Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential

Members of the gut microbiota genus Bifidobacterium are widely distributed human and animal symbionts believed to exert beneficial effects on their hosts. However, in-depth genomic analyses of animal-associated species and strains are somewhat lacking, particularly in wild animal populations. Here, to examine patterns of host specificity and carbohydrate metabolism capacity, we sequenced whole genomes of Bifidobacterium isolated from wild-caught small mammals from two European countries (UK and Lithuania). Members of Bifidobacterium castoris, Bifidobacterium animalis and Bifodobacterium pseudolongum were detected in wild mice (Apodemus sylvaticus, Apodemus agrarius and Apodemus flavicollis), but not voles or shrews. B. castoris constituted the most commonly recovered Bifidobacterium (78% of all isolates), with the majority of strains only detected in a single population, although populations frequently harboured multiple co-circulating strains. Phylogenetic analysis revealed that the mouse-associated B. castoris clades were not specific to a particular location or host species, and their distribution across the host phylogeny was consistent with regular host shifts rather than host-microbe codiversification. Functional analysis, including in vitro growth assays, suggested that mouse-derived B. castoris strains encoded an extensive arsenal of carbohydrate-active enzymes, including putative novel glycosyl hydrolases such as chitosanases, along with genes encoding putative exopolysaccharides, some of which may have been acquired via horizontal gene transfer. Overall, these results provide a rare genome-level analysis of host specificity and genomic capacity among important gut symbionts of wild animals, and reveal that Bifidobacterium has a labile relationship with its host over evolutionary time scales

The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s–1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37–50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environmen

Polyplax gracilis Fahrenholz 1910

Polyplax gracilis Fahrenholz, 1910 Polyplax gracilis Fahrenholz, 1910: 715. Records in Baltic States: Latvia (Lapina 1959; Grinbergs 1980b). Hosts: M. minutus (LV). Europeandistribution: France, Germany, Hungary, Italy, Poland, Romania, Russia, Slovakia,(Blagoveshchensky 1964; Wegner 1966; Beaucournu 1968; Voicu & Straton 1968; Piotrowski 1970; Krištofik & Dudich 2000a; Manilla 2003; Vas et al. 2012).Published as part of Kitrytė, Neringa & Baltrūnaitė, Laima, 2023, Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist, pp. 1-46 in Zootaxa 5353 (1) on page 19, DOI: 10.11646/zootaxa.5353.1.1, http://zenodo.org/record/842673

Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist

Kitrytė, Neringa, Baltrūnaitė, Laima (2023): Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist. Zootaxa 5353 (1): 1-46, DOI: 10.11646/zootaxa.5353.1.1, URL: http://dx.doi.org/10.11646/zootaxa.5353.1.

Haemogamasus hirsutosimilis Willmann 1952

Haemogamasus hirsutosimilis Willmann, 1952 Haemogamasus hirsutosimilis Willmann, 1952: 403. Records in Baltic States: Latvia (Lapina 1959; 1988; Grinbergs 1960; 1961a; 1961d; 1980a; Arzamasov 1968; Salmane 2001), Lithuania (Podėnaitė 1960; 1979; Kadytė & Jezerskienė 1986; Arnastauskienė et al. 1989; Kitrytė et al. 2022; current study). Hosts: S. araneus (LV), A. agrarius (LT), A. flavicollis (LV, LT), A. amphibius (LV), C. glareolus (LV, LT). European distribution: Austria, Belarus, Germany, Hungary, Moldova, Poland, Romania, Russia, Slovakia, Sweden, Ukraine, the United Kingdom (Bregetova et al. 1955; Bregetova 1956; Pirjanik 1962; Evans & Till 1966; Mahnert 1971a; Edler 1972; Haitlinger 1980; 2011; 2015; Ambros 1987; Schmölzer & Neudorf 1995; Chikilevskaya et al. 1998; Mašán & Fenďa 2010; Maaz et al. 2018).Published as part of Kitrytė, Neringa & Baltrūnaitė, Laima, 2023, Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist, pp. 1-46 in Zootaxa 5353 (1) on page 9, DOI: 10.11646/zootaxa.5353.1.1, http://zenodo.org/record/842673

Ixodes apronophorus Schulze 1924

Ixodes apronophorus Schulze, 1924 Ixodes apronophorus Schulze, 1924: 281. Records in Baltic States: Estonia (Kužilnõi 1961), Latvia (Grinbergs 1961a; 1961b; Andersone 1963; Salmane 2012), Lithuania (Podėnaitė 1979; Arnastauskienė et al. 1989). Hosts: M. musculus (LV), A. amphibius (EE, LV), C. glareolus (LT). European distribution: Austria, Belarus, Belgium, Bulgaria, the Czech Republic, Denmark, France, Germany, Hungary, Moldova, the Netherlands, Poland, Romania, Russia, Slovakia, Switzerland, Ukraine, the United Kingdom (Feider 1965; Sosnina et al. 1969; Aeschlimann et al. 1970; Černy 1972; Gilot et al. 1976b; Filippova 1977; Martyn 1988; Jaenson et al. 1994; Petney et al. 2012; Hornok et al. 2020; Rubel & Brugger 2022; Karbowiak et al. 2023).Published as part of Kitrytė, Neringa & Baltrūnaitė, Laima, 2023, Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist, pp. 1-46 in Zootaxa 5353 (1) on page 16, DOI: 10.11646/zootaxa.5353.1.1, http://zenodo.org/record/842673

Megabothris walkeri

Megabothris walkeri (Rothschild, 1902) Ceratophyllus walkeri Rothschild, 1902: 225. Records in Baltic States: Estonia (Vilbaste 1959; Daiter 1961a; Pototski 1989; 1990b; Pototski et al. 1993), Latvia (Eglitis 1957; Lapina 1959; Grinbergs 1960; 1961a; 1961d; 1964; 1976; Andersone 1963), Lithuania (Likevičienė 1957; Kadytė 1964; Arnastauskienė et al. 1989; Lipatova & Paulauskas 2010; Lipatova 2015; current study). Hosts: S. araneus (LV, LT), A. agrarius (LV, LT), A. flavicollis (LV, LT), M. minutus (LT), M. musculus (LT), R. norvegicus (LV), A. oeconomus (LT), A. amphibius (LV), C. glareolus (EE, LV, LT), M. agrestis (EE, LV, LT), M. arvalis (LV, LT). Host specificity: moderately specific parasite of voles of the genus Microtus ( S i = 0.75). European distribution: Austria, Belarus, Belgium, Czech Republic, Denmark, Finland, France, Germany, the Netherlands, Norway, Poland, Romania, Russia, Slovakia, Switzerland, Ukraine, the United Kingdom (Rosický 1944; Séguy 1944; Cooreman 1950; Smit 1962; 1967; 1969; Mehl 1967; Adamovich 1971; Suciu 1973; Weidner 1973; George 1974; Chikilevskaya 1977; Haitlinger 1977b; 2011; 2015; Libois 1979; Vashchonok 1996; Striese et al. 2012; Baláž & Zigová 2020).Published as part of Kitrytė, Neringa & Baltrūnaitė, Laima, 2023, Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist, pp. 1-46 in Zootaxa 5353 (1) on page 24, DOI: 10.11646/zootaxa.5353.1.1, http://zenodo.org/record/842673

Pulex Linnaeus 1758

Genus Pulex Linnaeus, 1758 Pulex Linnaeus, 1758: 614.Published as part of Kitrytė, Neringa & Baltrūnaitė, Laima, 2023, Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist, pp. 1-46 in Zootaxa 5353 (1) on page 29, DOI: 10.11646/zootaxa.5353.1.1, http://zenodo.org/record/842673

Ceratophyllus fringillae

Ceratophyllus fringillae (Walker, 1856) Pulex fringillae Walker, 1856: 4. Records in Baltic States: Lithuania (Podėnaitė 1979). Hosts: unidentified host. European distribution: Austria, Belgium, Czech Republic, Denmark, Finland, France, Italy, Germany, Greece, the Netherlands, Poland, Russia, Sweden, Switzerland, the United Kingdom, former Yugoslavia (Séguy 1944; Cooreman 1950; Rosický 1950; Niewiadomska 1953; Smit 1962; 1969; Weidner 1973; George 1974; Vashchonok 1996; Iori et al. 2003). Notes: These records are questionable (also suggested by Pakalniškis & Žygutienė 2004) since fleas of this species are specific parasites of birds (Vashchonok 1996; Brinck-Lindroth & Smit 2007).Published as part of Kitrytė, Neringa & Baltrūnaitė, Laima, 2023, Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist, pp. 1-46 in Zootaxa 5353 (1) on page 22, DOI: 10.11646/zootaxa.5353.1.1, http://zenodo.org/record/842673

Laelaps clethrionomydis Lange 1955

Laelaps clethrionomydis Lange, 1955 Laelaps clethrionomydis Lange, 1955: 330. Records in Baltic States: Latvia (Lapina 1959; 1988; Arzamasov 1968; Grinbergs 1982b; Salmane 2001), Lithuania (Kitrytė et al. 2022; current study). Hosts: S. araneus (LV, LT), A. flavicollis (LV), M. minutus (LT), C. glareolus (LV, LT). Host specificity: moderately specific parasite of C. glareolus ( S i = 0.71). European distribution: Austria, Belarus, Bulgaria, Finland, Hungary, Norway, Romania, Russia, Slovakia, Sweden (Bregetova et al. 1955; Bregetova 1956; Edler 1969; Mahnert 1971a; Mehl 1979; Haitliger 1980; Ambros 1987; Schmölzer & Neudorf 1995; Chikilevskaya et al. 1998; Beron 2007; Mašán & Fenďa 2010; Huhta 2015).Published as part of Kitrytė, Neringa & Baltrūnaitė, Laima, 2023, Ectoparasitic mites, ticks (Acari: Trombidiformes, Mesostigmata, Ixodida) and insects (Insecta: Psocodea, Siphonaptera) of ground-dwelling small mammals in the Baltic States. An annotated checklist, pp. 1-46 in Zootaxa 5353 (1) on page 12, DOI: 10.11646/zootaxa.5353.1.1, http://zenodo.org/record/842673