16S Gene Sequences Research Articles

S1 gene based phylogeny of Israel variant-2 infectious bronchitis virus isolated in Turkey in a five year period.

Infectious bronchitis (IB) is an important disease that causes severe economic loses in the poultry industry worldwide. Furthermore, the spread of new variants poses a challenge for diagnosis and control of the disease. This study investigated the situation of infectious bronchitis virus (IBV), specifically the Israel variant-2 (IS var-2) also known as GI-23 genotype, in Turkey. Between 2014 and 2019, 214 flocks vaccinated against H120 from Marmara, Western Black Sea, and Inner Anatolia were examined, with 127 (59.3%) flocks testing positive for IBV, of which 92 (72.4%) were positive for IS var-2. Of the latter samples, 60 were randomly selected and subjected to full S1 gene sequencing. The analysis indicated that the field strain in Turkey was located on the same branch as the GI-23 genotype, which is one of the most frequently observed wild-type cluster found in the Middle East. The DNA similarities between the GI-23 isolates from 2014 to 2019 were 99%. In conclusion, the IS var-2 genotype has been circulating in broiler flocks in Turkey. It is recommended that establishing the vaccine strategy it should be considered the current circulating strains for the prevention and control of the disease among poultry.

Impact of the Ileal Microbiota on Surgical Site Infections in Crohn's Disease: A Nationwide Prospective Cohort.

Surgery is performed in 50-70% of Crohn's disease [CD] patients, and its main risk is surgical site infection [SSI]. The microbiota has been extensively assessed in CD but not as a potential risk factor for septic morbidity. The objective of this study was to assess the impact of the gut microbiota on SSI in CD. We used the multicentric REMIND prospective cohort to identify all patients who experienced SSI after ileocolonic resection for CD, defined as any postoperative local septic complication within 90 days after surgery: wound abscess, intra-abdominal collection, anastomotic leakage or enterocutaneous fistula. The mucosa-associated microbiota of the ileal resection specimen was analysed by 16S gene sequencing in 149 patients. The variable selection and prediction were performed with random forests [R package VSURF] on clinical and microbiotal data. The criterion of performance that we considered was the area under the Receiver Operating Characteristic [ROC] curve [AUC]. SSI occurred in 24 patients [16.1%], including 15 patients [10.1%] with major morbidity. There were no significant differences between patients with or without SSI regarding alpha and beta diversity. The top selected variables for the prediction of SSI were all microbiota-related. The maximum AUC [0.796] was obtained with a model including 14 genera, but an AUC of 0.78 had already been obtained with a model including only six genera [Hungatella, Epulopiscium, Fusobacterium, Ruminococcaceae_ucg_009, Actinomyces and Ralstonia]. The gut microbiota has the potential to predict SSI after ileocolonic resection for CD. It might play a role in this frequent postoperative complication.

Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence.

ABSTRACTWaterlogging causes a significant reduction in soil oxygen levels, which in turn negatively affects soil nutrient use efficiency and crop yields. Rhizosphere microbes can help plants to better use nutrients and thus better adapt to this stress, while it is not clear how the plant-associated microbes respond to waterlogging stress. There are also few reports on whether this response is influenced by different sequencing methods and by different soils. In this study, using partial 16S rRNA sequencing targeting the V4 region and two full-length 16S rRNA sequencing approaches targeting the V1 to V9 regions, the effects of waterlogging on soybean rhizosphere bacterial structure in two types of soil were examined. Our results showed that, compared with the partial 16S sequencing, full-length sequencing, both LoopSeq and Pacific Bioscience (PacBio) 16S sequencing, had a higher resolution. On both types of soil, all the sequencing methods showed that waterlogging significantly affected the bacterial community structure of the soybean rhizosphere and increased the relative abundance of Geobacter. Furthermore, modular analysis of the cooccurrence network showed that waterlogging increased the relative abundance of some microorganisms related to nitrogen cycling when using V4 sequencing and increased the microorganisms related to phosphorus cycling when using LoopSeq and PacBio 16S sequencing methods. Core microorganism analysis further revealed that the enriched members of different species might play a central role in maintaining the stability of bacterial community structure and ecological functions. Together, our study explored the role of microorganisms enriched at the rhizosphere under waterlogging in assisting soybeans to resist stress. Furthermore, compared to partial and PacBio 16S sequencing, LoopSeq offers improved accuracy and reduced sequencing prices, respectively, and enables accurate species-level and strain identification from complex environmental microbiome samples.IMPORTANCE Soybeans are important oil-bearing crops, and waterlogging has caused substantial decreases in soybean production all over the world. The microbes associated with the host have shown the ability to promote plant growth, nutrient absorption, and abiotic resistance. High-throughput sequencing of partial 16S rRNA is the most commonly used method to analyze the microbial community. However, partial sequencing cannot provide correct classification information below the genus level, which greatly limits our research on microbial ecology. In this study, the effects of waterlogging on soybean rhizosphere microbial structure in two soil types were explored using partial 16S rRNA and full-length 16S gene sequencing by LoopSeq and Pacific Bioscience (PacBio). The results showed that full-length sequencing had higher classification resolution than partial sequencing. Three sequencing methods all indicated that rhizosphere bacterial community structure was significantly impacted by waterlogging, and the relative abundance of Geobacter was increased in the rhizosphere in both soil types after suffering waterlogging. Moreover, the core microorganisms obtained by different sequencing methods all contain species related to nitrogen cycling. Together, our study not only explored the role of microorganisms enriched at the rhizosphere level under waterlogging in assisting soybean to resist stress but also showed that LoopSeq sequencing is a less expensive and more convenient method for full-length sequencing by comparing different sequencing methods.

Genome Sequence and Assessment of Safety and Potential Probiotic Traits of Lactobacillus johnsonii CNCM I-4884.

The probiotic strain Lactobacillus johnsonii CNCM I-4884 exhibits anti-Giardia activity in vitro and in vivo in a murine model of giardiasis. The aim of this study was the identification and characterization of the probiotic potential of L. johnsonii CNCM I-4884, as well as its safety assessment. This strain was originally classified as Lactobacillus gasseri based on 16S gene sequence analysis. Whole genome sequencing led to a reclassification as L. johnsonii. A genome-wide search for biosynthetic pathways revealed a high degree of auxotrophy, balanced by large transport and catabolic systems. The strain also exhibits tolerance to low pH and bile salts and shows strong bile salt hydrolase (BSH) activity. Sequencing results revealed the absence of antimicrobial resistance genes and other virulence factors. Phenotypic tests confirm that the strain is susceptible to a panel of 8 antibiotics of both human and animal relevance. Altogether, the in silico and in vitro results confirm that L. johnsonii CNCM I-4884 is well adapted to the gastrointestinal environment and could be safely used in probiotic formulations.

A surveillance for avian coronavirus infectious bronchitis virus, infectious laryngotracheitis virus, avian metapneumovirus, and avian reovirus in poultry flocks with respiratory signs in Türkiye

In this study, avian coronavirus infectious bronchitis virus (IBV), infectious laryngotracheitis virus (ILTV), avian metapneumovirus (AMPV), and avian reovirus (ARV) were evaluated in broiler and layer flocks. For this purpose, tracheal swabs from 48 broiler and 45 layer flocks with respiratory signs were inoculated SPF embryonated chicken eggs for virus isolation. The viruses were identified by real-time PCR. Results showed that the most common virus in both broiler and layer farms was IBV with incidence rates of 58.33% and 46.67%, respectively. ILTV, AMPV, and ARV incidences in the samples were found to be 22.22%, 13.33%, and 4.44% in layer flocks while 2.08%, 8.33%, and 20.83% in broilers, respectively. The numbers of IBV+AMPV and IBV+ARV coinfections were 5 (11.11%) and 1 (2.22%) in layers, whereas, 1 (2.08%) and 5 (10.42%) broilers, respectively. In addition, 2 broiler flocks (4.17%) had triple infection with IBV, AMPV, and ARV. ILTV was detected always alone from the samples of layer and broiler flocks. Sequencing of S1 gene of selected IBV TR/L45 and TR/B42 isolates showed similarities with IS/1494/06 (HM131453) at the rates of 98.98% and 99.69%, respectively, while TR/L37, TR/L38, and TR/L39 isolates were identical to 4/91 (KF377577) vaccine strain at the rates of 99.01%, 99.01%, and 98.76%, respectively. Sequencing analysis of the ICP4 and TK genes of ILTV isolates revealed that they were all field strains with low virulence. The present data represent actual information on the genotypes of IBV and ILTV circulating in poultry flocks in Türkiye.

Antifungal activity of bacterial strains from maize silks against Fusarium verticillioides.

Fusarium verticillioides is pathogenic to maize and mycotoxin-producer, causing yield losses, feed and food contamination, and risks to human and animal health. Endophytic (ISD04 and IPR45) and epiphytic (CT02 and IM14) bacteria from maize silks were tested in vitro and greenhouse against F. verticillioides and for hydrolytic enzyme production (cellulase, pectinase, protease, lipase, and chitinase). The strains preliminarily identified as Achromobacter xylosoxidans (ISD04), Pseudomonas aeruginosa (IPR45), and Bacillus velezensis (CT02 and IM14) by 16S gene sequencing. All strains showed antifungal activity in vitro with inhibition values from 58.5 to 100%; they changed hyphae morphology and inhibited the conidial germination by up to 100% (IPR45). The four strains produced at least one enzyme with antifungal activity. The microbiolized seeds reduced the fungal development in stored grains and stalk rot severity in the greenhouse by 72.6% (ISD04). These results highlight the potential of these strains as biocontrol agents against F. verticillioides.

Reclassification of Gall Midges (Diptera: Cecidomyiidae: Cecidomyiini) from Amaranthaceae, with Description of Ten New Species Based on an Integrative Taxonomic Study.

Simple SummaryPlants of the family Amarantaceae are hosts to hundreds of gall-midge taxa (Diptera: Cecidomyiidae), one of which is the genus Halodiplosis, which has been known so far from 99 species, almost all of which are from Central Asia. Immature stages have never been described in this genus nor have molecular data been used in its classification. In preparation for the description of 10 new species from Israel, we conducted a thorough review of the taxonomic literature on Halodiplosis (almost all of which is in Russian) and found that this genus should be divided into several genera based on morphological and life-history attributes. As a result, we reinstated the genus Asiodiplosis for most of the species in this group, all of which develop in complex bud galls. This leaves only 14 species in Halodiplosis, which live in galls induced by other gall-midges or develop in plant tissues without causing distinct galls. Here we describe nine Asiodiplosis species and one Halodiplosis species from Israel based on morphological and molecular data, including the first description of larvae and pupae for these genera. This work demonstrates the value of combining morphological, molecular, and life-history data to resolve the systematics of taxonomically difficult groups.The genus Halodiplosis includes 99 species restricted to host-plants of the Amaranthaceae, virtually all of which are from Central Asia. The discovery of numerous undescribed species putatively belonging to this genus in Israel instigated an exhaustive review of the original descriptions of all known species in this genus. This study revealed that the generic concept of Halodiplosis and some of the genera synonymized under it should be redefined based on morphological and life-history attributes, such that Halodiplosis is limited to only 13 species developing in plant tissues without obvious gall formation or as inquilines in galls of other cecidomyiids. Revised status were proposed for Asiodiplosis, Onodiplosis, and Desertomyia, all species of which are gall inducers. A detailed morphological study of the Israeli species combined with data on their life history and an analysis of mitochondrial COI and 16S gene sequences revealed nine gall-inducing species belonging to Asiodiplosis and one inquilinous species belonging to Halodiplosis. All ten species (Asiodiplosis admirabilis n.sp., A. bimoda n.sp., A. delicatula n.sp., A. largifica n.sp., A. mohicana n.sp., A. mucronata n.sp., A. paradoxa n.sp., A. pillosaeconspicua n.sp., A. stellata n.sp., and Halodiplosis fugax n.sp.) are described here as new to science, including the first descriptions of larvae and pupae for these genera.

Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil

AbstractAmazonia encompasses extensive forests in areas that are periodically inundated by overflowing rivers. The inundation depth and duration vary according to the slope of the terrain and distance to major water bodies. This creates a flooding gradient from the lowest lying seasonally flooded forest up into the unflooded forest, which directly affects the biota. However, the effect of this gradient on soil organisms remains elusive. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity from soil and litter samples along the flooding gradient in central‐western Amazonia using 16S and 18S gene sequences, respectively. We characterize the below‐ground diversity and community composition based on amplicon sequence variants (ASVs). We examine relationships between the soil biota and the flooding gradient, soil properties, and above‐ground woody plant diversity. The flooding gradient does not explain below‐ground biodiversity, nor is below‐ground diversity explained by the above‐ground woody plant diversity. We uncover several taxonomic groups—such as Patescibacteria—not previously reported from Amazonian seasonally flooded forests. The flooding gradient and woody plant diversity partly explain the community composition of soil bacteria. Although the effects of the flooding gradient, soil properties, and above‐ground woody plant diversity are difficult to quantify, our results indicate that flood stress may influence below‐ground bacterial community composition.

Abstract 11575: The Effects of Tlr4 Deletion on Aortic Stiffness and Gut Microbiota Composition in High Fat Diet-Fed Mice

Introduction: We have previously shown that alterations to the gut microbiota are an important mediator of diet-induced cardiometabolic dysfunction. One potential mechanism by which these microbial alterations may affect cardiometabolic function is via lipopolysaccharide (LPS), a component of gram-negative bacteria that can enter circulation following dysbiosis-related intestinal permeability. Once in circulation, LPS binds to toll-like receptor 4 (TLR4) in various tissues and induces a robust inflammatory response. TLR4 null mice are partially protected from obesity-related metabolic dysfunction, but it’s unclear if this mutation offers protection from vascular dysfunction. Methods: 24 male mice lacking the TLR4 receptor (KO) and 24 C57BL/6 wild type male mice (WT) were fed either a control diet (CON) containing 4% fat or a high fat diet containing 60% fat (HFD) for 6 months, yielding the following four experimental group: WT+CON; WT+HFD; KO+CON; KO+HFD. After 6 months, mice underwent measurement arterial stiffness (via pulse wave velocity), and glucose tolerance (via ip glucose tolerance test). The gut microbiota was analyzed by 16S gene sequencing. Results: Mice fed a high fat diet increased body weight, although the magnitude of weight gain was attenuated in KO+HFD vs WT+HFD (p<0.05). Oral administration of FITC-dextran was used to determine intestinal permeability, HFD fed mice exhibited an increase intestinal permeability, compared to their respective control groups (p<0.05). Circulating LPS binding protein was increased in both HFD groups compared to WT. Aortic pulse wave velocity was increased in WT+HFD but not KO+HFD. Glucose tolerance was higher in WT+CON compared to the other three experimental groups. Microbiota shifts occurred between groups, and surprisingly, genotype was the main driver of these shifts, followed by diet (explaining 27% and 22% respectively). Conclusions: These data indicate that deletion of TLR4 in male mice partially protects from arterial stiffness. These data support the supposition that LPS signaling downstream of gut dysbiosis may be an important factor in diet-induced vascular dysfunction.

Effect of Lactobacillus dominance modified by Korean Red Ginseng on the improvement of Alzheimer's disease in mice

BackgroundGut microbiota influence the central nervous system through gut-brain-axis. They also affect the neurological disorders. Gut microbiota differs in patients with Alzheimer's disease (AD), as a potential factor that leads to progression of AD. Oral intake of Korean Red Ginseng (KRG) improves the cognitive functions. Therefore, it can be proposed that KRG affect the microbiota on the gut-brain-axis to the brain. MethodsTg2576 were used for the experimental model of AD. They were divided into four groups: wild type (n = 6), AD mice (n = 6), AD mice with 30 mg/kg/day (n = 6) or 100 mg/kg/day (n = 6) of KRG. Following two weeks, changes in gut microbiota were analyzed by Illumina HiSeq4000 platform 16S gene sequencing. Microglial activation were evaluated by quantitative Western blot analyses of Iba-1 protein. Claudin-5, occludin, laminin and CD13 assay were conducted for Blood-brain barrier (BBB) integrity. Amyloid beta (Aβ) accumulation demonstrated through Aβ 42/40 ratio was accessed by ELISA, and cognition were monitored by Novel object location test. ResultsKRG improved the cognitive behavior of mice (30 mg/kg/day p < 0.05; 100 mg/kg/day p < 0.01), and decreased Aβ 42/40 ratio (p < 0.01) indicating reduced Aβ accumulation. Increased Iba-1 (p < 0.001) for reduced microglial activation, and upregulation of Claudin-5 (p < 0.05) for decreased BBB permeability were shown. In particular, diversity of gut microbiota was altered (30 mg/kg/day q-value<0.05), showing increased population of Lactobacillus species. (30 mg/kg/day 411%; 100 mg/kg/day 1040%). ConclusionsKRG administration showed the Lactobacillus dominance in the gut microbiota. Improvement of AD pathology by KRG can be medicated through gut-brain axis in mice model of AD.

Changes in microbial community phylogeny and metabolic activity along the water column uncouple at near sediment aphotic layers in fjords

Fjords are semi-enclosed marine systems with unique physical conditions that influence microbial community composition and structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial community structure and metabolic potential in response to environmental conditions. Photosynthetic production in euphotic zones sustains deeper aphotic microbial activity via organic matter sinking, augmented by large terrestrial inputs. Previous studies do not consider both prokaryotic and eukaryotic communities when linking metabolic potential and activity, community composition, and environmental gradients. To address this gap we profiled microbial functional potential (Biolog Ecoplates), bacterial abundance, heterotrophic production (3H-Leucine incorporation), and prokaryotic/eukaryotic community composition (16S and 18S rRNA amplicon gene sequencing). Similar factors shaped metabolic potential, activity and community (prokaryotic and eukaryotic) composition across surface/near surface sites. However, increased metabolic diversity at near bottom (aphotic) sites reflected an organic matter influence from sediments. Photosynthetically produced particulate organic matter shaped the upper water column community composition and metabolic potential. In contrast, microbial activity at deeper aphotic waters were strongly influenced by other organic matter input than sinking marine snow (e.g. sediment resuspension of benthic organic matter, remineralisation of terrestrially derived organic matter, etc.), severing the link between community structure and metabolic potential. Taken together, different organic matter sources shape microbial activity, but not community composition, in New Zealand fjords.

Recent advances in environmental DNA‐based biodiversity assessment and conservation

Recent advances in environmental DNA‐based biodiversity assessment and conservation

Phylogeography and population differentiation in Hepatozoon canis (Apicomplexa: Hepatozoidae) reveal expansion and gene flow in world populations

BackgroundHepatozoon canis is a protozoan transmitted to dogs and other wild carnivores by the ingestion of ticks containing mature oocysts and is considered the principal cause of canine hepatozoonosis in the world. Here, we examined ribosomal RNA 18S gene sequence variation to determine the genetic differences and phylogeographic diversity of H. canis from various geographical areas around the world.MethodsWe used 550 publicly available sequences of H. canis from 46 countries to assess haplotype relationships, geographical structure, genetic diversity indices, and relationships among populations. We performed neutrality tests and pairwise comparisons of fixation index (FST) values between groups and pairwise comparisons of FST values between populations. To determine whether populations are structured, analyses of molecular variance (AMOVAs) and spatial analysis of molecular variance (SAMOVA) were performed.ResultsThe dataset of H. canis yielded 76 haplotypes. Differentiation among populations indicated that there is no phylogeographical structure (GST = 0.302 ± 0.0475). Moreover, when samples were grouped by continents a significant FST was obtained, meaning that populations were genetically differentiated. The AMOVA showed that 57.4% of the genetic variation was explained by differences within populations when all locations were treated as a single group and revealed that there is no population structure when populations are grouped into two, three, and four groups (FCT, p > 0.05), suggesting that dispersal between populations is high. SAMOVA revealed significant FCT values for groups K = 5. The Tajima’s D and Fu’s Fs show that populations have undergone recent expansion, and the mismatch distribution analysis showed population expansion (multimodal distribution).ConclusionsThe current molecular data confirmed that H. canis does not show phylogeographic or population structure. The haplotypes exhibit low genetic differentiation, suggesting a recent expansion due to gene flow among populations. These results provide pivotal information required for future detailed population genetic analysis or to establish control strategies of this parasite.Graphical abstract

Diversity analysis of antagonistic microbes against bacterial leaf and fungal sheath blight diseases of rice

BackgroundBiocontrol is an effective strategy in the integrated management of plant diseases, now more as a necessity than choice, in the present era of environmental and health awareness. Microbial diversity is a wonder by nature that inspires to explore and accordingly, the diversity analysis of the isolated microbes revealed their morphological and molecular differences. The DNA provides a common platform to store the microbial information in the form of databases in public domain that can be used by anyone from anywhere.ResultsExploration for native microbes in the present study resulted in isolation of different isolates of Trichoderma and Bacillus. The microbes were identified using morphological traits and molecular markers and the key conserved 18S and 16S gene sequences submitted with the appropriate repositories. Nucleotide analysis indicated a close phylogenetic relationship between BIK 2 and BIK 3 (Bacillus isolates) and within all the 5 Trichoderma isolates. The percent disease reduction of Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (Xoo) was more in plants treated with consortia of the Trichoderma (61.13%) and Bacillus (53.59%) isolates, respectively. Screening of plant growth promotion activities, percentage increase in root (41.00%) and shoot length (44.77%) were found to be maximum in Trichoderma consortia treated plants.ConclusionsThree Bacillus and one Trichoderma strains, viz., B. velezensis, B. subtilis and B. paralicheniformis and Trichoderma asperellum, were identified and found to be effective against R. solani and Xoo pathogens of rice. In vitro and in vivo studies indicated that TAIK1 and BIK3 were found to be the most potential isolates among others isolated. Ability to improve plant growth was more pronounced by consortia of microbes.

IDENTIFICATION AND ISOLATION OF DOMINANT BACTERIA IN TRADITIONAL ISFAHAN CHEESE AND DETERMINATION IF EFFECTIVE COMPOUNDS IN FLAVOR

Cheese production by native starter cultures instead of commercial ones is beneficial in respect of higher quality, nutrient content, immunogenicity and having beneficial microorganism. The objective of the presented study was molecular identifying of microorganism and exploring its active ingredients in native cheese. MRS and M17 media were used to culture bacteria in 15, 37 and 45°c for 24, 48 and 72 hours and then morphologic and biochemical tests were used to identifying the species. Predominant species were detected using 16S rRNA and gene sequencing. Active ingredients and fatty acid profile was studied by GC lactobacili, lactococci and enterococci were identified as the predominant bacteria. Acid palmitic had the highest concentration among the saturated fatty acid, with 42.47%, and acid meristic and acid lauric acid were next with the 13.22% and 3.9% concentration respectively, among the unsaturated fatty acids.

Species-Level Profiling of Ixodes pacificus Bacterial Microbiomes Reveals High Variability Across Short Spatial Scales at Different Taxonomic Resolutions.

Background and Aims: Outbreaks of severe and chronic tick-borne diseases (TBDs) are on the rise. This is through the transmission of infectious disease agents to humans during tick feeding. The transmission rate and extent of microbial exchange, however, vary based on the tick microbiome composition. While select microbes are determined to be members of the normal tick microbiome and others are clearly recognized mammalian and/or avian pathogens, the status of many other members of the tick microbiota with respect to human and alternate host pathogenesis remains unclear. Moreover, the species-level 16S microbiome of prominent TBD vectors, including Ixodes pacificus, have not been extensively studied. To elucidate the I. pacificus microbiome composition, we performed a pan-domain species-specific characterization of the bacterial microbiome on adult I. pacificus ticks collected from two regional parks within Western California. Our methods provide for characterizing nuances within cohort microbiomes and their relationships to geo-locale of origin, surrounding fauna, and prevalences of known and suspected pathogens in relation to current TBD epidemiological zones. Methods: Ninety-two adult I. pacificus bacterial microbiomes were characterized using a high-fidelity, pan-domain, species-specific, full-length 16S rRNA amplification method using circular consensus sequencing performed on the Pacific Biosciences Sequel platform. Data analyses were performed with the MCSMRT data analysis package and database. Results: The species-specific I. pacificus microbiome composition illustrates a complex assortment of microflora, including over 900 eubacterial species with high taxonomic diversity, which was revealed to vary by sex and geo-locale, though the use of full-length 16S gene sequencing. The TBD-associated pathogens, such as Borrelia burgdorferi, Anaplasma phagocytophilum, and Rickettsia monacensis, were identified along with a host of bacteria previously unassociated with ticks. Conclusion: Species-level taxonomic classification of the I. pacificus microbiome revealed that full-length bacterial 16S gene sequencing is required for the granularity to elucidate the microbial diversity within and among ticks based on geo-locale.

Description of larvae of Eleotris perniger (Teleostei: Eleotridae) in transition from saltwater to freshwater from Montserrat, West Indies

Larvae of the Smallscaled Spinycheek Sleeper (Eleotris perniger) in transition from saltwater to freshwater were identified using COI and 16S gene sequences and the morphology and color pattern were then described. Available freshwater habitat for this species on Montserrat is minimal and continued existence is threatened by potential water withdrawals.

The bacterial microbiota of Hunner lesion interstitial cystitis/bladder pain syndrome.

To undertake the first comprehensive evaluation of the urinary microbiota associated with Hunner lesion (HL) interstitial cystitis/bladder pain syndrome (IC/BPS). Despite no previous identification of a distinct IC/BPS microbial urotype, HL IC/BPS, an inflammatory subtype of IC/BPS, was hypothesized most likely to be associated with a specific bacterial species or microbial pattern. The bacterial microbiota of midstream urine specimens from HL IC/BPS and age- and gender-matched IC/BPS patients without HL (non-HL IC/BPS) were examined using the pan-bacterial domain clinical-level molecular diagnostic Pacific Biosciences full-length 16S gene sequencing protocol, informatics pipeline and database. We characterized the differential presence, abundances, and diversity of species, as well as gender-specific differences between and among HL and non-HL IC/BPS patients. A total of 59 patients with IC/BPS were enrolled (29 HL, 30 non-HL; 43 women, 16 men) from a single centre and the microbiota in midstream urine specimens was available for comparison. The species abundance differentiation between the HL and non-HL groups (12 species) was not significantly different after Bonferroni adjustments for multiple comparisons. Similarly, the nine differentiating species noted between female HL and non-HL patients were not significantly different after similar statistical correction. However, four species abundances (out of the 10 species differences identified prior to correction) remained significantly different between male HL and non-HL subjects: Negativicoccus succinivorans, Porphyromonas somerae, Mobiluncus curtisii and Corynebacterium renale. Shannon diversity metrics showed significantly higher diversity among HL male patients than HL female patients (P = 0.045), but no significant diversity differences between HL and non-HL patients overall. We were not able to identify a unique pathogenic urinary microbiota that differentiates all HL from all non-HL IC/BPS. It is likely that the male-specific differences resulted from colonization/contamination remote from the bladder. We were not able to show that bacteria play an important role in patients with HL IC/BPS.

Assessment of Evolutionary Relationships for Prioritization of Myxobacteria for Natural Product Discovery.

Discoveries of novel myxobacteria have started to unveil the potentially vast phylogenetic diversity within the family Myxococcaceae and have brought about an updated approach to myxobacterial classification. While traditional approaches focused on morphology, 16S gene sequences, and biochemistry, modern methods including comparative genomics have provided a more thorough assessment of myxobacterial taxonomy. Herein, we utilize long-read genome sequencing for two myxobacteria previously classified as Archangium primigenium and Chondrococcus macrosporus, as well as four environmental myxobacteria newly isolated for this study. Average nucleotide identity and digital DNA–DNA hybridization scores from comparative genomics suggest previously classified as A. primigenium to instead be a novel member of the genus Melittangium, C. macrosporus to be a potentially novel member of the genus Corallococcus with high similarity to Corallococcus exercitus, and the four isolated myxobacteria to include another novel Corallococcus species, a novel Pyxidicoccus species, a strain of Corallococcus exiguus, and a potentially novel Myxococcus species with high similarity to Myxococcus stipitatus. We assess the biosynthetic potential of each sequenced myxobacterium and suggest that genus-level conservation of biosynthetic pathways support our preliminary taxonomic assignment. Altogether, we suggest that long-read genome sequencing benefits the classification of myxobacteria and improves determination of biosynthetic potential for prioritization of natural product discovery.

Microbiome Preprocessing Machine Learning Pipeline.

Background16S sequencing results are often used for Machine Learning (ML) tasks. 16S gene sequences are represented as feature counts, which are associated with taxonomic representation. Raw feature counts may not be the optimal representation for ML.MethodsWe checked multiple preprocessing steps and tested the optimal combination for 16S sequencing-based classification tasks. We computed the contribution of each step to the accuracy as measured by the Area Under Curve (AUC) of the classification.ResultsWe show that the log of the feature counts is much more informative than the relative counts. We further show that merging features associated with the same taxonomy at a given level, through a dimension reduction step for each group of bacteria improves the AUC. Finally, we show that z-scoring has a very limited effect on the results.ConclusionsThe prepossessing of microbiome 16S data is crucial for optimal microbiome based Machine Learning. These preprocessing steps are integrated into the MIPMLP - Microbiome Preprocessing Machine Learning Pipeline, which is available as a stand-alone version at: https://github.com/louzounlab/microbiome/tree/master/Preprocess or as a service at http://mip-mlp.math.biu.ac.il/Home Both contain the code, and standard test sets.