate of R. invermaius, Paraglomus laccatum, and Claroideoglomus etunicatum, respectively. For all five R. irregularis isolates, high variability in the ITS region and the absence of ecotopic-related molecular characters in the ITS2 region were demonstrated. The NCBI data is still insufficient for accurate AMF identification of Acaulospora sp. isolates from the genus to the species level.Грибы арбускулярной микоризы (АМГ) образуют один из наиболее распространенных симбиозов с большинством наземных растений. АМГ снабжают растение различными минеральными элементами, в первую очередь, фосфором, а также улучшают водоснабжение. Поиск наиболее симбиотически эффективных штаммов АМГ и создание на их основе микробных препаратов – важная задача современной биологии. Идентификация AМГ очень сложна. Это связано, прежде всего, с высоким генетическим полиморфизмом AMГ, а также с трудностями их выращивания без растения-хозяина. Морфологическая идентификация AMГ часто ненадежна из-за большого числа криптических видов. В последние годы увеличивается число работ по изучению биологического разнообразия AMГ, проводимых современными методами на основе NGS (Next Generation Sequencing), в частности Illumina MiSeq. В настоящее время остается много вопросов по идентификации АМГ. К наиболее важным из них относятся: выбор маркера для генетического штрих-кодирования AMГ – консервативных или вариабельных последовательностей, а также выбор праймеров – специфичных для AMГ или универсальных. В настоящей работе мы успешно использовали универсальные праймеры ITS3 и ITS4 для секвенирования с Illumina MiSeq региона 5.8S рДНК – ITS2, содержащего как консервативные, так и вариабельные участки. Этот подход для идентификации AMГ оказался достаточно эффективным и позволил достоверно идентифицировать 8 из 9 изолятов до уровня вида: 5 – Rhizophagus irregularis, 1 – R. invermaius, 1 – Paraglomus laccatum, 1 – Claroideoglomus etunicatum. Для всех изолятов R. irregularis показаны высокая вариабельность в области ITS и отсутствие связи c экотопом клад, образуемых ITS на филогенетических деревьях. Для изолята Acaulospora sp., определенного до рода, дан- ные NCBI все еще недостаточны для точной идентификации AMГ рода Acaulospora до вида.

Rhizosphere bacteria are key determinants of plant health and productivity. In this study, we used PCR-based next-generation sequencing to reveal the diversity and community composition of bacteria in the cotton rhizosphere from samples collected in Xinjiang Province, China. We identified 125 bacterial classes within 49 phyla from these samples. Proteobacteria (33.07% of total sequences), Acidobacteria (19.88%), and Gemmatimonadetes (11.19%) dominated the bacterial community. Marked differences were evident in the α-diversity of rhizosphere bacteria during different cotton plant growth and development stages. The operational taxonomic unit (OTU) numbers were highest in seedling and bud stages and decreased at the flowering and fruit-boll-opening stages. Forty-three OTUs from the Proteobacteria were common to all four periods of cotton development. Proteobacteria were more abundant in the rhizospheres of cotton from southern Xinjiang than from northern Xinjiang, while the opposite trend was observed for Acidobacteria. Gemmatimonadetes frequency was broadly the same in both northern and southern Xinjiang. These results suggest that there is abundant diversity in the microbiota of cotton rhizosphere soil. Proteobacteria and Actinobacteria dominated this microbial niche and bacterial communities in the seedling, bud, flowering, and boll-opening stages appear to be more similar to one another than to communities at the other growth stages.

Ulleungdo and Dokdo are volcanic islands with an oceanic climate located off the eastern coast of South Korea. In the present study, we used barcoded Illumina MiSeq to analyze eukaryotic microalgal genera collected from Seonginbong, the highest peak on Ulleungdo, and from groundwater sites on Dongdo and Seodo Islands, which are part of Dokdo. Species richness was significantly greater in the Seonginbong samples than in the Dongdo and Seodo samples, with 834 operational taxonomic units (OTUs) identified from Seonginbong compared with 203 OTUs and 182 OTUs from Dongdo and Seodo, respectively. Taxonomic composition analysis was also used to identify the dominant microalgal phyla at each of the three sites, with Chlorophyta (green algae) the most abundant phyla on Seonginbong and Dongdo, and Bacillariophyta (diatoms) the most abundant on Seodo. These findings suggest that differences in the abundances of Chlorophyta and Bacillariophyta species in the Seonginbong, Dongdo, and Seodo samples are due to variations in species richness and freshwater resources at each sampling location. To the best of our knowledge, this is the first report to detail freshwater microalgal communities on Ulleungdo and Dokdo. As such, the number of species identified in the Seonginbong, Dongdo, and Seodo samples might be an indicator of the ecological differences among these sites and varying characteristics of their microbial communities. Information regarding the microalgal communities also provides a basis for understanding the ecological interactions between microalgae species and other eukaryotic microorganisms. Ulleungdo and Dokdo are volcanic islands with an oceanic climate located off the eastern coast of South Korea. In the present study, we used barcoded Illumina MiSeq to analyze eukaryotic microalgal genera collected from Seonginbong, the highest peak on Ulleungdo, and from groundwater sites on Dongdo and Seodo Islands, which are part of Dokdo. Species richness was significantly greater in the Seonginbong samples than in the Dongdo and Seodo samples, with 834 operational taxonomic units (OTUs) identified from Seonginbong compared with 203 OTUs and 182 OTUs from Dongdo and Seodo, respectively. Taxonomic composition analysis was also used to identify the dominant microalgal phyla at each of the three sites, with Chlorophyta (green algae) the most abundant phyla on Seonginbong and Dongdo, and Bacillariophyta (diatoms) the most abundant on Seodo. These findings suggest that differences in the abundances of Chlorophyta and Bacillariophyta species in the Seonginbong, Dongdo, and Seodo samples are due to variations in species richness and freshwater resources at each sampling location. To the best of our knowledge, this is the first report to detail freshwater microalgal communities on Ulleungdo and Dokdo. As such, the number of species identified in the Seonginbong, Dongdo, and Seodo samples might be an indicator of the ecological differences among these sites and varying characteristics of their microbial communities. Information regarding the microalgal communities also provides a basis for understanding the ecological interactions between microalgae species and other eukaryotic microorganisms.

Background We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation “short-read” and third-generation “long-read” sequencing methods. Results We focused on short-read assemblers, hybrid assemblers, and analysis of the genomic structure with particular emphasis on insertion sequences and the Francisella pathogenicity island. The A5-miseq pipeline performed best for MiSeq data, Mira for Ion Torrent data, and ABySS for HiSeq data from eight short-read assembly methods. Two approaches were applied to benchmark long-read and hybrid assembly strategies: long-read-first assembly followed by correction with short reads (Canu/Pilon, Flye/Pilon) and short-read-first assembly along with scaffolding based on long reads (Unicyler, SPAdes). Hybrid assembly can resolve large repetitive regions best with a “long-read first” approach. Conclusions Genomic structures of the Francisella pathogenicity islands frequently showed misassembly. Insertion sequences (IS) could be used to perform an evolutionary conservation analysis. A phylogenetic structure of insertion sequences and the evolution within the clades elucidated the clade structure of the highly conservative F. tularensis.

Five Staphylococcus saprophyticus strains were isolated from the fermented milk product nono in Nigeria and were sequenced using an Illumina MiSeq platform. The genome sizes ranged from 2.53 to 2.60 Mbp, while the GC contents ranged from 32.99 to 33.07 mol%. The genomes possessed 2,505 to 2,687 protein-coding sequences.

Paranemachilus genilepis (Zhu 1983) is a small and benthic loach species that mainly distributes in the Guangxi Province, China. To date, little was known about the genetic information of this species as no molecular sequence has been published. In this study, the complete mitochondrial genome of P. genilepis was reported using the Illumina MiSeq platform. The genome was 16,563 base pairs (bp) in length and its structure was identical to most genomes of bony fishes. Phylogenetic analyses supported two clades (I and II) among Nemacheilidae species and P. genilepis was sister to Oreonectes furcocaudalis.

The introduction of Next Generation Sequencing (NGS) into forensic casework requires a detailed appraisal of how the technology can assist with improving current CE based methods bearing in mind the investment required to implement this significantly different method into operational forensic laboratories. To this end an initial assessment was conducted which involved the typing of 53 samples using the Verogen ForenSeq™ DNA Signature Prep Kit in conjunction with the Illumina MiSeq FGx™ DNA Sequencer. Concordance was checked for Autosomal and Y-STRs present in both the Verogen kit and the Promega PowerPlex® Fusion 6C kit when typed by allele size alone. In addition all alleles typed were analysed for sequence structure with NGS versus size calling with CE in order to ascertain the likely benefit of analysing STRs by sequence as opposed to size alone.

Rotavirus A (RVA) causes acute diarrhoea in children and less frequently in adults. However, the knowledge about the genotype distribution of RVA strains circulating in adults is limited particularly in developing countries. This study aimed to characterise the RVA strains detected from adult patients with diarrhoea in Nepal. A total of 47 RVA positive stool samples from adult patients with diarrhoea in Kathmandu, Nepal during 2007–2008 were examined for the G and P genotypes by sequencing. Nearly half (49%) of the samples were genotyped as G9P[8] (n = 23), G1P[8], G2P[4] (n = 5 each), G12P[8] (n = 4), G12P[6] (n = 3), G1P[6] (n = 2), G3P[8] and G9P[6] (n = 1 each). Interestingly, two G11P[25] and one G9P[19] strains detected were further subjected to Illumina MiSeq next generation sequencing to determine their whole genome sequences. The genotype constellations of RVA/Human-wt/NPL/TK2615/2008/G11P[25] and RVA/Human-wt/NPL/TK2620/2008/G11P[25] were I12-R1-C1-M1-A1-N1-T1-E1-H1, whereas that of RVA/Human-wt/NPL/TK1797/2007/G9P[19] was I5-R1-C1-M1-A8-N1-T1-E1-H1. The 11 genes of TK2615 and TK2620 were virtually identical, and they were either porcine-like or unique except the VP2 and NSP1 genes which were of human RVA origin. The two G11P[25] strains were also very similar to KTM368, another G11P[25] isolated from a child in Nepal in 2004. On the other hand, no gene of TK1797 was likely to be of human RVA origin. The observation that porcine-like RVAs were detected from adult patients justifies further studies to explore the role of adults in the interspecies transmission of animal RVA to humans.

Accurate library quantification is very important during post-pooling captured target sequencing. There are a number of methods available to quantify libraries prior to sequencing, but no gold standard for the quantification of libraries exists. In this study, we compared common library quantification methods (Labchip, Qubit 3.0, qPCR with three primer sets) with ultra-low coverage sequencing (MiSeq with and without insert size correction). Cost, time and quantification accuracy were considered. We found that Qubit and MiSeq were better than qPCR and LabChip at predicting the final concentration. Also we revealed that MiSeq with insert size correction was the most accurate method for library quantification prior to target sequencing. This method allows for correction shifts in the ratio due to enrichment. Ultra-low coverage sequencing by Illumina MiSeq is the most accurate method for library quantification prior to pooling and post-pooling target enrichment.

Whole genome sequencing of bacterial isolates has become a daily task in many laboratories, generating incredible amounts of data. However, data acquisition is not an end in itself; the goal is to acquire high‐quality data useful for understanding genetic relationships. Having a method that could rapidly determine which of the many available run metrics are the most important indicators of overall run quality and having a way to monitor these during a given sequencing run would be extremely helpful to this effect. Therefore, we compared various run metrics across 486 MiSeq runs, from five different machines. By performing a statistical analysis using principal components analysis and a K‐means clustering algorithm of the metrics, we were able to validate metric comparisons among instruments, allowing for the development of a predictive algorithm, which permits one to observe whether a given MiSeq run has performed adequately. This algorithm is available in an Excel spreadsheet: that is, MiSeq Instrument & Run (In‐Run) Forecast. Our tool can help verify that the quantity/quality of the generated sequencing data consistently meets or exceeds recommended manufacturer expectations. Patterns of deviation from those expectations can be used to assess potential run problems and plan preventative maintenance, which can save valuable time and funding resources.

The changes in the bacterial community composition in a channel catfish nursery pond with a cage–pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage–pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

This article describes the whole genome sequencing data from 5 extrapulmonary tuberculosis clinical isolates. The whole genome sequencing was carried out on Illumina MiSeq platform to identify single nucleotide variations (SNVs) associated with drug resistance. A total of 214 SNVs in the coding and promoter regions were identified in the whole genome sequencing analysis. Among the identified SNVs, 18 SNVs were identified in genes known to be associated with first and second line drug resistance. The data is related to the research article “Whole genome sequencing of Mycobacterium tuberculosis isolates from extrapulmonary sites” (Sharma et al., 2017) [1].

Gordonia sp. strain X0973 is a Gram-positive, weakly acid-fast, aerobic actinomycete obtained from a human abscess with Gordonia araii NBRC 100433T as its closest phylogenetic neighbor. Here, we report using Illumina MiSeq and PacBio reads to assemble the complete and circular genome sequence of 3.75 Mbp with 3,601 predicted coding sequences.

The coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an Iraqi patient was sequenced for the first-time using Illumina MiSeq technology. There was a D614G mutation in the spike protein-coding sequence. This report is valuable for better understanding the spread of the virus in Iraq.

Bacillus subtilis subsp. subtilis MD 32 was isolated from kimchi. The strain was sequenced using an Illumina MiSeq platform, and the genome size was 4,238,856 bp with a GC content of 43.41 mol%. The genome encoded 4,396 proteins, with 45 tRNAs, 6 rRNAs, and 5 noncoding RNAs.

Introduction of new methods requires meticulous evaluation before they can be applied to forensic genetic case work. Here, a custom QIAseq Targeted DNA panel with 164 ancestry informative markers was assessed using the MiSeq sequencing platform. Concordance, sensitivity, and the capability for analysis of mixtures were tested. The assay gave reproducible and nearly concordant results with an input of 10 and 2 ng DNA. Lower DNA input led to an increase in both locus and allele drop-outs, and a higher variation in heterozygote balance. Locus or allele drop-outs in the samples with less than 2 ng DNA input were not necessarily associated with the overall performance of a locus. Thus, the QIAseq assay will be difficult to implement in a forensic genetic setting where the sample material is often scarce and of poor quality. With equal or near equal mixture ratios, the mixture DNA profiles were easily identified by an increased number of imbalanced heterozygotes. For more skewed mixture ratios, the mixture DNA profiles were identified by an increased noise level. Lastly, individuals from Great Britain and the Middle East were investigated. The Middle Eastern individuals showed a greater affinity with South European populations compared to North European populations.

The complete mitochondrial DNA sequence of the Japanese field vole Microtus montebelli was determined using Illumina MiSeq platform. The assembled genome was 16,307 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes. According to phylogenetic analysis of 13 protein-coding genes, M. montebelli and other Microtus species consist of paraphyletic clades and M. montebelli is most closely related to M. kikuchii, a species endemic to Taiwan.

Microbacterium sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42 Mb and one plasmid of 34.22 kb.

The diversity indices of eukaryotic microalgal groups in the Jeonglyeongchi, Waegok, and Wangdeungjae marshes of Mount Jiri, Korea, were measured using Illumina MiSeq and culture-based analyses. Waegok marsh had the highest species richness, with a Chao1 value of 828.00, and the highest levels of species diversity, with Shannon and Simpson index values of 6.36 and 0.94, respectively, while Wangdeungjae marsh had the lowest values at 2.97 and 0.75, respectively. The predominant species in all communities were Phagocata sibirica (Jeonglyeongchi, 68.64%), Aedes albopictus (Waegok, 34.77%), Chaetonotus cf. (Waegok, 24.43%), Eimeria sp. (Wangdeungjae, 26.17%), and Eumonhystera cf. (Wangdeungjae, 22.27%). Relative abundances of the microalgal groups Bacillariophyta (diatoms) and Chlorophyta (green algae) in each marsh were respectively: Jeonglyeongchi 1.38% and 0.49%, Waegok 7.0% and 0.3%, and Wangdeungjae 10.41% and 4.72%. Illumina MiSeq analyses revealed 34 types of diatoms and 13 types of green algae. Only one diatom (Nitzschia dissipata) and five green algae (Neochloris sp., Chlamydomonas sp., Chlorococcum sp., Chlorella vulgaris, Scenedesmus sp.) were identified by a culture-based analysis. Thus, Illumina MiSeq analysis can be considered an efficient tool for analyzing microbial communities. Overall, our results described the environmental factors associated with geographically isolated mountain marshes and their respective microbial and microalgal communities.

Here we report the whole genome sequence of Lactobacillus fermentum HFD1 strain, the producer of antibacterial peptides. The genome consists of one circular chromosome with 2101878 bp in length and GC-content of 51.8%, and includes linear DNA with 5386 bp in length with 100% identity to bacteriophage phiX174. The analysis of the genome has revealed 2049 genes encoding for proteins including 867 proteins without known function and 70 genes encoding for RNAs (10 rRNAs, 59 tRNAs and 1 tmRNA). Putative genes responsible for the biosynthesis of 4 antimicrobial peptides were identified. The NCBI Bioproject has been deposited at NCBI under the accession number PRJNA615901 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA615901/ ) and consist of full annotated genome and raw sequence data.

Paenibacillus species are important spoilage organisms in the dairy industry. The genomes of five Paenibacillus species which were isolated from dairy products in Canada were sequenced using the Illumina MiSeq platform. Draft genomes ranging from 5.1 to 7.1 Mb with GC contents of 49 to 53% were generated.

Kluyveromyces marxianus (K. marxianus) is an increasingly popular industrially relevant yeast. It is known to possess a highly efficient non-homologous end joining (NHEJ) pathway that promotes random integration of non-homologous DNA fragments into its genome. The nature of the integration events was traditionally analyzed by Southern blot hybridization. However, the precise DNA sequence at the insertion sites were not fully explored. We transformed a PCR product of the Saccharomyces cerevisiae URA3 gene (ScURA3) into an uracil auxotroph K. marxianus otherwise wildtype strain and picked 24 stable Ura+ transformants for sequencing analysis. We took advantage of rapid advances in DNA sequencing technologies and developed a method using a combination of Illumina MiSeq and Oxford Nanopore sequencing. This approach enables us to uncover the gross chromosomal rearrangements (GCRs) that are associated with the ScURA3 random integration. Moreover, it will shine a light on understanding DNA repair mechanisms in eukaryotes, which could potentially provide insights for cancer research.

Helicobacter pylori (H.pylori) infection is etiologically associated with severe diseases including gastric cancer, but its pathogenicity is deeply shaped by the exceptional genomic diversification and geographic variation of the species. The clinical relevance of strains colonizing Africa is still debated. This study aimed to explore genomic features and virulence potentials of H. pylori KE21, a typical African strain isolated from a native Kenyan patient diagnosed with a gastric cancer. A high-quality circular genome assembly of 1,648,327 bp (1590 genes) obtained as a hybrid of Illumina Miseq short reads and Oxford Nanopore MinION long reads, clustered within hpAfrica1 population. This genome revealed a virulome and a mobilome encoding more than hundred features potentiating a successful colonization, persistent infection, and enhanced disease pathogenesis. Furthermore, through an experimental infection of gastric epithelial cell lines, strain KE21 showed the ability to promote interleukin-8 production and to induce cellular alterations resulting from the injection of a functional CagA oncogene protein into the cells. This study shows that strain KE21 is potentially virulent and can trigger oncogenic pathways in gastric epithelial cells. Expended genomic and clinical explorations are required to evaluate the epidemiological importance of H. pylori infection and its putative complications in the study population.

Ligilactobacillus salivarius TUCO-L2 was isolated from llama milk in Bio-Bio, Chile, and sequenced with the Illumina MiSeq platform. TUCO-L2 genome sequencing revealed a genome size of 1,600,747 bp with 1,691 protein-coding genes and a GC content of 33%. This draft genome sequence will contribute to a better understanding of the microbiome of llama milk.

The genomes of three clinical isolates of Salmonella enterica subsp. houtenae were sequenced using an Illumina MiSeq instrument. These isolates came from the urine and cerebrospinal fluid of a dog treated for hind-limb paresis with immunosuppressive drugs. S. enterica subsp. houtenae has also been implicated in brain infections in humans.

Microsatellite markers have become a popular and useful tool for investigating evolutionary processes at shallow taxonomic scales such as within a species or between extremely closely related species. Rhododendron sect. Pentanthera is a closely related group of deciduous azaleas that demonstrate both naturally occurring and horticulturally derived hybridization. Two species, flame azalea and Cumberland azalea, represent a particularly recalcitrant evolutionary problem, which will benefit from the development of rapidly evolving molecular markers. Microsatellite markers were specifically developed for Rhododendron calendulaceum, the flame azalea, for use in studies of genetic structure and potential hybridization with its close relative Rhododendron cumberlandense, the Cumberland azalea. Forty-eight primer pairs designed from paired-end Illumina MiSeq data were screened for robust amplification. Sixteen of these pairs were PCR-amplified in the presence of fluorescently labeled primers and genotyped in 66 flame azalea individuals from three geographically dispersed populations. Fifteen primer pairs were both reliable and polymorphic and exhibit ample variability for use in downstream population-level investigations. Cross-amplification in all other members of Rhododendron sect. Pentanthera was highly successful, suggesting broad utility across the entire clade. The novel microsatellite markers presented here functioned well within the target species and amplified with high success in the remaining members of the clade. They represent a significant improvement to the genetic toolkit available for Rhododendron sect. Pentanthera, and particularly for the flame/Cumberland azalea evolutionary problem.

A potentially therapeutic Twort-like myophage, Esa1, with specificity toward Staphylococcus aureus was isolated from lake water. We report the complete genome sequence of ESa1, assembled using both MinION and Illumina MiSeq reads, consisting of 153,106 bp, with 30.3% GC content, 253 protein coding sequences, 4 tRNAs, and 10,437-bp direct terminal repeats.

Complete genome sequences of eight isolates of Salmonella enterica subsp. enterica from Canadian wild birds were determined by MinION and Illumina MiSeq sequencing. Assembled chromosomes had an average size of 4,833,662 bp. Salmonella enterica serovar Worthington obtained from partridge and quail carried 267-kb plasmids, which contained multiple antimicrobial resistance genes.

The knowledge surrounding the bovine vaginal microbiota and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal bacterial community and estradiol concentrations at the time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-d Co-Synch + controlled internal drug release estrus synchronization protocol. At AI, a double-guarded uterine culture swab was used to sample the anterior vaginal tract. Immediately after swabbing the vaginal tract, blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) vs. nonpregnant (n = 49) between 41 and 57 d post-AI. Additionally, heifers were classified into low (1.1 to 2.5 pg/mL; n = 21), medium (2.6 to 6.7 pg/mL; n = 30), and high (7.2 to 17.6 pg/mL; n = 27) concentration of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4 region from the 16S rRNA gene using the Illumina Miseq platform. Alpha diversity was compared via ANOVA and beta diversity was compared via PERMANOVA. There were no differences in the Shannon diversity index (alpha diversity; P = 0.336) or Bray–Curtis dissimilarity (beta diversity; P = 0.744) of pregnant vs. nonpregnant heifers. Overall, bacterial community composition in heifers with high, medium, or low concentrations of estradiol did not differ (P = 0.512). While no overall compositional differences were observed, species-level differences were present within pregnancy status and estradiol concentration groups. The implications of these species-level differences are unknown, but these differences could alter the vaginal environment thereby influencing fertility and vaginal health. Therefore, species-level changes could provide better insight rather than overall microbial composition in relation to an animal’s reproductive health.