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Eimeria is an important coccidian enteric parasite that infects a wide range of hosts and can cause substantial economic losses in the poultry and livestock industries. It is common for multiple Eimeria species to infect individual hosts, and this can make species identification difficult due to morphological similarities between species and mixed chromatograms when using Sanger sequencing. Relatively few studies have applied next-generation amplicon sequencing (NGS) to determining the genetic diversity of Eimeria species in different hosts. The present study screened 408 faecal samples from a range of hosts including livestock and wildlife using a previously developed quantitative polymerase chain reaction (qPCR) at the 18S locus and conducted amplicon NGS on the positives using a ~ 455-bp fragment of the 18S locus. A total of 41 positives (10.1%) were identified by qPCR from various hosts and NGS was successful for 38 of these positives. Fifteen Eimeria species and three genotypes were detected by NGS: E. ferrisi, E. kanyana, E. potoroi, E. quokka, E. setonicis, E. trichosuri, E. reichenowi, E. angustus, E. ahsata, E. auburnensis, E. bovis, E. brasiliensis, E. christenseni, E. crandallis, E. ovinoidalis, Eimeria sp. (JF419345), Eimeria sp. (JF419349) and Eimeria sp. (JF419351). Mixed infections were detected in 55.3% (21/38) of positive samples. The most striking finding was the identification of the same species in different hosts. This could be due to contamination and/or mechanical transmission or may provide support for previous studies suggesting that Eimeria species can infect not just closely related hosts but different genera and further research is required. This is also the first study to audit Eimeria populations in livestock (sheep and cattle) by NGS and could be applied in the future to determine the extent of pathogenic species and outcomes of Eimeria control strategies. [ABSTRACT FROM AUTHOR]

A new Isospora species is described from New Holland honeyeaters (Phylidonyris novaehollandiae). Sporulated oocysts (n = 25) were characterised as subspheroidal, 29–32 × 28–31 (29.8 × 29.4); length/width (L/W) ratio 1.01–1.02 (1.01). Wall bi-layered, 1.3–1.6 (1.5) thick, outer layer smooth, c.2/3 of total thickness. Micropyle and oocyst residuum absent, but usually two polar granules are present. Sporocysts (n = 25) ovoidal, 18–19 × 12–14 (18.4 × 12.3); L/W ratio 1.42–1.53 (1.50). Stieda body present, flattened, c. 0.5 deep × 2.5 wide; sub-Stieda present, rounded, c. 2.5 deep × 3.5 wide; para-Stieda body absent; sporocyst residuum present, usually a distinctly irregular body consisting of numerous small granules that appear to be membrane-bound. Sporozoites vermiform, with robust anterior and posterior refractile bodies. Molecular characterization was conducted at the 18S and 28S ribosomal RNA and the mitochondrial (mt) cytochrome oxidase (COI) loci. Phylogenetic analysis of genomic 18S and mt COI sequences indicated that Isospora phylidonyrisae n. sp. was genetically similar to Isospora coronoideae, isolated from an Australian raven (Corvus coronoides) in Western Australia, with a 99.3% and 98.4% homology, respectively. The 28S rRNA sequence was most similar to Isospora anthochaerae (KF766053) and Isospora manorinae (KT224381), both with a 98.2% genetic similarity. Based on morphological and genetic data, this isolate is a new species of Isospora , which is named Isospora phylidonyrisae n. sp. after its host. [Display omitted] • Description of I. phylidonyrisae n. sp. in a New Holland Honeyeater. • Morphology study: Unique to any of the reported Isospora spp.. • Genetic study: 99.3% and 99.4% similar to I. coronoideae at 18S and mtCOI locus, respectively. [ABSTRACT FROM AUTHOR]

Key message: The vacuolar processing enzyme gene TaVPE3cB is identified as a candidate gene for a QTL of wheat pith-thickness on chromosome 3B by BSR-seq and differential expression analyses. The high pith-thickness (PT) of the wheat stem could greatly enhance stem mechanical strength, especially the basal internodes which support the heavier upper part, such as upper stems, leaves and spikes. A QTL for PT in wheat was previously discovered on 3BL in a double haploid population of ‘Westonia’ × ‘Kauz’. Here, a bulked segregant RNA-seq analysis was applied to identify candidate genes and develop associated SNP markers for PT. In this study, we aimed at screening differentially expressed genes (DEGs) and SNPs in the 3BL QTL interval. Sixteen DEGs were obtained based on BSR-seq and differential expression analyses. Twenty-four high-probability SNPs in eight genes were identified by comparing the allelic polymorphism in mRNA sequences between the high PT and low PT samples. Among them, six genes were confirmed to be associated with PT by qRT-PCR and sequencing. A putative vacuolar processing enzyme gene TaVPE3cB was screened out as a potential PT candidate gene in Australian wheat ‘Westonia’. A robust SNP marker associated with TaVPE3cB was developed, which can assist in the introgression of TaVPE3cB.b in wheat breeding programs. In addition, we also discussed the function of other DEGs which may be related to pith development and programmed cell death (PCD). A five-level hierarchical regulation mechanism of stem pith PCD in wheat was proposed. [ABSTRACT FROM AUTHOR]

A growing body of evidence supports the concept of a systemic response to non-severe thermal trauma. This provokes an immunosuppressed state that predisposes paediatric patients to poor recovery and increased risk of secondary morbidity. In this study, to understand the long-term systemic effects of non-severe burns in children, targeted mass spectrometry assays for biogenic amines and tryptophan metabolites were performed on plasma collected from child burn patients at least three years post injury and compared to age and sex matched non-burn (healthy) controls. A panel of 12 metabolites, including urea cycle intermediates, aromatic amino acids and quinolinic acid were present in significantly higher concentrations in children with previous burn injury. Correlation analysis of metabolite levels to previously measured cytokine levels indicated the presence of multiple cytokine-metabolite associations in the burn injury participants that were absent from the healthy controls. These data suggest that there is a sustained immunometabolic imprint of non-severe burn trauma, potentially linked to long-term immune changes that may contribute to the poor long-term health outcomes observed in children after burn injury. [ABSTRACT FROM AUTHOR]

• B. amyloliquefaciens SC06 exhibited protective properties against hepatic inflammation and hepatocyte necrosis induced by LPS through inhbit the bile acid-associated-NLRP3 inflammasome pathway. • B. amyloliquefaciens SC06 administration efficiently overcomes LPS-induced bile acid metabolism anomalies. • B. amyloliquefaciens SC06 was unable to directly inhibit the activation of NLRP3 inflammasome. • Taurochenodeoxycholic acid (TCDCA) activated inflammatory vesicles and exacerbates LPS-induced inflammatory injury. The involvement of the inflammatory response has been linked to the development of liver illnesses. As medications with the potential to prevent and cure liver illness, probiotics have garnered an increasing amount of interest in recent years. The present study used a piglet model with acute liver injury (ALI) induced by lipopolysaccharides (LPS) to investigate the regulatory mechanisms of Bacillus amyloliquefaciens SC06. Our findings indicated that SC06 mitigated the liver structural damage caused by LPS, as shown by the decreased infiltration of inflammatory cells and the enhanced structural integrity. In addition, After the administration of SC06, there was a reduction in the increased levels of the liver damage markers. In the LPS group, there was an increase in the mRNA expression of inflammatory cytokines, apoptosis cell rate, and genes associated with apoptosis, while these alterations were mitigated by SC06 administration. Furthermore, SC06 prevented pigs from suffering liver damage by preventing the activation of the NLRP3 inflammasome, which was normally triggered by LPS. The examination of serum metabolic pathways found that ALI was related to several metabolic processes, including primary bile acid biosynthesis, pentose and glucuronate interconversions and the metabolism of phenylalanine. Significantly, our research revealed that the administration of SC06 effectively controlled the concentrations of bile acids in the serum. The correlation results also revealed clear relationships between bile acids and liver characteristics and NLRP3 inflammasome-related genes. However, in vitro experiments revealed that SC06 could not directly inhibit NLRP3 activation under ATP, monosodium urate, and nigericin stimulation, while taurochenodeoxycholic acid (TCDCA) activated NLRP3 inflammasome related genes. In conclusion, our study proved that the hepaprotective effect of SC06 on liver injury, which was closely associated with the restoration of bile acids homeostasis and NLRP3 inflammasome inhibition. [ABSTRACT FROM AUTHOR]

[Display omitted] • Rosa roxburghii Tratt, known as the king of vitamin C, shows stronger relief for colitis compared to vitamin C alone. • It surpasses vitamin C in alleviating inflammation, repairing intestinal barriers, and regulating intestinal flora. • Rosa roxburghii Tratt alleviates colitis by downregulating the colonic B cell receptor pathway and its downstream signals. Rosa roxburghii Tratt (RRT), a traditional Chinese plant known as the 'King of Vitamin C (VitC; ascorbic acid, AsA)', contains a wealth of nutrients and functional components, including polysaccharides, organic acids, flavonoids, triterpenes, and high superoxide dismutase (SOD) activity. The various functional components of RRT suggest that it may theoretically have a stronger potential for alleviating colitis compared to VitC. This study aims to verify whether RRT has a stronger ability to alleviate colitis than equimolar doses of VitC and to explore the mechanisms underlying this improvement. Results showed that RRT significantly mitigated body weight loss, intestinal damage, elevated inflammation levels, and compromised barriers in mice induced by Dextran sulfate sodium (DSS). Additionally, RRT enhanced the diversity and composition of intestinal microbiota in these DSS-induced mice. Colon RNA sequencing analysis revealed that compared to VitC, RRT further downregulated multiple immune-related signaling pathways, particularly the B cell receptor (BCR) pathway, which is centered around genes like Btk and its downstream PI3K-AKT, NF-κB, and MAPK signaling pathways. Correlation analysis between microbiota and genes demonstrated a significant relationship between the taxa improved by RRT and the key genes in the BCR and its downstream signaling pathways. Overall, RRT exhibited superior capabilities in alleviating DSS-induced colitis compared to VitC by decreasing intestinal inflammation and modulating BCR and its downstream signaling pathways, potentially regulated by the improved intestinal microbiota. [ABSTRACT FROM AUTHOR]

Metabolic phenotyping using mass spectrometry (MS) is being applied to ever increasing sample numbers in clinical and epidemiology studies. High-throughput and robust methods are being developed for the accurate measurement of metabolites associated with disease. Traditionally, quantitative assays have utilized triple quadrupole (QQQ) MS based methods; however, the use of such focused methods removes the ability to perform discovery-based metabolic phenotyping. An integrated workflow for the hybrid simultaneous quantification of 34 biogenic amines in combination with full scan high-resolution accurate mass (HRAM) exploratory metabolic phenotyping is presented. Primary and secondary amines are derivatized with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate prior to revered-phase liquid chromatographic separation and mass spectrometric detection. Using the HRAM-MS data, retrospective phenotypic data mining could be performed, demonstrating the versatility of HRAM-MS instrumentation in a clinical and molecular epidemiological environment. Quantitative performance was assessed using two MS detector platforms: Waters TQ-XS (QQQ; n = 3) and Bruker Impact II QToF (HRAMS-MS; n = 2) and three human biofluids (plasma, serum and urine). Finally, each platform was assessed using a certified external reference sample (NIST SRM 1950 plasma). Intra- and inter-day accuracy and precision were comparable between the QQQ and QToF instruments (<15%), with excellent linearity (R2 > 0.99) over the quantification range of 1–400 μmol L−1. Quantitative values were comparable across all instruments for human plasma, serum and urine samples, and calculated concentrations were verified against certified reference values for NIST SRM 1950 plasma as an external reference. As a real-life biological exemplar, the method was applied to plasma samples obtained from SARS-CoV-2 positive patients versus healthy controls. Both the QQQ and QToF approaches were equivalent in being able to correctly classify SARS-CoV-2 positivity. Critically, the use of HRAM full scan data was also assessed for retrospective exploratory mining of data to extract additional biogenic amines of biomarker interest beyond the 34 quantified targets. Image 1 • Quantitative/exploratory assay to target 34 amino acids, and simultaneously collect exploratory data. • Extensive intra-laboratory validation of quantitative performance (QToF vs QQQ). • Exemplar application to metabolically phenotype individuals infected with SARS-CoV-2 virus. • Demonstration of retrospective data mining and feature extraction from exploratory data. [ABSTRACT FROM AUTHOR]

An Isospora species, Isospora amphiboluri, originally described by Canon in 1967 and later by McAllister et al. (1995), was isolated from a central netted dragon (Ctenophorus nuchalis) housed at a wildlife rehabilitation centre in Perth, Western Australia. Sporulated oocysts of Isospora amphiboluri (n = 30) are spherical, 24.2 (26.5–23.0) μm in length and 23.9 (22.4–25.9) μm in width, with a shape index of 1.01. The bilayered oocyst wall is smooth and light-yellow in color. Polar granule, oocyst residuum and micropyle are absent. The sporocysts are lemon-shaped, 15.7 (15.2–18.0) × 10.2 (8.9–11.2) μm, with a shape index (length/width) of 1.53. Stieda and substieda bodies are present, the Stieda body being small and hemidome-shaped and the substieda half-moon-shaped. Each sporocyst contains four vermiform sporozoites arranged head to tail. The sporozoites are 11.7 (9.9–16.2) × 3.0 (2.4–3.5) μm, with a shape index (length/width) of 3.87. A sporocyst residuum is present. Sporozoites contain a central nucleus with a finely distributed granular residuum. Comparison of oocyst measurements and their features with other valid Isospora species from hosts in the Agamid family confirmed that this Isospora species is Isospora amphiboluri. Molecular characterization of I. amphiboluri at the 18S rRNA and MTCOI loci showed the highest similarity with I. amphiboluri from the central bearded dragon, 99.8% and 99.7% respectively. This is the first report of I. amphiboluri from a central netted dragon in Australia. [Display omitted] • Description of I. amphiboluri in a new host - central netted dragon. • Morphology study: With the same features of I. amphiboluri reported before. • Genetic study: 99.8% and 99.7% similar to I. amphiboluri at 18S and mtCOI locus, respectively. • First time identified I. amphiboluri in Australia. [ABSTRACT FROM AUTHOR]

A novel Eimeria Schneider, 1875 species is described from an Australian pied oystercatcher Haematopus longirostris Vieillot, in Western Australia. The pied oystercatcher was admitted to the Kanyana Wildlife Rehabilitation Centre (KWRC), Perth, Western Australia in a poor body condition, abrasion to its right hock and signs of partial delamination to its lower beak. Investigation into potential medical causes resulted in a faecal sample being collected and screened for gastrointestinal parasites. Unsporulated coccidian oocysts were initially observed in the faeces and identified as Eimeria upon sporulation. The sporulated oocysts (n = 20) are ellipsoidal, 20-21 × 12-13 μm in shape and have thick bi-layered walls which are c.2/3 of the total thickness. Micropyle is present, robust and protruding, and occasionally has a rounded polar body attached to the micropyle. Within the oocyst, a residuum, in addition, two to five polar granules are present. There are four ellipsoidal sporocysts 9-11 × 5-6 μm with flattened to half-moon shaped Stieda bodies. Sub-Stieda body and para-Stieda body are absent. The sporocysts contain sporocyst residuums composed of a few spherules scattered among the sporozoites. Within the sporozoites, anterior and posterior refractile bodies are present, but the nucleus is indiscernible. To further characterise the novel Eimeria species from H. longirostris, molecular analysis was conducted at the 18S ribosomal RNA locus, using PCR amplification and cloning. Two cloned sequences from the novel Eimeria were compared with those from other Eimeria spp. with the highest genetic similarity of 97.6% and 97.2% from Clone 1 and 2, respectively with Eimeria reichenowi (AB544308) from a hooded crane (Grus monacha Temminck) in Japan. Both sequences grouped in a clade with the Eimeria spp. isolated from wetland birds, which include Eimeria paludosa (KJ767187) from a dusky moorhen (Gallinula tenebrosa Gould) in Western Australia, Eimeria reichenowi (AB544308) and Eimeria gruis (AB544336) both from hooded cranes. Based on the morphological and molecular data, this Eimeria sp. is a new species of coccidian parasite and is named Eimeria haematopusi n. sp. after its host H. longirostris., (© 2024. Crown.)

A new Eimeria Schneider, 1875 species is described from an Australian pelican Pelecanus conspicillatus Temminck, 1824 in Western Australia. Sporulated oocysts (n = 23) subspheroidal, 33-35 × 31-33 (34.1 × 32.0) μm; length/width (L/W) ratio 1.0-1.1 (1.07). Wall bi-layered, 1.2-1.5 (1.4) μm thick, outer layer smooth, c.2/3 of total thickness. Micropyle absent, but 2 or 3 polar granules surrounded by a thin membrane, apparently residual, are present. Sporocysts (n = 23) elongate ellipsoidal or capsule shaped, 19-20 × 5-6 (19.5 × 5.6) μm; L/W ratio 3.4-3.8 (3.51). Stieda body vestigial and barely discernible, 0.5 × 1.0 μm; sub-Stieda and para-Stieda bodies absent; sporocyst residuum present, composed of a few dense spherules dispersed among the sporozoites. Sporozoites with robust anterior and posterior refractile bodies and centrally located nucleus. Molecular analysis was conducted at three loci; the 18S and 28S ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene. At the 18S locus, the new isolate shared 98.6% genetic similarity with Eimeria fulva Farr, 1953 (KP789172), which was identified from a goose in China. At the 28S locus, the new isolate shared the highest similarity of 96.2% with Eimeria hermani Farr, 1953 (MW775031) identified from a whooper-swan (Cygnus cygnus (Linnaeus, 1758)) in China. At the COI gene locus, this new isolate was most closely related to Isospora sp. isolate COI-178 and Eimeria tiliquae [25,26], presented 96.5% and 96.2% genetic similarity, respectively. Based on the morphological and molecular data, this isolate is a new species of coccidian parasite, which is named Eimeria briceae n. sp., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have influenced the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Four species of the Eimeriidae, Eimeria anatis Scholtyseck, 1955, Eimeria aythyae Farr, 1965, Eimeria krylovi Svanbaev & Rakhmatullina, 1967 and Tyzzeria perniciosa Allen, 1936, were morphologically identified from oöcysts recovered from a Pacific black duck, Anas superciliosa Gmelin. Additionally, genotypic characterization of E. anatis is provided via sequencing of the mitochondrial cytochrome c oxidase subunit 1 ( cox 1) and the small subunit ribosomal RNA (18S) genes. The four species are redescribed, providing additional morphological details. The validity of genera and coccidian species parasitizing birds of the order Anseriformes such as Wenyonella Hoare, 1933 and some Tyzzeria spp. are discussed. Molecular phylogenetic analyses for the cox 1 and 18S rRNA genes resulted in monophylies of Eimeria spp. from Anseriformes which included the sequences obtained from E. anatis oöcysts., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

A new coccidian species, Isospora lunulatae n. sp., from the western wattlebird Anthochaera lunulata Gould in Western Australia is described and characterised molecularly. Microscopic analysis of a faecal sample identified subspheroidal oöcysts measuring 27-34 × 26-31 (30.6 × 29.4) μm ( n  = 20), with a length/width (L/W) ratio of 1.0-1.1 (1.0). Oöcysts have a bi-layered wall, 0.9-1.2 (1.0) μm thick; the outer layer is smooth, representing c. 2/3 of total thickness. Micropyle and oöcyst residuum are both absent, but a polar granule is present. Sporocysts are ovoidal, 17-19 × 10-12 (18.3 × 10.7) μm, with a L/W ratio of 1.6-1.8 (1.7) and occupying about 21% of the area (each one) within the oöcyst. Stieda body is flattened to rounded, measuring on average 0.9 × 1.8 μm; sub-Stieda body is rounded to rectangular, measuring on average 1.5 × 2.6 μm; para-Stieda body is absent. Sporocyst residuum has an irregular shape consisting of numerous granules and appears membrane-bound. Sporozoites are vermiform 12.8 × 3.0 μm on average, with prominent striations at the more pointed end and two refractile bodies below striations. Segments of three gene loci (18S rRNA, 28S rRNA and cox 1) were sequenced and I . lunulatae n. sp. exhibited 99.6% genetic similarity to Isospora phylidonyrisae Yang, Brice, Berto & Ryan, 2021 at the 18S rRNA gene locus, 99.8% genetic similarity to Isospora anthochaerae Yang, Brice & Ryan, 2014 and shared a 98.1% genetic similarity with Isospora manorinae Yang, Brice, Jian & Ryan, 2016 at the cox 1 gene locus. Morphological and molecular data support the distinct species status of the new species., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2021 Published by Elsevier B.V.)

A new coccidian species, Isospora lugensae n. sp., was described from a single Kerguelen petrel (Lugensa brevirostris). Sporulated oocysts (n = 25) were characterized as subspheroidal to ellipsoidal measuring 24-25 μm × 21-23 μm (24.8 × 22.2 μm) in length/width (L/W), respectively, with a ratio of 1.07-1.14 μm (1.12). They contained a bi-layered wall with a thickness of 0.8-1.2 μm (1.0) and the outer layer smooth, with c.2/3 of total thickness. The oocyst contained two polar granules with both micropyle and oocyst residuum absent. Ovoidal sporocysts (n = 25) measured 15-16 μm × 10-11 μm (15.7 × 10.8 μm) in L/W, with a ratio of 1.41-1.49 μm (1.46). A flattened to knob-like Stieda body was present (c.0.5 μm deep × 2.5 μm wide) as well as a rounded to trapezoidal sub-Stieda (c.1.5 μm deep × 3.0 μm wide); however, no para-Stieda body was detected. The sporocyst residuum was composed of scattered spherules of different sizes, while vermiform sporozoites contained a refractile body, nucleus and visible striations. Analysis of the full-length mitochrondrial (mtDNA) genome revealed 3 protein-coding genes, (CytB, COI and COIII), 18 LSU and 14 small subunit (SSU) rDNA fragments, without transfer RNA genes with a total length of 6257 bp. Phylogenetic analysis of genomic SSU ribosomal sequences indicated that Isospora lugensae n. sp. is genetically similar to Eimeria reichenowi, isolated from a red-crowned crane (Grus japonensis) from Japan, with a 96.6% homology. The mtDNA sequence is most similar to Isospora serinuse with a 95.8% genetic similarity. Based on morphological and molecular data, this isolate is a new species of coccidian parasite that to date has only been found in a Kerguelen petrel.

A new Eimeria species is described from a common bronzewing pigeon (Phaps chalcoptera) (Latham, 1790) in Western Australia. Sporulated oocysts of Eimeria chalcoptereae n. sp. (n = 30) are subspheroidal, 22-25 × 21-24 (23.5 × 22.6) μm; length/width (L/W) ratio 1.0-1.1 (1.04) μm. Wall bi-layered, 1.0-1.4 (1.2) μm thick, outer layer smooth, c.2/3 of total thickness. Micropyle barely discernible. Oocyst residuum is absent, but 2 to 3 small polar granules are present. Sporocysts (n = 30) ellipsoidal, 13-14 × 7-8 (13.5 × 7.2) μm; L/W ratio 1.8-2.0 (1.88). Stieda body present, flattened to half-moon-shaped, 0.5 × 2.0 μm; sub-Stieda present, rounded to trapezoidal, 1.5 × 2.5 μm; para-Stieda body absent; sporocyst residuum present, usually as an irregular body consisting of numerous small granules that appear to be membrane-bound. Sporozoites vermiform, with a robust refractile body and centrally located nucleus. Isolated Eimeria oocysts were analysed at the 18S and 28S ribosomal RNA and the mitochondrial cytochrome oxidase (COI) loci. Analyses revealed that Eimeria chalcoptereae n. sp. shared the highest number of molecular features with an Eimeria sp. previously identified from a domestic pigeon in Australia (KT305927-29), with similarities at these three loci of 98.53%, 97.32% and 94.93%, respectively. According to morphological and molecular analysis, the isolated coccidian parasite is a new species of Eimeria named Eimeria chalcoptereae n. sp. after its host, the common bronzewing pigeon (Phaps chalcoptera) (Columbiformes: Columbidae) (Latham, 1790).