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Borrelia burgdorferi s.s. is a Gram-negative spirochaete, the aetiological agent of Lyme disease, the most common vector-borne disease in the Northern hemisphere. Reports on the presence of B. burgdorferi in central Mexico have been strongly criticized, since these were based only on unspecific serological methods. Furthermore, the worldwide genetic diversity of B. burgdorferi s.s. has not been evaluated. For this reason, the aim of the present study was to confirm the presence of B. burgdorferi in the central area of Mexico and to evaluate its relationship with regard to the global genetic diversity of B. burgdorferi s.s. To achieve this, fragments of the flagellin and the outer surface protein A genes were amplified from ear biopsies of the arboreal wild endemic mice Habromys schmidlyi. With these sequences, a concatenated Bayesian analysis was performed to confirm the identity of B. burgdorferi s.s. Afterwards, the global genetic diversity of this bacterial species was evaluated using our sequences and those available in GenBank. A prevalence of 10.4% (5/48) of H. schmidlyi infected with Borrelia sp. was detected, and the phylogenetic analyses confirmed the identity of B. burgdorferi s.s. Using both genes, the genetic diversity was low. However, genetic structuring analyses revealed that populations of western United States and those from Mexico formed slightly different genetic groups, separated from the populations of the rest of the world. Our study not only confirms the presence of this bacterium in central Mexico, but also shows the most southern record of this bacterium so far. It also highlights the importance of H. schmidlyi as a new potential host of this bacterial species. Our study also provides first genetic data on an incipient process of divergence in B. burgdorferi s.s. populations of eastern United States and central Mexico.

A novel, obligately anaerobic bacterium (strain SURF-ANA1T) was isolated from deep continental subsurface fluids at a depth of 1500 m below surface in the former Homestake Gold Mine (now Sanford Underground Research Facility, in Lead, South Dakota, USA). Cells of strain SURF-ANA1Twere Gram-negative, helical, non-spore-forming and were 0.25–0.55×5.0–75.0 µm with a wavelength of 0.5–0.62 µm. Strain SURF-ANA1Tgrew at 15–50 °C (optimally at 40 °C), at pH 4.8–9.0 (pH 7.2) and in 1.0–40.0 g l−1NaCl (10 g l−1NaCl). The strain grew chemoheterotrophically with hydrogen or mono-, di- and polysaccharides as electron donors. The major cellular fatty acids in order of decreasing abundance (comprising >5% of total) were 10-methyl C16:0, iso-C15:0, C18:2and C18:0dimethyl acetal (DMA) and C20:0methylene-nonadecanoic acid. Phylogenetic analysis based on the 16S rRNA gene sequence of strain SURF-ANA1Tindicated a closest relationship with the recently characterizedRectinema cohabitans(99%). Despite high sequence identity, because of its distinct physiology, morphology and fatty acid profile, strain SURF-ANA1Tis considered to represent a novel species within the genusRectinema, for which the nameRectinema subterraneumsp. nov. is proposed. To our knowledge, this is the first report of an isolate within the phylumSpirochaetesfrom the deep (>100 m) terrestrial subsurface. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and genomic sequences of strain SURF-ANA1Tare KU359248 and GCF 009768935.1, respectively. The type strain ofRectinema subterraneumis SURF-ANA1T(=ATCC TSD-67=JCM 32656).

Borrelia burgdorferi is the causative agent of Lyme disease and is transmitted to vertebrate hosts by Ixodes spp. ticks. The spirochaete relies heavily on its arthropod host for basic metabolic functions and has developed complex interactions with ticks to successfully colonize, persist and, at the optimal time, exit the tick. For example, proteins shield spirochaetes from immune factors in the bloodmeal and facilitate the transition between vertebrate and arthropod environments. On infection, B. burgdorferi induces selected tick proteins that modulate the vector gut microbiota towards an environment that favours colonization by the spirochaete. Additionally, the recent sequencing of the Ixodes scapularis genome and characterization of tick immune defence pathways, such as the JAK–STAT, immune deficiency and cross-species interferon-γ pathways, have advanced our understanding of factors that are important for B. burgdorferi persistence in the tick. In this Review, we summarize interactions between B. burgdorferi and I. scapularis during infection, as well as interactions with tick gut and salivary gland proteins important for establishing infection and transmission to the vertebrate host., Borrelia burgdorferi has a complex life cycle with several different hosts, causing Lyme disease when it infects humans. In this Review, Fikrig and colleagues discuss how B. burgdorferi infects and interacts with its tick vector to ensure onward transmission.

Lyme disease, as one of tick-borne diseases, has been a current epidemiological problem in Poland and in the world for several years. The proportion of borreliosis infections caused by B. burgdorferi spirochaetes is increasing. Difficulties diagnosing this disease with conventional methods have led to growing molecular biology research aimed at developing improved diagnostic tools. Molecular biology methods include all techniques that allow the detection and analysis of nucleic acids. Among them there are methods based on PCR reaction, molecular typing methods (MLST), new generation sequencing (NGS). The current development of this field gives great research opportunities. With regard to B. burgdorferi spirochete, molecular biology is used to: confirm Lyme borreliosis, identify and type Borreliella spirochetes, detect them in tick vectors or intermediate hosts, as well as to identify co-infections between different Borreliella species and other tick-borne pathogens. They are meant to significantly improve diagnostic analyzes. This paper reviews the current methods used for the detection and identification of B. burgdorferi. Molecular mechanisms for the survival of spirochetes in the host, infection vectors and clinical picture of Lyme disease were also discussed.

A Gram-stain-negative, obligatory anaerobic spirochaete (RCC2812T) was isolated from a faecal sample obtained from an individual residing in a remote Amazonian community in Peru. The bacterium showed highest 16S rRNA gene sequence similarity to the pig intestinal spirochete Treponema succinifaciens (89.48 %). Average nucleotide identity values between strain RCC2812T and all available Treponema genomes from validated type strains were all T was 41.24 mol%. Phenotypic characterization using the API-ZYM and API 20A systems confirmed the divergent position of this bacterium within the genus Treponema . Strain RCC2812T could be differentiated from the phylogenetically most closely related T. succinifaciens by the presence of alkaline phosphatase and α -glucosidase activities. Unlike T. succinifaciens , strain RCC2812T grew equally well with or without serum. Strain RCC2812T is the first commensal Treponema isolated from the human faecal microbiota of remote populations, and based on the collected data represents a novel Treponema species for which the name Treponema peruense sp. nov. is proposed. The type strain is RCC2812T (=LMG 31794T=CIP 111910T).

Simple Summary Borreliae are spirochaetes, which represent a heterogeneous phylum within bacteria. Spirochaetes are indeed distinguished from other bacteria for their spiral shape, which also characterizes Borreliae. This review describes briefly the organization of the phylum Spirocheteales with a digression about its pathogenicity and historical information about bacteria isolation and characterization. Among spirochaetes, Borrelia genus is here divided into three groups, namely the Lyme group (LG), the Echidna-Reptile group (REPG) and the Relapsing Fever group (RFG). Borreliae Part 1 deals with Lyme group and Echidna-Reptile group Borreliae, while the subject of Borreliae Part 2 is Relapsing Fever group and unclassified Borreliae. Lyme group Borreliae is organized here in sections describing ecology, namely tick vectors and animal hosts, epidemiology, microbiology, and Borrelia genome organization and antigen characterization. Furthermore, the main clinical manifestations in Lyme borreliosis are also described. Although included in the Lyme group due to their particular clinical features, Borrelia causing Baggio Yoshinari syndrome and Borrelia mayonii are described in dedicated paragraphs. The Borrelia Echidna-Reptile group has been recently characterized including spirochaetes that apparently are not pathogenic to humans, but infect reptiles and amphibians. The paragraph dedicated to this group of Borreliae describes their vectors, hosts, geographical distribution and their characteristics. Abstract Borreliae are divided into three groups, namely the Lyme group (LG), the Echidna-Reptile group (REPG) and the Relapsing Fever group (RFG). Currently, only Borrelia of the Lyme and RF groups (not all) cause infection in humans. Borreliae of the Echidna-Reptile group represent a new monophyletic group of spirochaetes, which infect amphibians and reptiles. In addition to a general description of the phylum Spirochaetales, including a brief historical digression on spirochaetosis, in the present review Borreliae of Lyme and Echidna-Reptile groups are described, discussing the ecology with vectors and hosts as well as microbiological features and molecular characterization. Furthermore, differences between LG and RFG are discussed with respect to the clinical manifestations. In humans, LG Borreliae are organotropic and cause erythema migrans in the early phase of the disease, while RFG Borreliae give high spirochaetemia with fever, without the development of erythema migrans. With respect of LG Borreliae, recently Borrelia mayonii, with intermediate characteristics between LG and RFG, has been identified. As part of the LG, it gives erythema migrans but also high spirochaetemia with fever. Hard ticks are vectors for both LG and REPG groups, but in LG they are mostly Ixodes sp. ticks, while in REPG vectors do not belong to that genus.

Integrons are bacterial genetic elements that can capture mobile gene cassettes. They are mostly known for their role in the spread of antibiotic resistance cassettes, contributing significantly to the global resistance crisis. These resistance cassettes likely originated from sedentary chromosomal integrons, having subsequently been acquired and disseminated by mobilised integrons. However, their taxonomic and environmental origins are unknown. Here, we use cassette recombination sites (attCs) to predict the origins of those resistance cassettes now spread by mobile integrons. We modelled the structure and sequence homology of 1,978 chromosomal attCs from 11 different taxa. Using these models, we show that at least 27% of resistance cassettes have attCs that are structurally conserved among one of three taxa (Xanthomonadales, Spirochaetes and Vibrionales). Indeed, we found some resistance cassettes still residing in sedentary chromosomal integrons of the predicted taxa. Further, we show that attCs cluster according to host environment rather than host phylogeny, allowing us to assign their likely environmental sources. For example, the majority of β-lactamases and aminoglycoside acetyltransferases, the two most prevalent resistance cassettes, appear to have originated from marine environments. Together, our data represent the first evidence of the taxonomic and environmental origins of resistance cassettes spread by mobile integrons., Ghaly et al. use cassette recombination sites to predict the origins of antibiotic resistance cassettes spread by mobile integrons. They find that more than a quarter of all resistance cassettes have recombination sites that are structurally conserved among one of three taxa (Xanthomonadales, Spirochaetes and Vibrionales).

The objectives of this study were (a) to evaluate skin biopsies of udder sores and negative control cows for the presence of mange and nonbacterial pathogens via histopathology and (b) to identify and compare bacterial abundance in the lesions of cows with udder sores and from the skin of healthy controls from the same farms. Cows from 3 dairy farms with (n = 23) and without (n = 12) udder sore lesions were enrolled, and punch biopsies (23 lesions, 23 negative control samples of cows with lesions, and 12 control samples of cows without lesions) were collected. The biopsies were evaluated histopathologically, and their 16S metagenome was analyzed. No signs of mange or viral or fungal infections were detected histopathologically in any samples. The α diversity of microbial populations decreased in lesions, across all farms, and the abundance of spirochaetes did not notably change, compared with controls. However, compared with control samples, the microbial fractions of Fusobacterium, Helcococcus spp., Anaerococcus spp., Porphyromonas spp., Prevotella spp., and Trueperella spp. increased several-fold in lesions. In summary, our results suggest that spirochaetes, viruses, and mange are unlikely to cause udder sores. Instead, sores were associated with a marked increase in the abundance of Fusobacterium, Helcococcus, Anaerococcus, Porphyromonas, Prevotella, and Trueperella. Future studies are needed to determine which of these bacteria initiates this polymicrobial infection.

Leptospirosis is a zoonotic disease that is caused by pathogenic spirochaetes of Leptospira spp. and it has become a public health concern in urban localities in the tropics. Rats are important reservoir animals for the transmission of leptospirosis in urban areas. Leptospirosis is considered endemic in Vietnam. However, information on the causative Leptospira genotypes and serotypes in the country is limited. We investigated the carrier status of Leptospira spp. in rats captured in Hanoi by culturing and DNA detection. Isolates were characterized using a serological method and multiple-locus variable-number tandem repeat analysis (MLVA). We captured 144 rats (1 Rattus argentiventer, 135 R. norvegicus, and 8 R. rattus) and obtained 17 L. interrogans, determined by rrs sequencing, from R. norvegicus (12.6%). Sixteen of the isolates were serogroup Bataviae. Five of the 16 isolates exhibited an MLVA type identical to that of the serovar Bataviae reference strain Van Tienen, while there were nine repeats for the other 11 isolates at VNTR31 compared with the reference strain. The remaining isolate grew poorly, and we were unable to determine its serogroup. However, it had an MLVA type matching those of serogroup Pomona strains isolated from R. norvegicus in Japan. Three different flaB sequences were detected in 23 out of 81 R. norvegicus kidney tissue samples (28.4%) using nested PCR followed by DNA sequencing. Two of the sequences were identical with those of serogroups Bataviae and Pomona, and no strain with another sequence was detected in the present study. The present study reveals a high prevalence rate of L. interrogans among R. norvegicus in Hanoi, Vietnam, indicating a potential risk of rat-borne leptospirosis in the area. The present study also demonstrates that a fastidious L. interrogans strain circulates among rats and that molecular detection is crucial in facilitating the accurate determination of reservoir animals.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause gastrointestinal symptoms in the patients, but the role of gut microbiota in SARS-CoV-2 infection remains unclear. Thus, in this study, we aim to investigate whether SARS-CoV-2 infection affects the composition and function of gut microbiota. In this study, we demonstrated for the first time that significant shifts in microbiome composition and function were appeared in both SARS-CoV-2-infected asymptomatic and symptomatic cases. The relative abundance of Candidatus_Saccharibacteria was significantly increased, whereas the levels of Fibrobacteres was remarkably reduced in SARS-CoV-2-infected cases. There was one bacterial species, Spirochaetes displayed the difference between patients and asymptomatic cases. On the genus level, Tyzzerella was the key species that remarkably increased in both symptomatic and asymptomatic cases. Analyses of genome annotations further revealed SARS-CoV-2 infection resulted in the significant ‘functional dysbiosis’ of gut microbiota, including metabolic pathway, regulatory pathway and biosynthesis of secondary metabolites etc. We also identified potential metagenomic markers to discriminate SARS-CoV-2-infected symptomatic and asymptomatic cases from healthy controls. These findings together suggest gut microbiota is of possible etiological and diagnostic importance for SARS-CoV-2 infection.

While many studies have developed microbial succession-based models for the prediction of postmortem interval (PMI) in terrestrial systems, similar well-replicated long-term decomposition studies are lacking for aquatic systems. Therefore, this study sought to identify temporal changes in bacterial community structure associated with porcine skeletal remains (n = 198) for an extended period in a fresh water lake. Every ca. 250 ADD, one cage, containing 5 ribs and 5 scapulae, was removed from the lake for a total of nineteen collections. Water was also sampled at each interval. Variable region 4 (V4) of 16S rDNA was amplified and sequenced for all collected samples using Illumina MiSeq FGx Sequencing platform; resulting data were analyzed with the mothur (v1.39.5) and R (v3.6.0). Bacterial communities associated with ribs differed significantly from those associated with scapulae. This difference was mainly attributed to Clostridia, Holophagae, and Spirochaete relative abundances. For each bone type, α-diversity increased with ADD; similarly, β-diversity bacterial community structure changed significantly with ADD and were explained using environmental parameters and inferred functional pathways. Models developed using 24 rib and 34 scapula family-level taxa allowed the prediction of PMSI with root mean square error of 522.97 ADD (~57 days) and 333.8 ADD (~37 days), respectively.

Background: Important evidence indicates that the intestinal tract microbiota plays a key role in esophageal squamous cell carcinoma (ESCC). Our objective is to analyze the composition of the ESCC-associated microbiota and characterize its contribution to the development of ESCC. Methods: The esophageal microbiota was prospectively investigated in 18 patients with ESCC and 11 patients with physiological normal (PN) esophagus by 16S rRNA gene profiling, using next-generation sequencing. The linear discriminant analysis effect size was used to assess the differences in microbial composition of PN esophagus and ESCC. Predictive functional profiling of microbial communities were obtained with PICRUSt. Findings: The microbiota composition in tumor tissues of ESCC patients is significantly different from that of patients with PN tissues. The ESCC microbiota was characterized by reduced microbial diversity, by decreased abundance of Bacteroidetes, Fusobacteria and Spirochactes. Employing these taxa into a microbial dysbiosis index demonstrated that dysbiosis microbiota had good capacity to discriminate between ESCC and PN esophagus. Functional analysis of the microbiota characterized that ESCC microbiota had altered nitrate reductase and nitrite reductase functions when compared with PN group. The observations were confirmed in other validation cohorts. Interpretation: Detailed analysis of the microbiota of the ESCC patients revealed that tumor exhibit a dysbiotic microbial community when compared with PN groups. We characterized microbial compositional changes, and further identified significant enrichments of Treponema amylovorum, Streptococcus infantis, Prevotella nigrescens, Porphyromonas endodontalis, Veillonella dispar, Aggregatibacter segnis, Prevotella melaninogenica, Prevotella intermedia, Prevotella tannerae, Prevotella nanceiensis and Streptococcus anginosus in ESCC oncogenic progression. Trial Registration: This GASTO1039 study was registered at http://www.chictr.org.cn/ (the Chinese Clinical Trial Registry: ChiCTR1800018897). Funding Statement: This research was supported by National Key R&D Program of China (2018YFC0910303), the National Natural Science Foundation of China (81572391, 81630072), Shenzhen Municipal Government (KQTD20170810160226082), Guangdong Basic and Applied Basic Research Foundation (2019A1515011874), and Guangzhou Municipal Science and Technology Bureau/Science and Technology program of Guangzhou city (201904010356). Declaration of Interests: Lu Gao is the employee of BGI Genomics, BGI-Shenzhen, China. The remaining authors declare no competing interests. Ethics Approval Statement: This prospective observational study was conducted according to a protocol approved by the respective Institutional Ethics Committees of the First Affiliated Hospital of Sun Yat-sen University and according to the Declaration of Helsinki.

Treponema spp. are spirochaetes or spiral bacteria that cause congenital infections as well as sexually and non-sexually...

Bovine digital dermatitis (BDD) is a common infectious disease of digital skin in cattle and an important cause of lameness worldwide, with limited treatment options. It is of increasing global concern for both animal welfare and food security, imposing a large economic burden on cattle farming industries each year. A polytreponemal etiology has been consistently identified, with three key phylogroups implicated globally: Treponema medium, Treponema phagedenis, and Treponema pedis. Pathogenic mechanisms which might enable targeted treatment/therapeutic development are poorly defined. This study used RNA sequencing to determine global differential mRNA expression in primary bovine foot skin fibroblasts following challenge with three representative BDD treponemes and a commensal treponeme, Treponema ruminis. A pro-inflammatory response was elicited by the BDD treponemes, mediated through IL-8/IL-17 signaling. Unexpectedly, the three BDD treponemes elicited distinct mechanisms of pathogenesis. T. phagedenis and T. pedis increased abundance of mRNA transcripts associated with apoptosis, while T. medium and T. pedis increased transcripts involved in actin rearrangement and loss of cell adhesion, likely promoting tissue invasion. The upregulation of antimicrobial peptide precursor, DEFB123, by T. phagedenis spirochaetes may present a microbial ecological advantage to all treponemes within BDD infected tissue, explaining their dominance within lesions. A commensal, T. ruminis, significantly dysregulated over three times the number of host mRNA transcripts compared to BDD treponemes, implying BDD treponemes, akin to the syphilis pathogen (Treponema pallidum), have evolved as “stealth pathogens” which avoid triggering substantial host immune/inflammatory responses to enable persistence and tissue invasion. Immunohistochemistry demonstrated increased IL-6, IL-8, RND1, and CFB protein expression in BDD lesions, confirming in vitro fibroblast observations and highlighting the system’s value in modeling BDD pathogenesis. Several unique shared gene targets were identified, particularly RGS16, GRO1, MAFF, and ZC3H12A. The three key BDD Treponema phylogroups elicited both distinct and shared pathogenic mechanisms in bovine foot skin; upregulating inflammation whilst simultaneously suppressing adaptive immunity. The novel gene targets identified here should enable future vaccine/therapeutic approaches.

We report here 16S rRNA gene amplicon sequence analysis of the gut microbiota in three species of deep-sea fish collected from Suruga Bay, Japan. Of the three species, two were dominated by the phylum Proteobacteria (genus Photobacterium), while one was dominated by the phyla Spirochaetes (genus Brevinema) and Tenericutes (unclassified Mycoplasmataceae).

Turtles are suspected to be involved in the epidemiology of Leptospira; however, data about the dissemination of this zoonotic pathogen among chelonians are scant. In the present study, the serum samples collected from 49 Trachemys scripta elegans living in a natural park of northern Italy were tested by a microagglutination test to measure detectable antibodies against different Leptospira serovars. Three (6.12%) turtles had agglutinins to the serovar Tarassovi, suggesting that they were exposed to the spirochaetes. Currently, it is not clear if Leptospira can cause disease in chelonians or if these animals can serve as reservoirs of leptospirae. Considering that chelonians often share the same environment with other animals and humans, and considering the One Health perspective, investigations to better understand the role of chelonians as a source of Leptospira infection are necessary.

The enteric, pathogenic spirochaete Brachyspira pilosicoli colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several in silico techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus Brachyspira . Our study revealed that an additional isolate that was unable to be species typed against any other Brachyspira lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the B. pilosicoli as random mutation (r/m=1.02). Comparative genomics has informed Brachyspira diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.

The gastrointestinal microbiota plays a pivotal role in maintaining animal health, immunity and reproductive performances. However, literature about the relationship between microbiota and reproductive performance is limited. The aim of the present study was to determine differences in the intestinal microbiota of broiler breeders with different egg laying rate. A total of 200 AA+ parent broiler breeders (41-week-old) were separated into two groups according to their different egg laying rate [average egg laying rate group (AR: 78.57 ± 0.20%) and high egg laying rate group (HR: 90.79 ± 0.43%). Feed conversion ratio (FCR), ovary cell apoptosis rate (ApoCR) and relative abdominal fat weight were lower (p = 0.01), while the hatchability rate of qualified egg was higher (p = 0.04) in HR group than that in AR group. Phascolarctobacterium abundance were lower (p = 0.012) in ileum of HR birds. Romboutsia (genus) in ileum was negatively related to the feed efficiency (r = −0.58, p < 0.05), Firmicutes (phylum) and Lactobacillus (genus) abundances in cecum were positively related to the egg laying rate (ELR) (r = 0.35 and 0.48, p < 0.05), feed efficiency (r = 0.42 and 0.43, p < 0.05), while Spirochaetes (phylum) and Sphaerochaeta (genus) abundances in cecum were negatively related to the ELR (r = −0.43 and −0.70, p < 0.05), feed efficiency (r = 0.54 and 0.48, p < 0.05), and positively related to ApoCR (r = 0.46 and 0.47, p < 0.05). Our results suggested that microbiota, such as Firmicutes (phylum) and Lactobacillus (genus) have positive relationship, while Spirochaetes (phylum) and Romboutsia (genus) abundances exert negative relationship with broiler breeders' reproductive performances.

To explore the changes in oral flora in people with functional dyspepsia (FD). Unstimulated saliva was collected from 21 FD patients diagnosed according to the Rome IV criteria and from 12 healthy controls (HCs) for 16SrRNA sequencing. The pH of saliva samples and community periodontal index (CPI) were tested. The prevalence of small intestinal bacterial overgrowth (SIBO) was obtained by the methane-and hydrogen-based breath test. At the phylum level, FD patients had a higher relative abundance of Spirochaetes and a lower relative abundance of Fusobacteria, TM7 and Proteobacteria than HCs (p Kingella and Abiotrophia genus levels showed significant changes between the FD and HC groups (p Intermedia was significantly different between FD and HC groups (p p p Kingella, Abiotrophia, and Intermedia may be diagnostic indicators of FD.

Bats have been implicated as reservoirs of relapsing fever group spirochaetes since the beginning of the last century. Recently, bat-associated spirochaetes have been reported as human pathogens. In 1968, a spirochaete was detected in blood of the bat Natalus tumidirostris captured inside the Macaregua cave, Colombia. Data on this microorganism were never published again. The aim of this study was to evaluate the presence of Borrelia DNA in blood from bats of Macaregua cave. We performed molecular analyses using a genus-specific real-time PCR targeting the 16S rRNA to detect DNA of Borrelia in blood samples from 46 bats captured in the Macaregua cave. Positive samples were submitted to a battery of PCRs aiming to amply Borrelia 16S rRNA, flaB, glpQ, p66, ospC, clpA, clpX, nifS, pepX, pyrG, recG, rplB and uvrA genes. Seventeen samples were positive for Borrelia after real-time PCR. With the exception of flaB gene, attempts to amplify further loci were unsuccessful. Nucleotide and amino acid divergences of four flaB haplotypes characterized from blood of Carollia perspicillata showed Borrelia burgdorferi sensu lato (Bbsl) as the most closely related group. A phylogenetic tree including 74 sequences of the genus confirmed this trend, since Borrelia genotypes detected in bats from Macaregua formed a monophyletic group basally positioned to Bbsl. Our results suggest that Borrelia genotypes characterized from bats roosting in the Macaregua cave might constitute a new taxon within the genus. This is the first molecular characterization of a Borrelia sp. in Colombia.

Bacterial ClpB is an ATP-dependent disaggregase that belongs to the Hsp100/Clp subfamily of the AAA+ ATPases and cooperates with the DnaK chaperone system in the reactivation of aggregated proteins, as well as promotes bacterial survival under adverse environmental conditions, including thermal and oxidative stresses. In addition, extensive evidence indicates that ClpB supports the virulence of numerous bacteria, including pathogenic spirochaete Leptospira interrogans responsible for leptospirosis in animals and humans. However, the specific function of ClpB in leptospiral virulence still remains to be fully elucidated. Interestingly, ClpB was predicted as one of the L. interrogans hub proteins interacting with human proteins, and pathogen–host protein interactions are fundamental for successful invasion of the host immune system by bacteria. The aim of this review is to discuss the most important aspects of ClpB’s function in L. interrogans, including contribution of ClpB to leptospiral virulence and pathogenesis of leptospirosis, a zoonotic disease with a significant impact on public health worldwide.

Gut microbiota composition can modulate neuroendocrine function, inflammation, and cellular and immunological responses against different pathogens, including viruses. Zika virus (ZIKV) can infect adult immunocompetent individuals and trigger brain damage and antiviral responses. However, it is not known whether ZIKV infection could impact the gut microbiome from adult immunocompetent mice. Here, we investigated modifications induced by ZIKV infection in the gut microbiome of immunocompetent C57BL/6J mice. Adult C57BL/6J mice were infected with ZIKV and the gut microbiota composition was analyzed by next-generation sequencing of the V4 hypervariable region present in the bacterial 16S rDNA gene. Our data showed that ZIKV infection triggered a significant decrease in the bacteria belonging to Actinobacteria and Firmicutes phyla, and increased Deferribacteres and Spirochaetes phyla components compared to uninfected mice. Interestingly, ZIKV infection triggered a significant increase in the abundance of bacteria from the Spirochaetaceae family in the gut microbiota. Lastly, we demonstrated that modulation of microbiota induced by ZIKV infection may lead to intestinal epithelium damage and intense leukocyte recruitment to the intestinal mucosa. Taken together, our data demonstrate that ZIKV infection can impact the gut microbiota composition and colon tissue homeostasis in adult immunocompetent mice.

Due to animal welfare issues, European Union has banned the use of conventional cages (CC) and non-EU countries including the US are also under constant public pressure to restrict their use in egg production. Very limited information is available on the composition of the microbial community of hens raised in different housing environments. This study was conducted to determine the effects of CC and enriched colony cages (EC) on cecal microbiota of two commercial laying hen strains, Hy-Line W36 (W36) and Hy-Line Brown (HB) during the late production stage (53, 58, 67, and 72 weeks of age). Cecal microbiota was studied by analyzing 16S rRNA gene sequences with Quantitative Insights Into Microbial Ecology (QIIME) 2 ver. 2018.8. Differentially abundant taxa were identified by Linear discriminant analysis Effect Size (LEfSe) analysis (P < 0.05, LDA score > 2.0). At phylum level, Actinobacteria was significantly enriched in W36 at all time points while Synergistetes (53 weeks), Spirochaetes (58 weeks), and Synergistetes and Spirochaetes (67 weeks) were significantly higher in HB. At genus level, Bifidobacterium (at all time points) and butyric acid producing genera such as Butyricicoccus and Subdoligranulum (58 and 72 weeks) were significantly higher in W36 as compared to HB. Moreover, Proteobacteria (72 weeks) and its associated genus Campylobacter (67 and 72 weeks) were significantly enriched in EC as compared to CC. Alpha diversity was significantly higher in HB (at all time points) and in EC (67 weeks) as compared to W36 and CC, respectively. Similarly, there was a significant difference in community structure (beta diversity) between W36 and HB (all time points) as well as between EC and CC (67 weeks). The effect of housing and strains was not only seen at the bacterial composition and structure but also reflected at their functional level. Notably, KEGG metabolic pathways predicted to be involved in carbohydrates degradation and amino acids biosynthesis by PICRUSt analysis were significantly different between W36 and HB housed at CC and EC. In sum, cecal microbiota composition, diversities, and their functional pathways were affected by housing type which further varied between two commercial laying hen strains, HB and W36. This suggests that both housing and genetic strains of laying hens should be considered for selection of the alternative housing systems such as enriched colony cage.

Here, we report the finished closed genomes of two environmental bacteria, Oceanispirochaeta crateria K2 and Thiospirochaeta perfilievii P (formally known as Spirochaeta perfilievii P). In addition, we provide methylation data and the associated enzymes predicted and confirmed to be responsible for each modified motif.

Autochthonous probiotics were proposed to have a higher capacity to compete with resident pathogens and were also more prone to dominate and persist over other potentially pathogenic microbes. Therefore, the aim of this study was conducted to investigate the potential autochthonous microbiota by revealing the differences in the intestinal microbiota composition of European eels (Anguilla anguilla) with different growth rates. The differences of diversity, an abundance of the intestinal microbiota, and compositions of all the libraries were identified. Moreover, the composition of the intestinal microbiota of European eels was affected by the growth rates. The dominant phylum of the intestinal microbiota of fast growth eels was Fusobacteria, while Spirochaetes was the dominant phylum of the intestinal microbiota of slow growth and medium growth eels. Cetobacterium was identified as the predominant genera of the intestinal microbiota of fast growth eels; there was a significant difference in this genus between fast growth eels and slow growth eels. Although the relative abundances of Plesiomonas, Turicibacter, Nitrospira, and Lachnospiraceae bacterium NK4A136 group were also increased with the growth rates, only Cetobacterium seemed to have great potential as the probiotics to European eels.

Made available in DSpace on 2020-12-10T17:40:40Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-03-06 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordination for the Improvement of Higher Education Personnel Leptospirosis is a zoonotic disease of global importance caused by an obligate aerobic spirochaete that infects a wide variety of domestic and wild animals. Natural hosts are asymptomatic or show moderate signs of the disease. Accidental hosts develop a severe, often lethal, form of the disease. All young southern tamanduas died suddenly at the zoo in the city of Joao Pessoa, Brazil. The animals were found dead without any noticeable clinical signs. Necropsy revealed extensive haemorrhage in the subcutaneous tissues, kidneys, lungs in addition to the presence of red fluid in the thoracic, abdominal and pericardial cavities. Histopathology of kidneys exhibited acute interstitial nephritis and tubular necrosis. Immunohistochemical staining revealed typical leptospiral wavy forms and aggregates in the lumen of several kidney tubules and lungs. Pathological and molecular investigations confirmedLeptospira interrogansinfection. The adult tamanduas did not present with clinical alterations. To our knowledge, this investigation is the first study to report that leptospirosis should be considered as a possible cause of death in tamanduas. This article warns of the risks of anthropization with respect to Leptospira transmission to tamanduas, other animals and humans. Univ Fed Paraiba, Areia, Paraiba, Brazil Univ Fed Campina Grande, Patos de Minas, Paraiba, Brazil Univ Estadual Paulista, Botucatu, SP, Brazil Univ Fed Santa Maria, Santa Maria, RS, Brazil Parque Zoobot Arruda Camara, Joao Pessoa, Paraiba, Brazil Univ Estadual Paulista, Botucatu, SP, Brazil CNPq: 429862/2016-4

The lagomorph infecting Treponema paraluisleporidarum is a close relative of the human syphilis-bacterium Treponema pallidum. There is a paucity of information on the epidemiology of hare syphilis and its relationship to the rabbit- and human-infecting treponemes that cause syphilis. In our study, we tested 734 serum samples from European brown hares (Lepus europaeus) collected between 2007 and 2019 in the federal state of Lower Saxony, Germany, for the presence of antibodies against Treponema paraluisleporidarum. Since T. paraluisleporidarum cross-reacts with T. pallidum antigen, we used a commercially available Treponema pallidum particle agglutination (TPPA) to test for the presence of antibodies. A high seropositivity (n = 405/734) was detected. An additional 233 serum samples were retested using a fluorescent treponemal antibody absorption test to confirm the results of the TPPA assay. Our results show that infection is widespread in Lower Saxony and suggest a horizontal (sexual) transmission mode since adult hares show significantly higher seropositivity than juveniles (odds ratio: 0.03 [95% CI 0.02-0.05], p

Leptospirosisis a zoonosis caused by spirochaetes from the species Leptospira. The more severe form of leptospirosis, known as Weil’s disease, is characterised by the triad of jaundice, renal impairment and haemorrhages. Pulmonary involvement occurs in 20%–70% of the patients, with severity ranging from non-productive cough to respiratory failure mainly due to pulmonary haemorrhage. Recognition of Weil’s disease in patients presenting with pulmonary symptoms can be difficult. This case illustrates a classic case of pulmonary haemorrhagic involvement in Weil’s disease.

Objective: This study was aimed to assess the effect of a novel postbiotic on bacterial community composition and structure within the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss), as well as evaluate its capacity to protect rainbow trout from Lactococcus garvieae infection. Results: After 30 days of dietary postbiotic supplementation, high-throughput 16S rRNA gene sequencing revealed that bacterial community composition, diversity and richness were significantly higher in treated fish than in control fish. The proportion of sequences affiliated to the phylum Tenericutes, and to a lesser extent, the phyla Spirochaetes and Bacteroidetes was increased in fish fed a postbiotic-enriched diet compared to control fish, whereas the abundance of Fusobacteria was higher in control fish. Moreover, the treated fish showed significantly (p < 0.05) improved protection against L. garvieae compared to control fish. Conclusions: These findings suggest that dietary postbiotic supplementation may represent an environmentally friendly strategy for preventing and controlling diseases in aquaculture.

The eastern subterranean termite (EST) Reticulitermes flavipes is an insect pest in the USA. Like all wood-feeding termites (WFT), EST relies on a complex system of microbes to meet its nutritional requirements. The microbiome of WFT is stable, but the relative abundance of bacteria changes depending on diet. The purpose of this study was to explore the microbial diversity within EST collected in Thibodaux and St. Francisville, LA and detect differences based on diet and location to determine if the microbiome has a strict structure. It was found that taxa did not differ much between nearby colonies, but relative abundance is impacted by the wood in the diet. Half of bacteria from the gut of termites on nuttall oak were Bacteroidales, of which 22.7% were members of the family Porphyromonadaceae. 44% of bacteria from termites on red maple were Spirochaetes. All Spirochaetes were members of the genus Treponema. Elusimicrobia, a phylum found exclusively within termites and wood-feeding cockroaches was not abundant in either St. Francisville colony. Taxa differed more between termite colonies from different locations, but the mircobiome of St. Francisville colonies appeared to begin diverging at the family level. Overall, the microbiome was typical of termites, harboring cellulolytic protozoa, nitrogen-fixing bacteria, acetogenic Spirochaetes, and methanogenic archaeans. This has implications in microbial ecology because the organisms are changing, but the function, digestion of lignocellulose, is not. A bacterium was isolated and identified from termite gut as Acinetobacter tandoii from our previous studies degraded various phenolics, including phenol, nitrophenol, dinitrophenol, trinitrophenol, and toluene.

Background Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the world’s domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fiber. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fiber degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity of the equine fecal microbiota to multiple species of equines. Core taxa shared by all the equine fecal samples (n = 70) were determined and an overview given of the microbiota across different equine types (horse, donkey, horse × donkey and zebra). Results Equine type was associated with differences in both fecal microbial concentrations and community composition. Donkey was generally most distinct from the other equine types, with horse and zebra not differing. Despite this, a common bacterial core of eight OTUs (out of 2070) and 16 genus level groupings (out of 231) was found in all the fecal samples. This bacterial core represented a much larger proportion of the equine fecal microbiota than previously reported, primarily due to the detection of predominant core taxa belonging to the phyla Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaetes. The majority of the core bacterial taxa lack cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and predominant. Conclusions Whilst differences were observed between equine types, a core fecal microbiota existed across all the equines. This core was composed primarily of a few predominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the predominant taxa needs to be addressed, as their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem.

Several studies have reported the effect of absorption of procyanidins and their contribution to the small intestine. However, differences between dietary interventions of procyanidins and interventions via antibiotic feeding in pigs are rarely reported. Following 16S rRNA gene Illumina MiSeq sequencing, we observed that both procyanidin administration for 2 months (procyanidin-1 group) and continuous antibiotic feeding for 1 month followed by procyanidin for 1 month (procyanidin-2 group) increased the number of operational taxonomic units, as well as the Chao 1 and ACE indices, compared to those in pigs undergoing antibiotic administration for 2 months (antibiotic group). The genera Fibrobacter and Spirochaete were more abundant in the antibiotic group than in the procyanidin-1 and procyanidin-2 groups. Principal component analysis revealed clear separations among the three groups. Additionally, using the online Molecular Ecological Network Analyses pipeline, three co-occurrence networks were constructed; Lactobacillus was in a co-occurrence relationship with Trichococcus and Desulfovibrio and a co-exclusion relationship with Bacillus and Spharerochaeta. Furthermore, metabolic function analysis by phylogenetic investigation of communities by reconstruction of unobserved states demonstrated modulation of pathways involved in the metabolism of carbohydrates, amino acids, energy, and nucleotides. These data suggest that procyanidin influences the gut microbiota and the intestinal metabolic function to produce beneficial effects on metabolic homeostasis.