<Emphasis Type="Italic">Parabacteroides chongii</Emphasis> sp. nov., isolated from blood of a patient with peritonitis

An obligate anaerobic, Gram-reaction-negative, non-sporeforming, non-motile, rod shaped bacterium designated YMC B3181^T was isolated from the blood of a patient with peritonitis. Strain B3181^T grew at 20 to 40°C with optimum growth at 37°C. 16S rRNA gene sequence similarity showed strain B3181^T belongs to the genus Parabacteroides and is closely related to Parabacteroides faecis 157^T (97.3%), Parabacteroides gordonii MS-1^T (96.6%), and Parabacteroides goldsteinii DSM 19448^T (95.7%). The G + C content of the genomic DNA was 42.3 mol%. The major cellular fatty acids were anteiso-C_15:0 and iso-C_17:0 3-OH, and the predominant respiratory quinones were MK-9 and MK-10 menaquinones. Genomic and chemotaxonomic data supported affiliation of B3181^T with the genus Parabacteroides. Strain B3181^T was phylogenetically and phenotypically different from recognized species of the genus Parabacteroides. Accordingly, this isolate belongs to a novel species for which the name Parabacteroides chongii sp. nov. (type strain YMC B3181^T = LMG 30065^T = KACC 19034^T) is proposed.     

Comparison of effects on colitis-associated tumorigenesis and gut microbiota in mice between Ophiocordyceps sinensis and Cordyceps militaris

Background: Gut microbiota plays an indispensable role in the treatment of inflammatory bowel disease (IBD) and colitis-associated cancer (CAC). As traditional medicinal fungi, previous studies have shown that Ophiocordyceps sinensis could better maintain intestinal health via promoting the growth of probiotics in vitro compared with Cordyceps militaris. However, the detailed pharmacological activities and clinical efficacy of O. sinensis and C. militaris are still elusive.Purpose: We aimed to evaluate the different actions of O. sinensis and C. militaris on colitis-associated tumorigenesis in Azoxymethane (AOM)/Dextran Sulfate Sodium (DSS)-treated mice and explore the potential gut microbiota-dependent mechanisms.Methods: C57BL/6 mice (Male, 4 weeks old) were used to construct the AOM/DSS-induced CAC mice model. The mice were administered with 0.6 mg/g/d O. sinensis or C. militaris for 12 weeks. It's worth noting that fecal microbiota transplantation (FMT) and antibiotic treatment were used to investigated the complex interactions between the medicinal fungi, gut microbiota and colonic tumorigenesis.Results: O. sinensis treatment significantly increased the body weight and survival rate, reduced the number of colon tumors, improved the damage of colon epithelial tissue, restored the crypt structure and alleviate the colonic inflammation in AOM/DSS-treated mice. RT-qPCR results indicated that O. sinensis partly regulated the Wnt/β-catenin signaling via alleviating the overexpression of β-catenin, TCF4 and c-Myc genes in adjacent noncancerous tissues. Compared with C. militaris, O. sinensis showed better anti-tumor activity. Gut microbiota analysis revealed that O. sinensis reversed the decline of gut microbiota diversity and the structural disorder induced by AOM/DSS. Spearman's correlation analysis showed that O. sinensis promoted the growth of Parabacteroides goldsteinii and Bifidobacterium pseudolongum PV8-2, which were positively correlated with the anti-tumor activity and the production of SCFAs. FMT combined with antibiotic treatment showed that horizontal fecal transfer derived from O. sinensis-treated mice improved the intestinal inflammation and alleviated the colitis-associated tumorigenesis, which was consistent with the direct ingestion of O. sinensis.Conclusion: O. sinensis could better attenuate colitis-associated tumorigenesis compared with C. militaris. These effects might be at least partially due to the increased abundance of probiotics, especially P. goldsteinii and B. pseudolongum PV8-2.     

A review of three cases of Clostridium aldenense bacteremia

Three cases of Clostridium aldenense bacteremia are reported. C. aldenense is also associated with intra-abdominal infections and closely resembles Clostridium clostridioforme and therefore may be misidentified. C. aldenense may be a more frequent pathogen than appreciated and is generally fluoroquinolone resistant.     

Isolation of Atypical Candida albicans from the North Sea

Isolates of Candida albicans with sparse filamentation and weak fermentation were isolated from the surface microlayer of the North Sea, but not from subsurface waters. Such atypical isolates may be misidentified by using normal taxonomic procedures.     

First record of Teleogryllus (Brachyteleogryllus) marini Otte & Alexander, 1983 (Orthoptera: Gryllidae) in korea and discussion of its continued misidentification using DNA barcoding

DNA barcoding is useful for identifying species that are difficult to distinguish via morphological analysis. However, if the public DNA barcode database includes misidentified DNA samples, subsequent molecular studies could generate incorrect results. Here, we report a misidentified DNA barcode for the North Coastal Black Field Cricket Teleogryllus (Brachyteleogryllus) marini. T. (B.) marini is routinely misidentified using DNA barcoding; it has been reported as Teleogryllus (Brachyteleogryllus) commodus since its misidentification in various studies of Asian samples. Here, we report the first occurrence of T. (B.) marini in Korea, along with its morphological diagnosis, bioacoustic signals, and DNA barcoding findings. T. (B.) marini is transferred to the subgenus Brachyteleogryllus from the subgenus Teleogryllus, based on the male genitalia morphology and phylogenetic analysis. Genetic distance analyses have shown that cytochrome c oxidase I barcoding is useful for species identification of the genus Teleogryllus, but detailed morphological investigations are essential for DNA barcoding before any molecular study.     

Isolation of bacteria from mouse caecal samples and description of Bacteroides sartorii sp. nov

Caecal samples from wild-type and TNF^deltaARE mice were cultured on selective media containing bile salts, amino acids or casein macro-peptides. Twenty-two strains were isolated and identified by 16S rRNA gene sequencing. Twenty-one strains showed >98% similarity to known bacteria (Blautia spp., Clostridium innocuum, Enterococcus spp., Escherichia coli, Lactobacillus murinus, Parabacteroides goldsteinii and Shigella dysenteriae). One additional isolate, strain A-C2-0, was a new bacterium. The closest relatives were Bacteroides massiliensis, Bacteroides dorei and Bacteroides vulgatus (≤94% similarity). Strain A-C2-0 is a Gram-negative rod that does not form spores and has a G + C content of DNA of 41.5%. Its major cellular fatty acid is C_{15:0 ANTEISO}, and its major respiratory quinone is MK-9. Cells are aerotolerant but grow only under strict anoxic conditions. They are resistant to cefotaxime and tobramycin. When compared with related Bacteroides spp., the new bacterium was positive for α-arabinosidase, negative for glutamyl glutamic acid arylamidase and did not metabolise galactose, glucose, fructose, mannose, raffinose and sucrose. Strain A-C2-0 therefore merits recognition as a member of a novel species within the genus Bacteroides, for which the name Bacteroides sartorii is proposed. The type strain is A-C2-0^T (= DSM 21941^T = CCUG 57211^T).     

A revision of Japanese species of the genus Psammoecus Latreille (Coleoptera,Silvanidae)

Japanese species of the genus Psammoecus Latreille, 1829 are taxonomically revised. Four new species, P. scitus sp. n. (misidentified with P. quadrimaculatus), P. labyrinthicus sp. n., P. boreas sp. n. and P. omotoensis sp. n. are described. Psammoecus bipunctatus (Fabricius, 1792), P. trimaculatus Motschulsky, 1858 (misidentified with P. triguttatus), P. simoni Grouvelle, 1892, P. fasciatus Reitter, 1874 and P. triguttatus are redescribed. Another described species whose distribution in Japan is questionable. P. quadrimaculatus is also redescribed. Lectotype and paralectotype of P. fasciatus and P. triguttatus are designated.     

The cave population of Chaerilus Simon, 1877 from Palawan,Philippines, and description of a new species (Scorpiones: Chaerilidae)

The study of an important collection of scorpions, belonging to the genus Chaerilus, recently collected from a cave in the Palawan Island, Philippines, allows the clarification of the identity of this population, often misidentified with Chaerilus chapmani Vachon & Lourenço, 1985 known from caves in the Gunong Mulu National Park in Sarawak (Borneo). Chaerilus agnellivanniorum sp. n. is described from the Puerto Princesa Underground River Cave in Palawan Island based on 14 specimens, males, females, and juveniles. The new species is totally distinct morphologically from Chaerilus chapmani, a true troglobitic species. Chaerilus agnellivanniorum sp. n. may also be a true troglobitic element, but with a less marked degree of regression for several characters. Some comments on the ecology of the new species and on regional biogeography of Borneo and Palawan islands are also proposed.     

Description of a new species of Distenia (Coleoptera,Disteniidae, Disteniini) from Southeastern China,with?records and diagnoses of similar species

A new species, Distenia orientalis sp. n. is described from Southeastern China. It was misidentified as Distenia gracilis (Blessig, 1872) but can be separated from the latter by the color of antennae and legs, structure differences on scape, maxillary palp, pronotum, tibiae, punctures on elytra, etc. Three related species are carefully diagnosed and treated.     

Does dishonesty really invite third-party punishment? Results of a more stringent test

Many experiments have demonstrated that people are willing to incur cost to punish norm violators even when they are not directly harmed by the violation. Such altruistic third-party punishment is often considered an evolutionary underpinning of large-scale human cooperation. However, some scholars argue that previously demonstrated altruistic third-party punishment against fairness-norm violations may be an experimental artefact. For example, envy-driven retaliatory behaviour (i.e. spite) towards better-off unfair game players may be misidentified as altruistic punishment. Indeed, a recent experiment demonstrated that participants ceased to inflict third-party punishment against an unfair player once a series of key methodological problems were systematically controlled for. Noticing that a previous finding regarding apparently altruistic third-party punishment against honesty-norm violations may have been subject to methodological issues, we used a different and what we consider to be a more sound design to evaluate these findings. Third-party punishment against dishonest players withstood this more stringent test.     

The isolation of methyl β-orsellinate from Stereocaulon alpinum and comments on the isolation of 4,6-dihydroxy-2- methoxy-3-methylacetophenone from stereocaulon species

Methyl β-orsellinate has been isolated from chloroform extracts of Stereocaulon alpinum. It is shown that methyl β-orsellinate was probably previously misidentified as 4,6-dihydroxy-2-methoxy-3-methylacetophenone during work on Stereocaulon vesuvianum. Reports of the isolation of the latter thus appear to be erroneous. The status of methyl β-orsellinate as a naturally occurring metabolite is discussed.     

Effects of Including Misidentified Sharks in Life History Analyses: A Case Study on the Grey Reef Shark Carcharhinus amblyrhynchos from Papua New Guinea

Fisheries observer programs are used around the world to collect crucial information and samples that inform fisheries management. However, observer error may misidentify similar-looking shark species. This raises questions about the level of error that species misidentifications could introduce to estimates of species’ life history parameters. This study addressed these questions using the Grey Reef Shark Carcharhinus amblyrhynchos as a case study. Observer misidentification rates were quantified by validating species identifications using diagnostic photographs taken on board supplemented with DNA barcoding. Length-at-age and maturity ogive analyses were then estimated and compared with and without the misidentified individuals. Vertebrae were retained from a total of 155 sharks identified by observers as C. amblyrhynchos. However, 22 (14%) of these were sharks were misidentified by the observers and were subsequently re-identified based on photographs and/or DNA barcoding. Of the 22 individuals misidentified as C. amblyrhynchos, 16 (73%) were detected using photographs and a further 6 via genetic validation. If misidentified individuals had been included, substantial error would have been introduced to both the length-at-age and the maturity estimates. Thus validating the species identification, increased the accuracy of estimated life history parameters for C. amblyrhynchos. From the corrected sample a multi-model inference approach was used to estimate growth for C. amblyrhynchos using three candidate models. The model averaged length-at-age parameters for C. amblyrhynchos with the sexes combined were L¯∞ = 159 cm TL and L¯0 = 72 cm TL. Females mature at a greater length (l₅₀ = 136 cm TL) and older age (A₅₀ = 9.1 years) than males (l₅₀ = 123 cm TL; A₅₀ = 5.9 years). The inclusion of techniques to reduce misidentification in observer programs will improve the results of life history studies and ultimately improve management through the use of more accurate data for assessments.     

Rhizamoeba neglecta n. sp. (Amoebozoa,Tubulinea) from the bottom sediments of freshwater Lake Leshevoe (Valamo Island,North-Western Russia), with notes on the phylogeny of the order Leptomyxida

A new species of Leptomyxida, named Rhizamoeba neglecta was found during studies of the amoeba fauna of the inner Lake Leshevoe located at Valamo archipelago (The Lake Ladoga, North-Western Russia). Light-microscopical and ultrastructural studies indicated that it represents a new species of Leptomyxida. The partial 18S rDNA sequence of this amoeba is very similar to that of Leptomyxa reticulata.. These organisms, however, are very different in LM morphology and biology. Organisms assigned to the genus Rhizamoeba do not form a single clade in the 18S rDNA tree. This may indicate that the genus is an artificial grouping or that a number of studied strains were misidentified. The phylogeny and the systematics of leptomyxids require further investigation.     

Metabolic labeling of fucosylated glycoproteins in Bacteroidales species

Members of the Bacteroidales order are among the most abundant gram-negative bacteria of the human colonic microbiota. These species decorate their cell-surface glycoproteins with fucosylated glycans, which are believed to play important roles in host intestinal colonization. Currently, there is no method for the enrichment of these glycoproteins for their identification. Here, we describe a chemical approach directed toward labeling and detecting fucosylated glycoproteins from cultured Bacteroidales species, namely Bacteroides fragilis and Parabacteroides distasonis. We treated these bacteria with an alkyne-bearing fucose analog, which is metabolically integrated into the bacterial surface fucosylated glycoproteins. The alkyne-tagged glycoproteins can then react with azide-bearing biophysical probes via bioorthogonal click chemistry for detection or glycoproteomic analysis.     

A review of the threadfin breams of the genusNemipterus (Nemipteridae) from Japan and Taiwan,with description of a new species

Species of the fish genusNemipterus (Nemipteridae) from Japan and Taiwan are reviewed. A key, diagnoses and synonymies are provided for 9 species, including a new species:N. aurora sp. nov. (previously misidentified asN. delagoae Smith);N. bathybius Snyder;N. furcosus (Valenciennes) [mistakenly referred to asN. peronii (Valenciennes)];N. hexodon (Quoy et Gaimard);N. japonicus (Bloch);N. peronii (Valenciennes) [previously referred to asN. tolu (Valenciennes), a junior synonym];N. thosaporni Russell [previously misidentified asN. marginatus (Valenciennes)];N. virgatus (Houttuyn); andN. zysron (Bleeker) [previously referred to asN. metopias (Bleeker), a junior synonym].N. aurora is described from specimens from Taiwan, the Gulf of Thailand, East Malaysia and Indonesia. It appears to be closely allied toN. bipunctatus (Ehrenberg) (N. delagoae is a junior synonym), an Indian Ocean species, but the two species are readily distinguished on the basis of colour pattern of the dorsal and anal fins:N. aurora has a broad orange-yellow submedial stripe along the dorsal fin, and a lemon submedial stripe on the anal fin; whereas inN. bipunctatus the dorsal fin is uniformly rosy, and the anal fin has 2–4 wavy yellow stripes.     

Two New Species of Anastrepha Schiner (Diptera, Tephritidae) Closely Related to Anastrepha pickeli Lima

Anastrepha entodonta n. sp. and Anastrepha hadropickeli n. sp. are described and illustrated. The new species belong to the spatulata group. Both species occur sympatrically with Anastrepha pickeli Lima in the semiarid region of the state of Minas Gerais, Brazil. Anastrepha hadropickeli occurs also in the semiarid of the state of Rio Grande do Norte, Brazil, where it was misidentified as A. pickeli.     

Species of Rhytismatales on Berberis from China

Three species of Rhytismatales on Berberis were found from Sichuan and Yunnan provinces in China. Two of them were described as new species to science, namely Hypoderma minteri and Lophodermium johnstonii. The third one was a known species, Hypoderma berberidis. The phylogenetic relationships of these species within the Rhytismatales were analyzed based on internal transcriber spacer ribosomal DNA. The results showed that the species of the Rhytismatales on Berberis, unlike most species on pines, were not closely related. Three ITS sequences from GenBank, named there as Lirula macrospora, were used in this study, but were found to be from misidentified sources. A key to species of Rhytismatales on Berberis worldwide is also given.     

Influence of different data cleaning solutions of point‐occurrence records on downstream macroecological diversity models

Digital point‐occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time‐consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. Taking North American Ephedra as a model, we examined how different data cleaning pipelines (using, e.g., the GBIF web application, and four different R packages) affect downstream species distribution models (SDMs). We also assessed how data differed from expert data. From 13,889 North American Ephedra observations in GBIF, the pipelines removed 31.7% to 62.7% false positives, invalid coordinates, and duplicates, leading to datasets between 9484 (GBIF application) and 5196 records (manual‐guided filtering). The expert data consisted of 704 records, comparable to data from field studies. Although differences in the absolute numbers of records were relatively large, species richness models based on stacked SDMs (S‐SDM) from pipeline and expert data were strongly correlated (mean Pearson''s r across the pipelines: .9986, vs. the expert data: .9173). Our results suggest that all R package‐based pipelines reliably identified invalid coordinates. In contrast, the GBIF‐filtered data still contained both spatial and taxonomic errors. Major drawbacks emerge from the fact that no pipeline fully discovered misidentified specimens without the assistance of taxonomic expert knowledge. We conclude that application‐filtered GBIF data will still need additional review to achieve higher spatial data quality. Achieving high‐quality taxonomic data will require extra effort, probably by thoroughly analyzing the data for misidentified taxa, supported by experts.     

Typification of the genus Dileptus Dujardin, 1841 (Ciliophora,Rhynchostomatia)

In their monograph of the dileptids, Vďačný and Foissner (2012) could not clarify the type species of the genus Dileptus Dujardin, 1841. Thus, they suggested that the problem be referred to the International Commission on Zoological Nomenclature. However, recently we discovered that Dujardin (1841) has originally typified Dileptus with Amphileptus anser sensu Ehrenberg (1838) which is in fact a misidentified Amphileptus margaritifer Ehrenberg, 1833, a common species also originally classified in Dileptus. Under Article 70.3.2 of the Code, Dileptus margaritifer (Ehrenberg, 1833) Dujardin, 1841, thoroughly redescribed by Foissner et al. (1995), is now the type of Dileptus. This has the great advantages of historical continuity and that new combinations (names) are not required.