Sayaka Tsuchida

Bifidobacterium moukalabense sp. nov., isolated from the faeces of wild west lowland gorilla (Gorilla gorilla gorilla).

Gram-staining-positive anaerobic rods were isolated from the faeces of a wild lowland gorilla (Gorilla gorilla gorilla) in Moukalaba-Doudou National Park, Gabon, and strain GG01(T) was taxonomically investigated. Based on phylogenetic analyses and specific phenotypic characteristics, the strain belonged to the genus Bifidobacterium. Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain GG01(T) formed a single monophyletic cluster and had a distinct line of descent. Based on 16S rRNA gene sequence similarity, the type strains of Bifidobacterium catenulatum JCM 1194(T) (98.3%) and Bifidobacterium pseudocatenulatum (98.1%) JCM 1200(T) were the most closely related to this novel strain, although it was clear that they belonged to different species. hsp60 sequences also supported these relationships. The DNA G+C content of this novel strain was 60.1 mol%. Bifidobacterium moukalabense sp. nov. (type strain GG01(T) = JCM 18751(T) = DSM 27321(T)) is proposed.

Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae

Intestinal microbiota are characterized by host-specific microorganisms, which have been selected through host-microbe interactions under phylogenetic evolution and transition of feeding behavior by the host. Although many studies have focused on disease-related intestinal microbiota, the origin and evolution of host-specific intestinal microbiota have not been well elucidated. Pig is the ideal mammal model to reveal the origin and evolution of host-specific intestinal microbiota because their direct wild ancestor and close phylogenetic neighbors are available for comparison. The pig has been recognized as a Lactobacillus-type animal. We analyzed the intestinal microbiota of various animals in Suidae: domestic pigs, wild boars and Red river hogs to survey the origin and evolution of Lactobacillus-dominated intestinal microbiota by metagenomic approach and following quantitative PCR confirmation. The metagenomic datasets were separated in two clusters; the wild animal cluster being characterized by a high abundance of Bifidobacterium, whereas the domesticated (or captured) animal cluster by Lactobacillus. In addition, Enterobacteriaceae were harbored as the major family only in domestic Sus scrofa. We conclude that domestication may have induced a larger Enterobacteriaceae population in pigs, and the introduction of modern feeding system further caused the development of Lactobacillus-dominated intestinal microbiota, with genetic and geographical factors possibly having a minor impact.

Molecular features of hookworm larvae (Necator spp.) raised by coproculture from Ugandan chimpanzees and Gabonese gorillas and humans.

Species composition of Necator hookworms was surveyed in (i) Ugandan chimpanzees living around farms and villages at Bulindi, (ii) Gabonese gorillas under habituation in Moukalaba-Doudou National Park (MDNP), and (iii) Gabonese villagers living adjacent to MDNP. Internal transcribed spacers (ITS) of rDNA and partial cytochrome c oxidase subunit 1 (Cox1) gene of mtDNA were analyzed from larvae obtained by coproculture. Three ITS types (I, II and III) and three Cox1 haplotype groups (A, B and C) were demonstrated. ITS type I and Cox1 haplotype group A, representing Necator americanus, were demonstrated in the hookworm larvae from Gabonese gorillas and humans, but not from Ugandan chimpanzees. Type II and haplotype groups B and C, presumably representing N. gorillae, were found in larvae from Ugandan chimpanzees and Gabonese gorillas and humans. These features were overall similar with those found previously in the Central African Republic. Meanwhile, type III was proven in a larva from a Gabonese gorilla as the first demonstration from a non-human primate. Cox1 haplotypes obtained from Ugandan chimpanzees formed a subgroup within group B, presumably reflecting dispersal and diversification processes of the apes.

Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans

Preservation of indigenous gastrointestinal microbiota is deemed to be critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we investigated cecal bacterial communities in wild Japanese rock ptarmigans (Lagopus muta japonica) and compared them with those in Svalbard rock ptarmigans (L. m. hyperborea) in captivity. Ultra-deep sequencing of 16S rRNA gene indicated that the community structure of cecal microbiota in wild rock ptarmigans was remarkably different from that in captive Svalbard rock ptarmigans. Fundamental differences between bacterial communities in the two groups of birds were detected at the phylum level. Firmicutes, Actinobacteria, Bacteroidetes and Synergistetes were the major phyla detected in wild Japanese rock ptarmigans, whereas Firmicutes alone occupied more than 80% of abundance in captive Svalbard rock ptarmigans. Furthermore, unclassified genera of Coriobacteriaceae, Synergistaceae, Bacteroidaceae, Actinomycetaceae, Veillonellaceae and Clostridiales were the major taxa detected in wild individuals, whereas in zoo-reared birds, major genera were Ruminococcus, Blautia, Faecalibacterium and Akkermansia. Zoo-reared birds seemed to lack almost all rock ptarmigan-specific bacteria in their intestine, which may explain the relatively high rate of pathogenic infections affecting them. We show evidence that preservation and reconstitution of indigenous cecal microflora are critical for successful ex situ conservation and future re-introduction plan for the Japanese rock ptarmigan.

Draft Genome Sequence of Lactobacillus gorillae Strain KZ01T, Isolated from a Western Lowland Gorilla

ABSTRACT Here, we report the draft genome sequence of Lactobacillus gorillae strain KZ01T isolated from a western lowland gorilla (Gorilla gorilla gorilla). This genome sequence will be helpful for the comparative genomics between human and nonhuman primate-associated Lactobacillus.

Lactobacillus gorillae sp. nov., isolated from the faeces of captive and wild western lowland gorillas (Gorilla gorilla gorilla)

Four strains of Gram-staining-positive, anaerobic rods were isolated from the faeces of western lowland gorillas (Gorilla gorilla gorilla). Three strains, KZ01(T), KZ02 and KZ03, were isolated at the Kyoto City Zoo, Japan, and one strain, GG02, was isolated in the Moukalaba-Doudou National Park, Gabon. These strains were investigated taxonomically. These strains belonged to the Lactobacillus reuteri phylogenetic group according to phylogenetic analysis based on 16S rRNA gene sequences and specific phenotypic characteristics. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains KZ01(T), KZ02, KZ03 and GG02 formed a single monophyletic cluster and had a distinct line of descent. Based on sequence similarity of the 16S rRNA gene, Lactobacillus fermentum JCM 1173(T) (96.6 %) was the closest neighbour to these novel strains, although it was clear that these strains belonged to a different species. Partial pheS sequences also supported these relationships. DNA-DNA relatedness between strain KZ01(T) and L. fermentum JCM 1173(T) was less than 22 % and the DNA G+C content of strain KZ01(T) was 50.7 mol%. The cell-wall peptidoglycan type was A4β (l-Orn-d-Asp) and the major fatty acids were C16 : 0, C18 : 1ω9c and C19 : 1 cyclo 9,10. Therefore, based on phylogenetic, phenotypic and physiological evidence, these strains represent a novel species of the genus Lactobacillus, for which the name Lactobacillus gorillae sp. nov. is proposed. The type strain is KZ01(T) ( = JCM 19575(T) = DSM 28356(T)).

Isolation of Streptococcus gallolyticus with very high degradability of condensed tannins from feces of the wild Japanese rock ptarmigans on Mt. Tateyama

None of the authors of this manuscript has any financial or personal relationship with other people or organizations that could inappropriately influence their work. ing on the snow-covered Mt. Tateyama, were at least 80 times more active in tannase than those previously shown in the strain from koala, Phascolarctos cinereus, and at least 8 times more active than those in the brushtail possum, Trichosurus vulpecula. Freshly defecated cecal feces, or rectal feces, were promptly collected from the snow following close observation (ca. 5 m distance) of the birds on Mt. Tateyama at the end of November 2014 and the middle of May 2015. A portion of the feces was streaked on a BL plate (Nissui, Tokyo, Japan), which was supplemented with 5% defibrinated chicken blood, or a GAM plate (Nissui, Tokyo, Japan). Plates were immediately placed in a plastic bag containing an Anaeropouch (Mitsubishi Gas Chemical, Tokyo, Japan) and then incubated at 41∞C in a portable incubator after returning to the Raicyo-so Lodge (15–30 minute after collection), where electricity was available. After overnight culture, plates were placed in a styrene foam box with cooling devices and transported to our laboratory. Visible colonies were chosen and re-streaked on the same plate medium. After purification, partial 16S rRNA gene sequences were determined as described previously (Tsuchida et al., 2014). Similar sequences were retrieved from public databases, and calculations for pairwise sequence similarities for 16S rRNA genes were made using MEGA version 6.06 (Tamura et al., 2013). Multiple sequence alignments were performed using the CLUSTAL W program (Thompson et al., 1994) and phylogenetic trees were constructed using the neighbor-joining method (Saitou and Nei, 1987). Tree topology was evaluated by a bootstrap analysis with 1000 replicates using CLUSTAL W. In accordance with Osawa (1990), we prepared tanninIsolation of Streptococcus gallolyticus with very high degradability of condensed tannins from feces of the wild Japanese rock ptarmigans on Mt. Tateyama

Decaying toxic wood as sodium supplement for herbivorous mammals in Gabon.

African rainforest harbors herbivores at high density. However, because plants and soils typically lack in some essential minerals, rainforest is not always a suitable habitat for herbivores. How they fulfill the mineral requirements is therefore an important question to animal ecology and conservation. Although large marshes, called ‘bais’, are often mentioned as efficient mineral-resource, little information on other sodium resources has still been available. Our laboratory works and field surveys found that a peculiar item, decaying wood stumps of Anthostema aubryanum, played as a major sodium resource for herbivores in Moukalaba-Doudou National Park, Gabon. When A. aubryanum is alive, the sodium content of its bark is low and its latex is toxic. Sodium is accumulated in decaying stumps (mean=1,343 mg/kg dry matter). Eight herbivores visited stumps to ingest the dead wood. Fecal sample analysis revealed that western lowland gorillas, a species most-frequently using the stumps, consumed large amount of the dead wood as regular food. Our findings suggest that decaying A. aubryanum is critical sodium-resources and is a key species for herbivores in our study area. Importance of the A. aubryanum may be particularly large there, because it is a limited sodium-rich material that is available year round. Our study site is known as the site where the densities of several herbivores are among the highest at Central Africa. The relatively high herbivores density in our study site may partly depend on decaying A. aubryanum as sodium resources.

Genomic Characteristics of Bifidobacterium thermacidophilum Pig Isolates and Wild Boar Isolates Reveal the Unique Presence of a Putative Mobile Genetic Element with tetW for Pig Farm Isolates

Genomic analysis was performed on seven strains of Bifidobacterium thermacidophilum, a Sus-associated Bifidobacterium. Three strains from the feces of domestic pigs (Sus scrofa domesticus) and four strains from the rectal feces of free-range Japanese wild boars (S. s. scrofa) were compared. The phylogenetic position of these isolates suggested by genomic analyses were not concordant with that suggested by 16S rRNA sequence. There was biased distribution of genes for virulence, phage, metabolism of aromatic compounds, iron acquisition, cell division, and DNA metabolism. In particular four wild boar isolates harbored fiber-degrading enzymes, such as endoglucanase, while two of the pig isolates obtained from those grown under an intensive feeding practice with routine use of antimicrobials, particularly tetracycline harbored a tetracycline resistance gene, which was further proved functional by disk diffusion test. The tetW gene is associated with a serine recombinase of an apparently non-bifidobacterial origin. The insertion site of the tetW cassette was precisely defined by analyzing the corresponding genomic regions in the other tetracycline-susceptible isolates. The cassette may have been transferred from some other bacteria in the pig gut.

Cecal Microbiome Analyses on Wild Japanese Rock Ptarmigans (Lagopus muta japonica) Reveals High Level of Coexistence of Lactic Acid Bacteria and Lactate-Utilizing Bacteria

Preservation of indigenous gastrointestinal microbiota is critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we compared the cecal microbial composition of wild living Japanese rock ptarmigans (Lagopus muta japonica) in different locations of Japanese mountains, and the dominant cecal microbial structure of wild Japanese rock ptarmigans is elucidated. Coriobacteraceae and Lachnospraceae were the two dominant bacterial families in all samples analyzed. At the genus level, 10 genera Olsenella, Actinomyces, Megasphaera, Slackia, Cloacibacillus, Bifidobacterium, Escherichia, Dialister, Megamonas, and Bilophila were dominant. These results reveal the high level of coexistence of lactic acid bacteria (Olsenella and Bifidobacterium) and lactate-utilizing bacteria (Megasphaera). This coexistence should be taken into account for the successful breeding of captive Japanese rock ptarmigans in the national conservation program.