Judicial Opinion 129

Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.

Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

Filling the gaps: missing taxon names at the ranks of class, order and family

The International Code of Nomenclature of Prokaryotes (ICNP) recently underwent some major modifications regarding the higher taxonomic ranks. On the one hand, the phylum category was introduced into the ICNP, which rapidly led to the valid publication of more than forty names of phyla. On the other hand, a decision on the retroactivity of Rule 8 regarding the names of classes was made, which removed most of the nomenclatural uncertainty that had affected those names during the last decade. However, it turned out that a number of names at the ranks of class, order and family are either not validly published or are validly published but illegitimate, although these names occur in the literature and are based on the type genus of a phylum with a validly published name. A closer examination of the literature for these and similar cases indicates that the names are unavailable under the ICNP either because of minor formal errors in the original descriptions, because another name should have been adopted for the taxon when the name was proposed, because of taxonomic uncertainties that were settled in the meantime, or because the names were placed on the list of rejected names. The purpose of this article is to fill the gaps by providing the missing formal descriptions and to ensure that the resulting taxon names are attributed to the original authors who did the taxonomic work.

Solving the remaining problems with names of classes. Request for an Opinion

The legitimacy, spelling and grammatical gender of names of classes validly published under the International Code of Nomenclature of Prokaryotes (ICNP) is reviewed in the aftermath of the decision to make Rule 8 of the ICNP non-retroactive regarding the formation of such names. This ruling removed most of the nomenclatural uncertainty that affected names of classes but some issues remain to be solved. Some previously legitimate names of classes became illegitimate by this decision while others retained their illegitimacy. The Judicial Commission is asked to conduct according clarifications. It is proposed to place the names at the rank of class Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988, Archaeobacteria Murray 1988, Bacteria Haeckel 1894 (Approved Lists 1980), Firmibacteria Murray 1988, Microtatobiotes Philip 1956 (Approved Lists 1980), Oxyphotobacteria (ex Gibbons and Murray 1978) Murray 1988, Photobacteria Gibbons and Murray 1978 (Approved Lists 1980), Proteobacteria Stackebrandt et al. 1988, Schizomycetes Nägeli 1857 (Approved Lists 1980) and Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980) on the list of rejected names. It is also requested to orthographically correct the names Aquificae Reysenbach 2002, Chrysiogenetes Garrity and Holt 2002, Gemmatimonadetes Zhang et al. 2003, Opitutae Choo et al. 2007 and Verrucomicrobiae Hedlund et al. 1998.

Lists of names of prokaryotic Candidatus taxa

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

Risk factors for the infection with Brachyspira hyodysenteriae in pig herds

Swine dysentery (SD), caused by infection with Brachyspira hyodysenteriae, is a serious disease in pig production worldwide. Quantitative risk factors triggering the occurrence of infection are unknown. The present case-control study aimed at identifying major risk factors related to presence of B. hyodysenteriae in pig herds. Twenty case herds and 60 randomly selected control herds with a minimum herd size of '10 sows/ 80 fattening pigs' were examined by means of a questionnaire-based interview and a herd examination. Herds with previous eradication of SD were excluded. Logistic regression models revealed that the 'positive/suspicious SD status of source herds', the regular application of treatment, purchasing more than 4 batches/ year, contact to foxes, diagnostics performed during last 12 months, liquid feeding systems, rats on farm, and >250 fatting places were associated with higher chances of a herd to be infected. On the contrary, having different sources of grower pigs within one batch, the presence of raptor birds and the presence of martens in the region were associated with fewer chances of being infected. The final multivariable logistic regression model identified purchasing more than 4 batches/ year (OR = 7.5, 95 % CI 1.8-54.3) and contact to foxes (OR = 5.9; 97.5 % CI 1.2-34.6) as the two main risk factors in our study. 'More than 4 batches/ year' implies continuous herd management supporting persistence of B. hyodysenteriae in an infected herd, but also increased number of purchases each increasing the risk of B. hyodysenteriae introduction by carrier pigs or transport vehicles. Foxes might be infected with B. hyodysenteriae by feeding on positive piglets and rodents. Besides, 'contact to foxes' might represent a lack in biosecurity. In conclusion, the risk factors detected underline the importance of biosecurity in SD prevention and control.

Acuticoccus sediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean and proposal of Acuticoccaceae fam. nov

A Gram-staining negative, aerobic, oval-shaped bacterium, designated strain PTG4-2^T, was isolated from deep-sea sediment of the Indian Ocean. Growth was observed with 1-9 % (w/v) NaCl with optimal growth with 3 %, at pH 6.0-10.0 with an optimum of pH 7.0, and at 4-40 °C with an optimum of 30 °C. Positive for catalase and oxidase. The results of a 16S rRNA gene sequence comparison indicated that PTG4-2^T was most closely related to Acuticoccus yangtzensis JL1095^T (97.3 %), followed by Acuticoccus kandeliae J103^T (96.5 %), all other species shared <93 % sequence similarity. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PTG4-2^T forms a distinct lineage within the genus Acuticoccus, and revealed that the genus Acuticoccus forms a novel family-level clade in the order Rhizobiales. The ANI and the DNA-DNA hybridization estimate values between PTG4-2^T and two type strains (A. yangtzensis JL1095^T and A. kandeliae J103^T) were 79.9-76.2 % and 23.1-20.8 %, respectively. PTG4-2^T contained Q-10 as the predominant ubiquinone. The principal fatty acids (>5 %) were summed feature 8 [C18 : 1ω7c/ω6c (72.2 %)], C18 : 0 (8.4 %), C20 : 1ω7c (6.4 %) and C16 : 0 (6.3 %). The polar lipids consisted of phosphatidylglycerol, three unidentified phospholipids, two unidentified glycolipids, one unidentified aminolipid and one unknown lipid. The DNA G+C content of PTG4-2^T is 69.2 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, PTG4-2^T should be classified as representing a novel species of the genus Acuticoccus, for which the name Acuticoccus sediminis sp. nov. is proposed, with the type strain PTG4-2^T (=MCCC 1A01274^T=KCTC 52323^T). In addition, a novel family, Acuticoccaceae fam. nov., is proposed to accommodate the genus Acuticoccus.

An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017

Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.

Paludirhabdus telluriireducens gen. nov., sp. nov. and Paludirhabdus pumila sp. nov., isolated from soil of a mountain wetland and emended description of Gorillibacterium massiliense

Two strains of Gram-stain-positive, endospore-forming, motile by means of peritrichous flagella, aerobic or facultative anaerobic, and rod-shaped bacteria that were designated ON8^T and ON6^T were isolated from soil collected from a mountain wetland in Gwang-ju, Republic of Korea. The isolates were catalase-positive and oxidase-negative. Cells of ON8^T and ON6^T grew at 15-35 °C (optimal 30 °C) and 15-40 °C (optimal 30 °C), respectively. The major menaquinone was MK-7 and the major cellular fatty acids (>10 % of the total) were anteiso-C15 : 0, iso-C15 : 0, C14 : 0 and C16 : 0. The predominant polar lipids were diphosphatidylglycerol, aminophospholipid and phospholipid. Meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C contents of strains ON8^T and ON6^T were 50.6 and 53.5 mol%, respectively, and the 16S rRNA gene sequence analysis showed that the nearest phylogenetic neighbour of both strains was Gorillibacterium massiliense G5^T (93.9 %), followed by the members of the genus Paenibacillus in the family Paenibacillaceae. The DNA-DNA hybridization relatedness value between ON8^T and ON6^T was 44.1 %, which indicated that they represented distinct species. Based on polyphasic characteristics, a novel genus is proposed with the name Paludirhabdus gen. nov., which consists of two species, Paludirhabdus telluriireducens sp. nov. (the type species; type strain ON8^T=KACC 19267^T=JCM 31958^T) and Paludirhabdus pumila sp. nov. (type strain ON6^T=KACC 19266^T=JCM 31957^T).

Characterization of Brachyspira communities from clinical cases of swine mucohaemorrhagic diarrhea through deep sequencing of the NADH oxidase (nox) gene

Swine dysentery is traditionally associated with Brachyspira hyodysenteriae, but the re-emergence of Brachyspira-associated disease in North America associated with a novel causative species, B. hampsonii, is now a concern for swine producers. The pathogenesis of Brachyspira-associated disease is not completely understood, and it is not known whether mixed infections of Brachyspira spp. are important in disease development. Deep sequencing of partial sequences of the nox gene amplified with genus-specific primers was used to detect Brachyspira spp. in 55 fecal samples from clinical cases of mucohaemorrhagic diarrhea in pigs from Western Canada that had been identified as positive for one or more Brachyspira species using established diagnostic tests. Synthetic mixtures of Brachyspira genomic DNA were included in the study to define detection limits for the technique and identify biases in detection of different species. Multiple species were detected in all clinical cases for which sufficient nox sequence data were generated (n = 47), indicating that mixed species Brachyspira infections are common, although in most cases, one species accounted for at least half of the sequences identified. In all cases, the species detected in the original diagnostic investigation of each case was also detected by nox sequencing. Results from synthetic communities indicated that the method was highly reproducible, but also indicated potential PCR bias against B. hampsonii genomovar I. Deep sequencing of the nox gene target is a suitable method for simultaneous detection of multiple Brachyspira species in clinical case material that may offer advantages over current, more targeted diagnostic approaches for investigating the significance of mixed infections in disease development.

A review of methods used for studying the molecular epidemiology of Brachyspira hyodysenteriae

Brachyspira (B.) spp. are intestinal spirochaetes isolated from pigs, other mammals, birds and humans. In pigs, seven Brachyspira spp. have been described, i.e. B. hyodysenteriae, B. pilosicoli, B. intermedia, B. murdochii, B. innocens, B. suanatina and B. hampsonii. Brachyspira hyodysenteriae is especially relevant in pigs as it causes swine dysentery and hence considerable economic losses to the pig industry. Furthermore, reduced susceptibility of B. hyodysenteriae to antimicrobials is of increasing concern. The epidemiology of B. hyodysenteriae infections is only partially understood, but different methods for detection, identification and typing have supported recent improvements in knowledge and understanding. In the last years, molecular methods have been increasingly used. Molecular epidemiology links molecular biology with epidemiology, offering unique opportunities to advance the study of diseases. This review is based on papers published in the field of epidemiology and molecular epidemiology of B. hyodysenteriae in pigs. Electronic databases were screened for potentially relevant papers using title and abstract and finally, Barcellos et al. papers were systemically selected and assessed. The review summarises briefly the current knowledge on B. hyodysenteriae epidemiology and elaborates on molecular typing techniques available. Results of the studies are compared and gaps in the knowledge are addressed. Finally, potential areas for future research are proposed.