16S rDNA Data Research Articles

Integrated microbiome and metabolomic analysis of Spodoptera litura under Metarhizium flavoviride qc1401 stress.

Metarhizium spp. have emerged as an alternative to chemical pesticides for protecting crops from insect pest. Here, we investigated midgut microbial community and metabolites of Spodoptera litura at three different timepoints after infection with Metarhizium flavoviride. The innate immune system of S. litura was activated with levels of polyphenol oxidase, carboxylesterase, multifunctional oxidase, and glutathione S-transferase activity significantly increasing. Exposure to the fungal pathogen also altered bacterial abundance and diversity in host's midgut, and these changes varied depending on the time elapsed since exposure. We identified more operational taxonomic units in the treated samples as compared to the control samples at all tested time points. A total of 372 metabolites were identified, and 88, 149, and 142 differentially accumulated metabolites (DAMs) were identified between the treatment and control groups at 3 timepoints after treatment, respectively. Based on the changes of DAMs in response to M. flavoviride infection at different timepoints and significantly enriched KEGG pathways, we speculated that "tyrosine metabolism," "galactose metabolism," "ATP-binding cassette transporters," "neuroactive ligand-receptor interaction," "purine metabolism," "arginine and proline metabolism," "beta-alanine metabolism," "lysosome," and "carbon metabolism" may participate in the metabolic-level defense response. An integrated pathway-level analysis of the 16S-rDNA and metabolomic data illustrated the connections and interdependencies between the metabolic responses of S. litura and the midgut microorganisms to M. flavoviride infection. This work emphasizes the value of integrated analyses of insect-pathogen interactions, provides a framework for future studies of critical microorganisms and metabolic determinants of these interactions, establishes a theoretical basis for the sustainable use of M. flavoviride.

Lepocreadiidae (Trematoda) associated with gelatinous zooplankton (Cnidaria and Ctenophora) and fishes in Australian and Japanese waters

We examined gelatinous zooplankton from off eastern Australia for lepocreadiid trematode metacercariae. From 221 specimens of 17 species of cnidarian medusae and 218 specimens of four species of ctenophores, infections were found in seven cnidarian and two ctenophore species. Metacercariae were distinguished using cox1 mtDNA, ITS2 rDNA and morphology. We identified three species of Prodistomum Linton, 1910 [P. keyam Bray & Cribb, 1996, P. orientale (Layman, 1930), and Prodistomum Type 3], two species of Opechona Looss, 1907 [O. kahawai Bray & Cribb, 2003 and O. cf. olssoni], and Cephalolepidapedon saba Yamaguti, 1970. Two species were found in cnidarians and ctenophores, three only in cnidarians, and one only in a ctenophore. Three Australian fishes were identified as definitive hosts; four species were collected from Scomber australasicus and one each from Arripis trutta and Monodactylus argenteus. Transmission of trematodes to these fishes by ingestion of gelatinous zooplankton is plausible given their mid-water feeding habits, although such predation is rarely reported. Combined morphological and molecular analyses of adult trematodes identified two cox1 types for C. saba, three cox1 types and species of Opechona, and six cox1 types and five species of Prodistomum of which only two are identified to species. All three genera are widely distributed geographically and have unresolved taxonomic issues. Levels of distinction between the recognised species varied dramatically for morphology, the three molecular markers, and host distribution. Phylogenetic analysis of 28S rDNA data extends previous findings that species of Opechona and Prodistomum do not form monophyletic clades.

Abstract 2795: An investigation to identify the phylogeny of bacterial communities in the pancreatic cancer microbiome by 16SrDNA sequencing and bioinformatic analysis

Abstract The microbiome refers to the diverse community of microorganisms, including bacteria, viruses, fungi, and other microbes, that inhabit various parts of the human body, such as the skin, mouth, gut, and other mucosal surfaces. The role of the microbiome in cancer is a complex and evolving area of research. While much is still being learned, there is evidence suggesting that the microbiome can influence cancer development and progression in several ways. Some bacteria within the microbiome can produce substances that may be either carcinogenic or protective against cancer. For instance, the conversion of certain dietary components by gut bacteria can produce metabolites that may either promote or inhibit cancer development. Different cancers may be associated with specific alterations in the microbiome, for example, the gut microbiome has been extensively studied in relation to colorectal cancer, with certain bacterial species potentially contributing to the development of this cancer. However, the role of microbiome in Pancreatic cancer is still not extensively studied, henceforth, we did a preliminary study to identify novel bacterial communities around pancreatic cancer microbiome by 16SrDNA sequencing in human pancreatic cancer xenograft model mice. Isolating total genomic DNA from the pancreatic model mice feces, 16SrDNA PCR was done using specific primers and the amplicon obtained as PCR product was confirmed by standard DNA gel electrophoresis with a 1 kb standard ladder to be 1.5kb in size universal for all bacterial 16SrDNA. The amplicon was then sent for Next Generation Sequencing at Zymo Research Corporation (CA). The resultant DNA sequences were analyzed by bioinformatics studies and their phylogeny identified by comparing with 16SrDNA data base. Differential abundance of the bacteria’s of the genera Lachnoclostridium, Robinsoniella, Alistipes, Akkermansia and Lactobacillus were observed analyzing the data along with other bacterial communities. We are currently continuing the project to identify more bacterial communities of significance in the pancreatic cancer microbiome and investigating the role and significance of these bacterial communities in pancreatic cancer tumor microenvironment. Acknowledgement This study was done by a joint collaboration between scientists and students of Elizabeth City State University (ECSU) campus of the University of North Carolina Systems and Mayo Clinic, Jacksonville. This research is supported by the NIH-NIGMS grant#T34GM100831-10 to Dr. H. Banerjee and a University of North Carolina General Administration Grant to Dr. Colby Hunter at ECSU. Citation Format: Hirendra N. Banerjee, Colby Hunter, Narendra Banerjee, Karrington Perry, Khadimou Dia, Anasua Banerjee, Santanu Bhattacharya, Hari Krishnareddy Rachamala, Enfang Wang, Shamit Dutta. An investigation to identify the phylogeny of bacterial communities in the pancreatic cancer microbiome by 16SrDNA sequencing and bioinformatic analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2795.

Aging of polypropylene plastic and impacts on microbial community structure in constructed wetlands

The COVID-19 pandemic has resulted in a substantial surge in the usage of disposable plastic masks, generating a significant volume of waste and contributing to environmental pollution. Wetland ecosystems function as crucial repositories for terrestrial pollutants and are highly effective in retaining disposable masks composed mainly of PP material. These masks can endure extended periods in wetlands, experiencing natural degradation that may have potential implications on wetland ecosystems. Our findings demonstrate the natural aging process of disposable masks, resulting in the generation of microplastics (MPs) ranging in diameter from 10 to 30 μm over a 180-day timeframe. Examination of 16S rDNA data unveiled temporal fluctuations in microbial diversity in the wetland ecosystem. Initially, microbial diversity displayed a modest incline, which was succeeded by a subsequent decrease. With the progressive accumulation of plastic within the wetland, an ongoing decline in microbial diversity linked to nitrogen transformation was observed. This study provides valuable insights into the retention of disposable masks by wetlands amidst the COVID-19 pandemic, along with their consequential effects on wetland ecosystems, specifically pertaining to nitrogen cycling. It underscores the urgency of augmenting the safeguarding measures for wetland ecosystems.

Genetic variation of the freshwater snail Indoplanorbis exustus (Gastropoda: Planorbidae) in Thailand, inferred from 18S and 28S rDNA sequences.

Indoplanorbis exustus, a freshwater pulmonate snail, is widely distributed in tropical and subtropical zones and plays a significant role as an intermediate host for trematode parasites. Various genetic markers have been used for species identification and phylogenetic studies of this snail. However, there are limited studies about their molecular genetics based on nuclear ribosomal DNA (rDNA) genes. A genetic analysis of I. exustus in Thailand was conducted based on the nuclear 18S rDNA (339 bp) and 28S rDNA (1036 bp) genes. Indoplanorbis snails were collected from 29 localities in 21 provinces covering six regions of Thailand. Nucleotide sequences from 44 snails together with sequences from the GenBank database were examined for phylogenetic relationships and genetic diversity. All sequences of the selected nucleotide regions exhibited a high level of similarity (99%) to the sequences of I. exustus in the GenBank database. The maximum likelihood tree based on the 18S and 28S rDNA fragment sequences of I. exustus in Thailand revealed only one group with clear separation from another genus in the family Planorbidae. The I. exustus 28S rDNA sequences showed intraspecific genetic divergence ranging from 0 to 0.78% and were classified into 8 different haplotypes. Conversely, the 18S rDNA data showed lower variation than the 28S rDNA data and revealed a single haplotype and intraspecific distances of zero among all sampled individuals. The haplotype network of 28S rDNA sequences of I. exustus in Thailand revealed six unique haplotypes and two haplotypes shared by at least two regions. Overall, both markers were successful in the identification of I. exustus. However, these markers, particularly the 18S rDNA, may not be suitable for genetic analysis within the species, particularly for population genetic studies, due to their limited variation as seen in this study. In summary, this study not only enhances understanding of genetic variation in I. exustus but is also useful for the selection of molecular markers in future genetic research.

Characterization of gut microbiome profile in children with confirmed wheat allergy.

Food allergies pose serious health risks, including life-threatening anaphylactic reactions, increased morbidity, and reduced quality of life. Wheat allergy is a common concern in Asia. There is growing interest in understanding the potential association between dysregulation of the gut microbiome and the development of food allergies. This study aimed to explore the gut microbiome of Thai children with wheat allergy and its potential association with allergic responses. Microbial abundance was assessed using Quantitative Insights into Microbial Ecology 2 (QIIME2) microbiome analysis based on 16S rDNA data. The correlation between microbial richness and relevant parameters was evaluated using the Spearman correlation analysis. Additionally, the microbial community functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). The gut microbiome analysis revealed significant differences between the two groups at the phylum and genus levels. Firmicutes (p = 0.012) and Verrucomicrobia (p < 0.001) were enriched in wheat-allergic children, whereas specific gut microbes such as Megamonas (p = 0.04), Romboutsia (p < 0.001), Fusobacterium (p < 0.001), Clostridium senso stricto1 (p < 0.001), and Turicibacter (p < 0.001) were more abundant in healthy children. Anaerostripes (p = 0.011), Erysipelatoclostridium (p < 0.001), Prevotella 2 (p < 0.001), Ruminiclostridium 5 (p < 0.001), and Clostridium innnocuum (p < 0.001) were enriched in children with a confirmed wheat allergy. Functional analysis indicated disparities in the pathways related to arginine and polyamine biosynthesis. These findings offer valuable insights into the gut microbiome of children with wheat allergy and its potential impact on symptom severity, laying the groundwork for further research and interventions aimed at addressing this health concern.

Description and molecular characterization of Trachactinolaimus persicus sp. n. from Iran (Nematoda, Dorylaimida, Actinolaimidae), with new insights into the taxonomy and evolutionary relationships of the genus.

A new species of the free-living nematode genus Trachactinolaimus, collected in natural habitats of northern Iran, is described, including morphological and molecular (28S-rDNA) data. Trachactinolaimus persicus sp. n. is characterized by its 1.95-2.44 mm long body, lip region weakly offset by depression and 18-20 μm wide, odontostyle 25-27 μm long, neck 540-636 μm long, pharyngeal expansion occupying one-half of the total neck length, bipartite uterus 2.6-3.9 body diameters long, vulva (V = 49-53) pore-like, tail long and filiform in both sexes (174-223 μm, c = 10.0-13.4, c' = 5.9-7.0 in females, 165-196 μm, c = 10.7-13.8, c' = 4.6-5.8 in males), spicules 68-75 μm long, and 12-14 almost contiguous ventromedian supplements with hiatus. Molecular data supports the monophyly of the genus and the hypothesis that Dorylaimidae are the sister group of actinolaims. The taxonomy of Trachactinolaimus is updated, including diagnosis, list of species, key to their identification, and a compendium of their main morphometrics. Dominiactinolaimus is regarded as its junior synonym.

Morphological and Molecular note on the identity of Mylonchulus sigmaturus Cobb, 1917 (Nematoda: Mylonchulidae) from Pakistan.

A species of predatory nematode, Mylonchulus sigmaturus Cobb, 1917, was recovered around the soil and roots of banana plants (Musa paradisiaca) from four different localities of Pakistan. The male of this species represents a new record from Pakistan. Morphological and morphometric data of the species have been contributed along with the molecular study. The phylogenetic analysis using 18S rDNA placed the Pakistani populations of M. sigmaturus with the same species in a clade with 100 posterior probabilities. The first input of 28S rDNA data placed Pakistani M. sigmaturus in a separate clade with 100 posterior probability support, however close with Prionchulus punctatus (Cobb, 1917) Andrássy, 1958 and Clarkus papillatus (Bastian, 1865) Jairajpuri, 1970.

Novel Microbial Signatures in the Faecal Microbiome Associated with Severe Alcoholic Hepatitis: Bacteroides Finegoldii and Veillonella Dispar

Background: Alcoholic hepatitis is associated with dysbiosis, resulting in compositional changes in the gut microbiome, endotoxin transfer to the portal vein, and activation of inflammatory signalling pathways in the liver. However, the microbiome signature of severe alcoholic hepatitis (AH) patients of Indian origin is unknown. Aim: To investigate the microbiome diversity of Indian AH patients in comparison to non-alcoholic healthy controls (HC). Methods: 16S rRNA amplicon-based metagenomics analysis of faecal samples at the time of AH diagnosis (n=12) was compared with HC (n=6), and correlation with survival status, co-occurrence networking, Linear Discriminant Analysis Effect Size (LEfSe), and the relationship between diet – microbiome were performed. Results: 16S rDNA data showed a significant abundance of the Enterobacteriaceae family belonging to the phylum Proteobacteria and a depletion of the phylum Firmicutes in AH. A species-level classification identified Klebsiella pneumonia, Klebsiella variicola, and Parabacteroides distasonis as having the highest predictive performance value with reference to mortality at 60 days. Apart from this, a unique finding was the abundance of Bacteroides finegoldii and Veillonella dispar in AH patients. Moreover, the co-occurrence networking analysis revealed a higher level of connectivity and complexity within the microbial community of AH patients compared to HC. Thus, indicating the significant positive association (Spearman r &gt; 0.7, p &lt; 0.01) among members of the Firmicutes, Bacteroidetes, and Proteobacteria phyla in AH. Wilcoxon-Rank Sum test (p &lt; 0.01) identified Firmicutes phyla occurrence associated with high carbohydrate intake and Actinobacteria phyla with low protein intake. Conclusion: The findings provide the baseline occurrence profile of the gut microbiome signature of liver damage and the diet-microbiome relationship in patients with severe AH. The study demonstrated an abundance of Proteobacteria phyla, indicating their role in inflammatory conditions, and further identified Bacteroides finegoldii and Veillonella dispar in severe AH patients. Additionally, Klebsiella pneumonia, Klebsiella variicola, and Parabacteroides distasonis were identified as mortality-predictive risk biomarkers.

Genetic characterisation of four Lamproglena spp. (Copepoda, Lernaeidae) from Africa and the first mitochondrial data.

Females of species of Lamproglena von Nordmann, 1832 are parasitic on the gills of teleost fishes and the 38 nominal species are based on mainly morphological data. Only four of these species have been genetically characterised and no mitochondrial data are available for the genus. The present study aimed to provide representative ribosomal DNA (rDNA) data for two additional species of Lamproglena from Africa: Lamproglena clariae Fryer, 1956 and Lamproglena hoi Dippenaar, Luus-Powell et Roux, 2001, alongside mitochondrial DNA (mtDNA) for these and two other African species, Lamproglena hemprichii von Nordmann, 1832 and Lamproglena monodi Capart, 1944. The four species were collected from Clariidae, Cyprinidae, Alestidae and Cichlidae, respectively. Representative 18S rDNA and 28S rDNA data were obtained for L. clariae and L. hoi, while cox1 mtDNA was obtained for all four species. The respective haplotypes supported the distinctness of all species using all three gene regions investigated. Interestingly, species appeared to be grouped more by geographical origin than host family, with L. hoi more closely related to other African species than to Asian species also collected from cyprinid hosts. Even though the results presented here greatly add to the molecular data available for Lamproglena, there are still 32 (>80%) species for which no genetic data are available. The interpretation of the results presented here is thus preliminary and much more data are required before the phylogeny of this genus, and other members of the family, such as Lernaea Linnaeus, 1758, can be studied appropriately.

Cerium oxide nanoparticles (nCeO2) exert minimal adverse effects on microbial communities in soils with and without biosolids amendment.

Increased use of nano-cerium oxide (nCeO2) in an array of industrial applications has raised environmental concerns due to potential increased loadings to the soil environment. This research investigated the potential adverse effects of nCeO2 (10-30 nm) on the soil microbial community in two exposure scenarios: direct application to soil, and indirect application to soil through chemical spiking of biosolids, followed by mixing into soil. Total Ce in test soils without, and with biosolids amendment, ranged from 44 to 770, and 73 to 664 mg Ce kg-1 soil, respectively. In order to help distinguish whether observed effects were elicited by the solid-phase colloids or the activity of dissolved Ce, a soluble Ce salt (Ce (NO3)3) treatment was included in select assays. A suite of tests was used to investigate effects on critical processes: microbial growth (heterotrophic plate count), microbial activity (organic matter (OM) decomposition, enzyme activity and, nitrification) and diversity (structural and functional). Although results showed significant inhibition on microbial growth in soil without biosolids amendment at ≥ 156 mg Ce kg-1 soil by week 5, these results were inconsistent and non-significant thereafter. In general, nCeO2 showed no evidence of consistent adverse effects on OM decomposition, nitrification, soil enzyme activities and functional diversity. Leucine aminopeptidase showed significant (p< 0.05) stimulatory effects over time at ≥ 44 mg Ce kg-1 in soils without biosolids, which was not observed in soils with biosolids amendment. The lack of inhibitory effects of nCeO2 may be attributed to its low solubility; Ce in soil extracts (0.01 M CaCl2) were all below detection (< 0.003 mg kg-1) in the nCeO2-spiked soils, but detectable in the Ce (NO3)3 samples. In contrast, soluble Ce at 359 mg Ce kg-1 showed a significant reduction in OM decomposition and effects on microbial genomic diversity based on the 16S rDNA data in soils with and without biosolids amendment (359 and 690 mg Ce kg-1). The nCeO2 behaviour and effects information described herein are expected to help fulfill data gaps for the characterization of this priority nanomaterial.

A Novel Phytogenic Formulation, EUBIO-BPSG, as a Promising One Health Approach to Replace Antibiotics and Promote Reproduction Performance in Laying Hens

Gut microbiota play a key role in health maintenance and disease pathogenesis in animals. Dietary phytochemicals are crucial factors shaping gut bacteria. Here, we investigated the function and mechanism of a phytogenic formulation, EUBIO-BPSG (BP), in laying hens. We found that BP dose-dependently improved health and egg production in 54-week-old hens. Furthermore, BP was correlated with increased fecal Lactobacillus, decreased Escherichia coli and Salmonella enterica, and reduced antibiotic resistance (AR) and antibiotic resistance genes (ARG) in chicken stools. The 16S rDNA data showed that BP increased seven genera of probiotics and reduced 13 genera of pathogens in chicken feces. In vitro co-culture experiments showed that BP at 4 µg/mL and above promoted growth of L. reuteri while large 100- and 200-fold higher doses suppressed growth of E. coli and S. enterica, respectively. Mechanistic studies indicated that L. reuteri and its supernatants antagonized growth of E. coli and S. enterica but not vice-versa. Five short-chain fatty acids and derivatives (SCFA) produced from L. reuteri directly killed both pathogens via membrane destruction. Furthermore, BP inhibited conjugation and recombination of ARG via interference with conjugation machinery and integrase activity in E. coli. Collectively, this work suggests that BP promotes host health and reproductive performance in laying hens through regulation of gut microbiota through increasing probiotics and decreasing pathogens and spreading ARG.

The enigmatic genusLoofilaimus(Nematoda, Dorylaimida, Loofilaimidae) revisited 25 years after, with remarkable new insights into its phylogeny

The evolutionary relationships of the nematode genus Loofilaimus are explored with an integrative approach, combining morphological and molecular (28S-rDNA) data. Never recorded since its original description in 1998, the finding of fresh specimens of its type and only species, L. phialistoma, allowed us to obtain SEM observations and sequencing, both for the first time, resulting in relevant aspects to elucidate its phylogeny. Morphologically, the genus is characterized by two autapomorphies affecting its lip region and pharynx. Molecular study revealed that it represents a very restricted evolutionary trend within Dorylaimida. The clade (Nygolaimina + (Loofilaimus + Dorylaimina)) is well supported. Loofilaimidae is accepted as a separate and valid family, which should also include Bertzuckermania.

First Report of Aphelenchoides Bicaudatus (Imamura, 1931) Filipjev and Schuurmans Stekhoven, 1941 Associated with Grass in South Africa.

Aphelenchoides bicaudatus associated with grass in South Africa was identified morphologically and molecularly. This population is characterized by a body length of 409 - 529 μm, a stylet length of 9.5 - 13 μm, a post-vulval uterine sac of 45 - 50 μm, and the characteristic tail bifurcated at the end with one prong longer than the other. Molecular analyses based on the 18S and ITS rDNA data confirmed the primary morphological identification of the A. bicaudatus species. The obtained phylogenetic trees revealed a close positioning of the South African population to other representatives of A. bicaudatus with the maximum (1.00) posterior probability value. Principal component analysis (PCA) also indicated a variation within the populations of A. bicaudatus. This is the first report of A. bicaudatus from South Africa.

An ancient alliance: Matching evolutionary patterns of cartilaginous fishes (Elasmobranchii) and chloromyxid parasites (Myxozoa).

Myxozoa is a group of endoparasitic cnidarians covering almost 2600 species but merely 53 species, mostly from the genus Chloromyxum, have been reported from sharks, rays, and skates (Elasmobranchii). Elasmobranchs play a key role in the study of evolutionary trajectories of myxozoans as they represent ancestral vertebrate hosts. Our study provides new data on Chloromyxum spp. from 57 elasmobranchs, covering 20 species from geographical regions and host groups not previously investigated, such as Lamniformes and Hexanchiformes, the most basal phylogenetic shark lineage. In total, 28% of elasmobranchs were infected with Chloromyxum spp., indicating high diversity. Of the seven distinguished species, six are formally described based on morphological, morphometric, and genetic (18S rDNA) data. Comprehensive co-phylogenetic analyses and ancestral state reconstruction revealed that parasite and host phylogenies are clearly correlated, resulting in a distinct phylogenetic separation of chloromyxids from selachid (shark) vs. batoid (ray and skate) hosts. Species infecting the most ancient elasmobranchs formed a sublineage, branching off in the middle of the Chloromyxum sensu stricto clade. Our findings indicate that chloromyxids likely invaded an ancestral elasmobranch prior the time of divergence of shark and batoid lineages. Our analyses did not show a clear phylogeographic pattern of Chloromyxum parasites, probably due to the cosmopolitan distribution and migratory behaviour of many elasmobranch hosts, but geographical sampling must be extended to confirm or refute this observation. This study provides a complex view on species diversity, phylogeny, evolution, host-parasite co-phylogeny, and the phylogeographic origin of Chloromyxum species from elasmobranchs. Our results highlight the importance of adding missing data from previously un- or undersampled geographical regions and host species which results in a more accurate estimate of myxozoan biodiversity and a better understanding of the evolution of this parasite group in their hosts and in the different oceans of our planet.

Natural association of the entomopathogenic nematode Heterorhabditis indica (Rhabditida: Heterorhabditidae) from the Philippines with the non-symbiotic bacterium Ochrobactrum anthropi (Proteobacteria: Brucellaceae)

BackgroundEntomopathogenic nematodes of the genera Heterorhabditis and Steinernema are widely used as biocontrol agents against diverse insect pests. Their association with symbiont bacteria is found to be the primary cause of insect mortality. The present study reported a comprehensive characterization of a local Philippine EPN isolate using congruent morpho-taxometrical and molecular data and the associated bacterium in the infective dauer juveniles.ResultsUsing an insect-baiting technique, a nematode isolate labeled F2H was recovered from the sandy soils in the coastal area of southern Philippines. Based on morphology and morpho-taxometrics, the F2H isolate collected from Iligan City was identified as Heterorhabditis indica. Analysis of the ITS region of rDNA revealed the highest sequence match to H. indica. The sequences of the bacterial 16S rDNA gene showed that the symbiont of H. indica presented 100% similitude with the sequences of Ochrobactrum anthropi. Further, pairwise alignment and phylogenetic analysis demonstrated that O. anthropi, O. lupini and O. cytisi shared 100% similarity and form a monophyletic clade. These strains have not presented any differences in the phylogenetic and 16S rDNA data, and O. lupini and O. cytisi should be considered a later heterotypic synonym of O. anthropi.ConclusionsThe description of H. indica-O. anthropi association was the first report in the Philippines. This provides additional account and collection of naturally isolated EPN-bacteria, contributing to limited knowledge on its diversity in the Philippines, which can be utilized in the biocontrol of pests after further comprehensive assessments.

A phylogenetic overview of Squamanita, with descriptions of nine new species and four new combinations

ABSTRACT Nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) sequence data from eight type specimens of previously described Squamanita species were obtained. Phylogenetic analysis of ITS and partial nuc 28S rDNA data revealed Squamanita as paraphyletic splitting into two monophyletic groups, which we recognize as the genera Squamanita and Dissoderma. We accept 14 Squamanita and nine Dissoderma species, provide the first sequences of 13 of these, and describe six new species of Squamanita and three new species of Dissoderma. We transfer three species of Squamanita into Dissoderma, one into Cystoderma, and treat S. basii and S. umbilicata as synonyms of D. paradoxum. Squamanita can be distinguished from Dissoderma by the generally larger fleshier basidiomata with a tricholomatoid or amanitoid stature and yellowish to tawny brown pileus and often similarly colored stipe. Most species have cheilo- and pleurocystidia. Species of Dissoderma are small, collybioid or mycenoid, lack cystidia, and the pileus and often upper stipe are purplish gray. Both genera parasitize basidiomata of other agarics.

Comparison of the Microbiome of Artisanal Homemade and Industrial Feta Cheese through Amplicon Sequencing and Shotgun Metagenomics.

Feta is the most renowned protected designation of origin (PDO) white brined cheese produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on, among other factors, its overall microbial ecosystem. In this study, we employed 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing, as well as shotgun metagenomics, to investigate the microbiome of artisanal homemade and industrial Feta cheese samples from different regions of Greece, which has very rarely been investigated. 16S rDNA data suggested the prevalence of the Lactococcus genus in the homemade samples, while Streptococcus and Lactobacillus genera prevailed in the industrial control samples. Species identification deriving from shotgun metagenomics corroborated these findings, as Lactococcus lactis dominated two homemade samples while Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were found to be dominating one industrial sample. ITS data revealed a complex diversity of the yeast population among the samples analyzed. Debaryomyces, Kluyveromyces, Cutaneotrichosporon, Pichia, Candida, and Rhodotorula were the major genera identified, which were distributed in a rather arbitrary manner among the different samples. Furthermore, a number of potential metagenome-assembled genomes (MAGs) could be detected among assembled shotgun bins. The overall analysis of the shotgun metagenomics supported the presence of different foodborne pathogens in homemade samples (e.g., Staphylococcus aureus, Listeria monocytogenes, Enterobacter cloacae, and Streptococcus suis), but with low to very low abundances. Concluding, the combination of both amplicon sequencing and shotgun metagenomics allowed us to obtain an in-depth profile of the artisanal homemade Feta cheese microbiome.

Bacillus velezensis LG37 absorbs and utilizes ammonia nitrogen from aquaculture water and enhances the toxicity tolerance of grass carp (Ctenopharyngodon idella) to ammonia (non-ionic ammonium)

High concentrations of ammonia nitrogen lead to multi-organ damage, decreased immunity, and metabolic disorders in aquaculture animals, which cause disease outbreaks. This study mainly screened probiotic strains for good control of the concentration of ammonia nitrogen and identified strain LG37 as Bacillus velezensis according to its morphological, 16S rDNA, phylogenetic, and genomic data analysis. This LG37 strain achieved efficiently purifies aquaculture water and enhances the toxicity tolerance of grass carp to ammonia. The experimental on growth characteristics showed that LG37 exhibited a satisfactory growth trend with 10 types of sugar, 17 types of amino acids, and 6 types of organic nitrogen as the carbon or nitrogen source. Under the conditions of initial dissolved oxygen at 6±1 mg/L, the temperature at 27±2°C, and pH 7±0.3. Through wastewater treatment equipment, which degraded ammonia nitrogen and the feed protein in grass carp culture wastewater reached up to 55.5% and 73.6% within one week, respectively. Moreover, in the acute toxicity test, when feed without LG37 was fed to grass carp, the safe concentration of ammonia nitrogen (non-ionic ammonium) was 3.37 mg/L (0.2 mg/L). When feed with LG37 was fed to grass carp, the safe concentration of ammonia nitrogen (non-ionic ammonium) was 5.11 mg/L (0.31 mg/L). Compared to feed without LG37, the feed with LG37 increased the toxicity tolerance of grass carp to ammonia nitrogen (non-ionic ammonium) by 51.63% (55%).

Study of Rhizosphere Microbial Community Structures of Asian Wild and Cultivated Rice Showed That Cultivated Rice Had Decreased and Enriched Some Functional Microorganisms in the Process of Domestication

Asian cultivated rice (Oryza sativa L.), domesticated from Asian wild rice, is a staple food crop for populations around the world. Asian cultivated rice has undergone physiological changes in the process of its evolution from Asian wild rice, and the closely related rhizosphere microorganisms may have changed in the process of plant domestication. However, the rhizosphere microorganisms of different Asian wild rice species and their related indica and japonica cultivated rice have not yet been illustrated clearly. This study aimed to illustrate the microbial community structures in the rhizosphere of Asian wild rice (common wild rice, nivara wild rice, medicinal wild rice, and spotted wild rice) and Asian cultivated rice (indica and japonica accessions) through the high-throughput sequencing of 16S rDNA, ITS amplifiers and metagenomic data. The results showed that there were significant differences between wild and cultivated rice in their rhizosphere microbial community structures. In view of the indica and japonica rice, the bacterial and fungal community structures of indica rice with the nivara wild rice and medicinal wild rice were more similar than the japonica rice species. The indica and japonica rice had the lowest proportion of Actinobacteria than the wild rice species, and indica rice has the highest relative abundance of Nitrospira. As for the microbial functions, methane metabolism and pyruvate metabolism were found to be the common pathway enriched in the rhizosphere of common and nivara wild rice in comparison with the indica and japonica rice; in addition, though it was found that the relative abundances of the pathogenic fungi in the rhizosphere soil of indica and japonica rice were significantly lower than that of the wild rice, the relative abundances of Magnaporthales and Ustilaginales were significantly higher in indica and japonica rice than that of the wild rice. This study is expected to provide a theoretical basis for the development and utilization of rhizosphere microbial resources for wild and cultivated rice.