Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae: characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prevot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov

Reduced sulfur compound formation from a leachate-saturated zone under changing temperature conditions

In the leachate-saturation zone of landfills, sulfate reduction is influenced by temperature and electron donors. This study assessed sulfate reduction behaviors under varied electron donor conditions by establishing multiple temperature variation scenarios based on stable temperature fields within the leachate-saturation zone. The results showed that temperature variations altered the microbial community structure and significantly influenced the sulfate reduction process. A more pronounced effect was observed with a temperature difference of 30 °C compared to one of 10 °C. In addition, sulfate reduction was influenced by the presence of electron donors and acceptors. In the middle and low-temperature regions (35 °C and 25 °C), sulfate reduction reaction of acidic organic matter was more significant, while alcohol and saccharide organic substances were more effective in promoting sulfate reduction at high-temperature regions (55 °C). Notably, a 30 °C temperature difference within the leachate-saturation zone significantly altered the microbial community structure, which influenced the sulfate reduction behavior. In particular, Firmicutes and Synergistota played essential roles in mediating the variance in sulfate reduction efficiency with a 30 °C decrease and 30 °C increase, respectively. The results also revealed that temperature changes within landfills were influenced by leachate migration, therefore, controlling leachate recharge can help prevent secondary risks associated with sulfate reduction processes.

Long-term intermittent caloric restriction remodels the gut microbiota in mice genetically prone to breast cancer

OBJECTIVES

Gut microbiota dysbiosis is among the risk factors for breast cancer development, together with genetic background and dietary habits. However, caloric restriction has been shown to remodel the gut microbiota and slow tumor growth. Here, we investigated whether the gut microbiota mediates the preventive effects of long-term chronic or intermittent caloric restriction on breast cancer predisposition.

METHODS

10-week-old transgenic breast cancer-prone mice were randomly assigned to dietary groups (ad libitum, chronic caloric restriction, and intermittent caloric restriction groups) and fed up to week 81. Stool samples were collected at weeks 10 (baseline), 17 (young), 49 (adult), and 81 (old). 16S rRNA gene sequencing was performed to identify the gut microbiota profile of the different groups. In order to investigate the breast cancer gut microbiota profile within genetically predisposed individuals regardless of diet, mammary tumor-bearing mice and mammary tumor-free but genetically prone mice were selected from the ad libitum group (n = 6).

RESULTS

Intermittent caloric restriction increased the microbial diversity of adult mice and modified age-related compositional changes. A total of 13 genera were differentially abundant over time. Pathogenic Mycoplasma was enriched in the re-feeding period of the old intermittent caloric restriction group compared with baseline. Furthermore, mammary tumor-free mice showed shared gut microbiota characteristics with mammary tumor-bearing mice, suggesting an early link between genetic predisposition, gut microbiota, and breast cancer development.

CONCLUSIONS

Our study revealed the role of gut microbes in the preventive effects of caloric restriction against breast cancer development, implying the significance of diet and microbiome interplay.

Bacteremia due to Lachnoanaerobaculum umeaense in a patient with acute myeloid leukemia during chemotherapy: A case report, and a review of the literature

The present case reports a bacteremia due to Lachnoanaerobaculum umeaense (a Gram-positive, filamentous, rod-shaped, anaerobic, spore-forming bacillus present in the human oral microbiota) in a patient treated for acute myeloid leukemia. After failed identification by MALDI-TOF, identification was done by sequencing of 16s rRNA. The patient was successfully treated with Amoxicillin-clavulanic acid and ciprofloxacin for seven days. Comparison of V1-V3 regions of the bacterial 16S rRNA gene gene with published sequences failed to classify the strain as pathogenic or non-pathogenic based on this phylogenetic classification alone. Although Lachnoanaerobaculum gingivalis are known to be associated with bacteremia in patients with acute myeloid leukemia, this clinical case of infection by L. umeaense argues for further studies that will lead to more efficient classification of the infection by these microorganisms.

Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet

The advent of long-read sequencing of microbiomes necessitates the development of new taxonomic profilers tailored to long-read shotgun metagenomic datasets. Here, we introduce Lemur and Magnet, a pair of tools optimized for lightweight and accurate taxonomic profiling for long-read shotgun metagenomic datasets. Lemur is a marker-gene-based method that leverages an EM algorithm to reduce false positive calls while preserving true positives; Magnet is a whole-genome read-mapping-based method that provides detailed presence and absence calls for bacterial genomes. We demonstrate that Lemur and Magnet can run in minutes to hours on a laptop with 32 GB of RAM, even for large inputs, a crucial feature given the portability of long-read sequencing machines. Furthermore, the marker gene database used by Lemur is only 4 GB and contains information from over 300,000 RefSeq genomes. Lemur and Magnet are open-source and available at https://github.com/treangenlab/lemur and https://github.com/treangenlab/magnet.

Eubacterium bacteremia - a retrospective observational study of a seldom found anaerobic pathogen

BACKGROUND

Human infections due to Eubacterium are rare and knowledge of the condition is limited. This study aimed to describe clinical characteristics and outcome in patients with Eubacterium bacteremia.

METHODS

Episodes of Eubacterium bacteremia were identified through the clinical microbiology laboratory in Lund, Sweden. Medical records were retrospectively reviewed. Blood isolates of Eubacterium were collected and antibiotic susceptibility testing was performed with agar dilution.

RESULTS

Seventeen patients with Eubacterium bacteremia were identified of whom six had monomicrobial bacteremia. The incidence was 1.7 cases of Eubacterium bacteremia per million inhabitants and year. The median age was 67 years (interquartile range 63-79 years), and six patients had some form of malignancy. Most of the patients an abdominal focus of infection and the 30-day mortality was low (n = 1).

CONCLUSIONS

Invasive infections with Eubacterium have a low incidence. The condition has a low mortality and an abdominal focus of infection, and malignancy, is common.

Oils with different degree of saturation: effects on ileal digestibility of fat and corresponding additivity and bacterial community in growing pigs

BACKGROUND

Oils are important sources of energy in pig diets. The combination of oils with different degree of saturation contributes to improve the utilization efficiency of the mixed oils and may reduce the cost of oil supplemented. An experiment was conducted to evaluate the effects of oils with different degree of saturation on the fat digestibility and corresponding additivity and bacterial community in growing pigs.

METHODS

Eighteen crossbred (Duroc × Landrace × Yorkshire) barrows (initial body weight: 29.3 ± 2.8 kg) were surgically fitted with a T-cannula in the distal ileum. The experimental diets included a fat-free basal diet and 5 oil-added diets. The 5 oil-added diets were formulated by adding 6% oil with different ratio of unsaturated to saturated fatty acids (U:S) to the basal diet. The 5 oils were palm oil (U:S = 1.2), canola oil (U:S = 12.0), and palm oil and canola oil were mixed in different proportions to prepare a combination of U:S of 2.5, 3.5 and 4.5, respectively.

RESULTS

The apparent and standardized ileal digestibility (AID and SID) of fat and fatty acids increased linearly (P < 0.05) as the U:S of dietary oils increased except for SID of fat and C18:2. The AID and SID of fat and fatty acids differed among the dietary treatments (P < 0.05) except for SID of unsaturated fatty acids (UFA) and C18:2. Fitted one-slope broken-line analyses for the SID of fat, saturated fatty acids (SFA) and UFA indicated that the breakpoint for U:S of oil was 4.14 (R2 = 0.89, P < 0.01), 2.91 (R2 = 0.98, P < 0.01) and 3.84 (R2 = 0.85, P < 0.01), respectively. The determined SID of fat, C18:1, C18:2 and UFA in the mixtures was not different from the calculated SID of fat, C18:1, C18:2 and UFA. However, the determined SID of C16:0, C18:0 and SFA in the mixtures were greater than the calculated SID values (P < 0.05). The abundance of Romboutsia and Turicibacter in pigs fed diet containing palm oil was greater than that in rapeseed oil treatment group, and the two bacteria were negatively correlated with SID of C16:0, C18:0 and SFA (P < 0.05).

CONCLUSIONS

The optimal U:S for improving the utilization efficiency of mixed oil was 4.14. The SID of fat and UFA for palm oil and canola oil were additive in growing pigs, whereas the SID of SFA in the mixture of two oils was greater than the sum of the values of pure oils. Differences in fat digestibility caused by oils differing in degree of saturation has a significant impact on bacterial community in the foregut.

Evidence of the cooperative response of Blattella germanica gut microbiota to antibiotic treatment

Gut microbiota plays a key role in host health under normal conditions. However, bacterial composition can be altered by external factors such as antibiotic (AB) intake. While there are many descriptive publications about the effects of AB on gut microbiota composition after treatment, the dynamics and interactions among the bacterial taxa are still poorly understood. In this work, we performed a longitudinal study of gut microbiome dynamics in B. germanica treated with kanamycin. The AB was supplied in three separate periods, giving the microbiota time to recover between each antibiotic intake. We applied two new statistical models, not focusing on pair-wise interactions, to more realistically study the interactions between groups of bacterial taxa and how some groups affect a single taxon. The first model provides information on the importance of a given genus, and the rest of the community, to define the abundance of that genus. The second model, on the other hand, provides details about the relationship between groups of bacteria, focusing on which community groups affect the taxa. These models help us to identify which bacteria are community-dependent in stress conditions, which taxa might be better adapted than the rest of the community, and which bacteria might be working together within the community to overcome the antibiotic. In addition, these models enable us to identify different bacterial groups that were separated in control conditions but were found together in treated conditions, suggesting that when the environment is more hostile (as it is under antibiotic treatment), the whole community tends to work together.

Genome-Based Reclassification of Strain KIST612, Previously Classified as Eubacterium limosum, into a New Strain of Eubacterium callanderi

The strain KIST612, initially identified as E. limosum, was a suspected member of E. callanderi due to differences in phenotype, genotype, and average nucleotide identity (ANI). Here, we found that E. limosum ATCC 8486T and KIST612 are genetically different in their central metabolic pathways, such as that of carbon metabolism. Although 16S rDNA sequencing of KIST612 revealed high identity with E. limosum ATCC 8486T (99.2%) and E. callanderi DSM 3662T (99.8%), phylogenetic analysis of housekeeping genes and genome metrics clearly indicated that KIST612 belongs to E. callanderi. The phylogenies showed that KIST612 is closer to E. callanderi DSM 3662T than to E. limosum ATCC 8486T. The ANI between KIST612 and E. callanderi DSM 3662T was 99.8%, which was above the species cut-off of 96%, Meanwhile, the ANI value with E. limosum ATCC 8486T was not significant, showing only 94.6%. The digital DNA-DNA hybridization (dDDH) results also supported the ANI values. The dDDH between KIST612 and E. callanderi DSM 3662T was 98.4%, whereas between KIST612 and E. limosum ATCC 8486T, it was 57.8%, which is lower than the species cut-off of 70%. Based on these findings, we propose the reclassification of E. limosum KIST612 as E. callanderi KIST612.

Lachnoanaerobaculum orale bacteremia in a patient with acute myeloid leukemia and stomatitis: An emerging pathogen

Background

Lachnoanaerobaculum orale is a newly described, obligately anaerobic gram-positive bacillus. The first report of invasive disease caused by L. orale was described in a patient with acute lymphocytic leukemia following systematic chemotherapy. Here we describe another case of L. orale bacteremia in a patient with a hematologic malignancy following chemotherapy-induced neutropenia.

Methods

We present a case of a 46-year-old woman with a recent diagnosis of AML who presented to Sunnybrook Health Sciences Center with febrile neutropenia following induction chemotherapy with daunorubicin-cytarabine (3 +7 regimen) with Gemtuzumab and Ozogamycin. Despite being on intravenous pipercillin-tazobactam she remained febrile. Following our clinical assessment and investigations, potential sources of infection included a swollen digit and severe mucositis.

Results

One blood culture from admission grew Lachnoanaerobaculum orale in the anaerobic bottle, identified by Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF). The isolate also underwent whole-genome sequencing using methods that have been described previously. Results demonstrated the organism was susceptible to cefoxitin, clindamycin, meropenem, metronidazole, penicillin, and piperacillin-tazobactam. We concluded that the source of this patient's bloodstream infection to be chemotherapy-induced stomatitis.

Conclusion

With the increasing use of intensive immunosuppressive regimens and hematopoietic stem cell transplantation for patients with hematologic malignancies, there has been an increase in the incidence and detection of bloodstream infections due to anaerobic organisms. This is only the second case report of L. orale bacteremia, highlighting its emerging role as an opportunistic pathogen in immunocompromised patients.

Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries

Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.

Microbiome and metabolome associated with white spot lesions in patients treated with clear aligners

White spot lesions (WSLs) have long been a noteworthy complication during orthodontic treatment. Recently, an increasing number of orthodontists have found that adolescents undergoing orthodontic treatment with clear aligners are at a higher risk of developing WSLs. The oral microbiota and metabolites are considered the etiologic and regulatory factors of WSLs, but the specific impact of clear aligners on the oral microbiota and metabolites is unknown. This study investigated the differences in the salivary microbiome and metabolome between adolescents with and without WSLs treated with clear aligners. Fifty-five adolescents (aged 11-18) with Invisalign appliances, 27 with and 28 without WSLs, were included. Saliva samples were analyzed using 16S rRNA gene sequencing and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); the data were further integrated for Spearman correlation analysis. The relative abundances of 14 taxa, including Actinobacteria, Actinomycetales, Rothia, Micrococcaceae, Subdoligranulum, Capnocytophaga, Azospira, Olsenella, Lachnoanaerobaculum, and Abiotrophia, were significantly higher in the WSL group than in the control group. Metabolomic analysis identified 27 potential biomarkers, and most were amino acids, including proline and glycine. The metabolites were implicated in 6 metabolic pathways, including alanine, aspartate and glutamate metabolism; glycine, serine and threonine metabolism; and aminoacyl-tRNA biosynthesis. There was a correlation between the salivary microbial and metabolomic datasets, reflecting the impact of clear aligners on the metabolic activity of the oral flora. A concordant increase in the levels of Lachnoanaerobaculum, Rothia, Subdoligranulum and some amino acids had predictive value for WSL development. In summary, when adolescents undergo long-term clear aligner therapy with poor oral hygiene habits, clear aligners can disrupt the balance of the oral microecosystem and lead to oral microbiota dysbiosis, thereby increasing the risk of developing WSLs. Our findings might contribute to the understanding of the pathogenesis of WSLs and provide candidate biomarkers for the diagnosis and treatment of WSLs associated with clear aligners.

Targeting the succinate receptor effectively inhibits periodontitis

Periodontal disease (PD) is one of the most common inflammatory diseases in humans and is initiated by an oral microbial dysbiosis that stimulates inflammation and bone loss. Here, we report an abnormal elevation of succinate in the subgingival plaque of subjects with severe PD. Succinate activates succinate receptor-1 (SUCNR1) and stimulates inflammation. We detected SUCNR1 expression in the human and mouse periodontium and hypothesize that succinate activates SUCNR1 to accelerate periodontitis through the inflammatory response. Administration of exogenous succinate enhanced periodontal disease, whereas SUCNR1 knockout mice were protected from inflammation, oral dysbiosis, and subsequent periodontal bone loss in two different models of periodontitis. Therapeutic studies demonstrated that a SUCNR1 antagonist inhibited inflammatory events and osteoclastogenesis in vitro and reduced periodontal bone loss in vivo. Our study reveals succinate’s effect on periodontitis pathogenesis and provides a topical treatment for this disease.

Periodontitis is the most prevalent adult oral disease. Guo et al. show elevation of succinate in periodontitis, which aggravates the disease through the succinate receptor (SUCNR1). They developed a gel formulation of a small compound specifically blocking SUCNR1 to prevent and treat periodontitis by inhibiting dysbiosis, inflammation, and bone loss.

First reported case of Lachnoanaerobaculum gingivalis bacteremia in an acute myeloid leukemia patient with oral mucositis during high dose chemotherapy

CASE DESCRIPTION

Lachnoanaerobaculum gingivalis is an obligate anaerobe identified in a human dental plaque in 2019. Here, we report the first case of L. gingivalis bacteremia in a patient with oral mucositis during chemotherapy. L. gingivalis was confirmed by 16S rRNA gene analysis but not by MALDI-TOF-MS.

CONCLUSION

During chemotherapy in patients with oral mucositis, we should consider the possibility of L. gingivalis bacteremia.

Influence of Factors Altering Gastric Microbiota on Bariatric Surgery Metabolic Outcomes

Little is known about the influence of gastric microbiota on host metabolism, even though the stomach plays an important role in the production of hormones involved in body weight regulation and glucose homeostasis. Proton pump inhibitors (PPIs) and Helicobacter pylori alter gut microbiota, but their impact on gastric microbiota in patients with obesity and the influence of these factors on the metabolic response to bariatric surgery is not fully understood. Forty-one subjects with morbid obesity who underwent sleeve gastrectomy were included in this study. The H. pylori group was established by the detection of H. pylori using a sequencing-based method (n = 16). Individuals in whom H. pylori was not detected were classified according to PPI treatment. Gastric biopsy specimens were obtained during surgery and were analyzed by a high-throughput-sequencing method. Patients were evaluated at baseline and 3, 6, and 12 months after surgery. β-Diversity measures were able to cluster patients according to their gastric mucosa-associated microbiota composition. H. pylori and PPI treatment are presented as two important factors for gastric mucosa-associated microbiota. H. pylori reduced diversity, while PPIs altered β-diversity. Both factors induced changes in the gastric mucosa-associated microbiota composition and its predicted functions. PPI users showed lower percentages of change in the body mass index (BMI) in the short term after surgery, while the H. pylori group showed higher glucose levels and lower percentages of reduction in body weight/BMI 1 year after surgery. PPIs and H. pylori colonization could modify the gastric mucosa-associated microbiota, altering its diversity, composition, and predicted functionality. These factors may have a role in the metabolic evolution of patients undergoing bariatric surgery.

IMPORTANCE The gut microbiota has been shown to have an impact on host metabolism. In the stomach, factors like proton pump inhibitor treatment and Helicobacter pylori haven been suggested to alter gut microbiota; however, the influence of these factors on the metabolic response to bariatric surgery has not been fully studied. In this study, we highlight the impact of these factors on the gastric microbiota composition. Moreover, proton pump inhibitor treatment and the presence of Helicobacter pylori could have an influence on bariatric surgery outcomes, mainly on body weight loss and glucose homeostasis. Deciphering the relationship between gastric hormones and gastric microbiota and their contributions to bariatric surgery outcomes paves the way to develop gut manipulation strategies to improve the metabolic success of bariatric surgery.

Acyloxyacyl hydrolase is a host determinant of gut microbiome-mediated pelvic pain

Dysbiosis of gut microbiota is associated with many pathologies, yet host factors modulating microbiota remain unclear. Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating condition of chronic pelvic pain often with comorbid urinary dysfunction and anxiety/depression, and recent studies find fecal dysbiosis in patients with IC/BPS. We identified the locus encoding acyloxyacyl hydrolase, Aoah, as a modulator of pelvic pain severity in a murine IC/BPS model. AOAH-deficient mice spontaneously develop rodent correlates of pelvic pain, increased responses to induced pelvic pain models, voiding dysfunction, and anxious/depressive behaviors. Here, we report that AOAH-deficient mice exhibit dysbiosis of gastrointestinal (GI) microbiota. AOAH-deficient mice exhibit an enlarged cecum, a phenotype long associated with germ-free rodents, and a "leaky gut" phenotype. AOAH-deficient ceca showed altered gene expression consistent with inflammation, Wnt signaling, and urologic disease. 16S sequencing of stool revealed altered microbiota in AOAH-deficient mice, and GC-MS identified altered metabolomes. Cohousing AOAH-deficient mice with wild-type mice resulted in converged microbiota and altered predicted metagenomes. Cohousing also abrogated the pelvic pain phenotype of AOAH-deficient mice, which was corroborated by oral gavage of AOAH-deficient mice with stool slurry of wild-type mice. Converged microbiota also alleviated comorbid anxiety-like behavior in AOAH-deficient mice. Oral gavage of AOAH-deficient mice with anaerobes cultured from IC/BPS stool resulted in exacerbation of pelvic allodynia. Together, these data indicate that AOAH is a host determinant of normal gut microbiota, and dysbiosis associated with AOAH deficiency contributes to pelvic pain. These findings suggest that the gut microbiome is a potential therapeutic target for IC/BPS.

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.

Highly multiplexed spatial mapping of microbial communities

Mapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density¹ and rich diversity² of species in environmental microbiomes and the limitations of optical imaging technology^3–6. Here, we introduce High Phylogenetic Resolution microbiome mapping by Fluorescence in situ Hybridization (HiPR-FISH), a versatile technology that uses binary encoding, spectral imaging, and machine learning based decoding to create micron-scale maps of the locations and identities of hundreds of microbial species in complex communities. We demonstrate the ability of 10-bit HiPR-FISH to distinguish 1023 E. coli isolates, each fluorescently labeled with a unique binary barcode. HiPR-FISH, in conjunction with custom algorithms for automated probe design and single-cell image analysis, reveals the disruption of spatial networks in the mouse gut microbiome in response to antibiotic treatment and the longitudinal stability of spatial architectures in the human oral plaque microbiome. Combined with super-resolution imaging, HiPR-FISH reveals the diverse ribosome organization strategies of human oral microbial taxa. HiPR-FISH provides a framework for analyzing the spatial ecology of environmental microbial communities at single-cell resolution.

Alkalibaculum sporogenes sp. nov., isolated from a terrestrial mud volcano and emended description of the genus Alkalibaculum

A novel anaerobic, endospore-forming bacterium (strain M08 DMB^T) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells of the strain were motile rods 1.3-2.0 µm long and 0.4 µm in diameter. The temperature range for growth was 5-42 °C, with an optimum at 30 °C. The pH range for growth was H 6.5-11.0, with an optimum at pH 8.0. Growth of strain M08 DMB^T was observed at NaCl concentrations of 0-5.0 % (w/v) with an optimum at 1.0 %. Strain M08 DMB^T utilized 3,4-dimethoxybenzoic acid, 2-methoxyphenol, carbon monoxide, glucose, fructose, mannose, xylose and yeast extract. The end product of glucose fermentation was acetate. The DNA G+C content of strain M08 DMB^T was 32.3 mol% (obtained via whole genome sequencing). The closest phylogenetic relative of strain M08 DMB^T was Alkalibaculum bacchi (family Eubacteriaceae, class Clostridia) with 95.17 % 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08 DMB^T is considered to represent a novel species of the genus Alkalibaculum, for which the name Alkalibaculum sporogenes sp. nov. is proposed. The type strain of Alkalibaculum sporogenes is M08 DMB^T (=KCTC 15840^T=VKM B-3387^T).

Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere

To explore how airborne microbial patterns change with height above the Earth’s surface, we flew NASA’s C-20A aircraft on two consecutive days in June 2018 along identical flight paths over the US Sierra Nevada mountain range at four different altitudes ranging from 10,000 ft to 40,000 ft. Bioaerosols were analyzed by metagenomic DNA sequencing and traditional culturing methods to characterize the composition and diversity of atmospheric samples compared to experimental controls. The relative abundance of taxa changed significantly at each altitude sampled, and the diversity profile shifted across the two sampling days, revealing a regional atmospheric microbiome that is dynamically changing. The most proportionally abundant microbial genera were Mycobacterium and Achromobacter at 10,000 ft; Stenotrophomonas and Achromobacter at 20,000 ft; Delftia and Pseudoperonospora at 30,000 ft; and Alcaligenes and Penicillium at 40,000 ft. Culture-based detections also identified viable Bacillus zhangzhouensis, Bacillus pumilus, and Bacillus spp. in the upper troposphere. To estimate bioaerosol dispersal, we developed a human exposure likelihood model (7-day forecast) using general aerosol characteristics and measured meteorological conditions. By coupling metagenomics to a predictive atmospheric model, we aim to set the stage for field campaigns that monitor global bioaerosol emissions and impacts.

Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types

Mutational signatures can reveal the history of mutagenic processes that cells were exposed to before and during tumorigenesis. We expect that as-yet-undiscovered mutational processes will shed further light on mutagenesis leading to carcinogenesis. With this in mind, we analyzed the mutational spectra of 36 Asian oral squamous cell carcinomas. The mutational spectra of two samples from patients who presented with oral bacterial infections showed novel mutational signatures. One of these novel signatures, SBS_AⁿT, is characterized by a preponderance of thymine mutations, strong transcriptional strand bias, and enrichment for adenines in the 4 bp 5′ of mutation sites. The mutational signature described in this manuscript was shown to be caused by colibactin, a bacterial mutagen produced by E. coli carrying the pks-island. Examination of publicly available sequencing data revealed SBS_AⁿT in 25 tumors from several mucosal tissue types, expanding the list of tissues in which this mutational signature is observed.

Dewaterability enhancement and sulfide mitigation of CEPT sludge by electrochemical pretreatment

Dewatering and sulfide control are the key challenges in treating chemically enhanced primary treatment (CEPT) sludge. In this study, an electrochemical pretreatment (EPT) approach with the input of 10 V/800 mA was explored for simultaneously improving the dewaterability of CEPT sludge and eliminating its sulfide production. The effects of different electrode materials (carbon and titanium) and EPT durations (from 5 to 15 min) were documented to reveal the underlying EPT mechanism. EPT with titanium electrodes (titanium-EPT) led to limited improvement in dewaterability and sulfide control. EPT with carbon electrodes (carbon-EPT) for 15 min, however, led to decreases in capillary suction time and specific resistance in filtration of over 80% and the suppression of about 99% of hydrogen sulfide (H₂S_(g)) production over 5 days of anaerobic storage. Analysis of the characteristics of treated CEPT sludge revealed that carbon-EPT disintegrated sludge flocs with ∼70% reduction in sludge particle sizes and release of aromatic and tyrosine protein-like substances, thus enhancing sludge dewaterability. The sulfur balance in the liquid and gaseous phases showed that most of the sulfur-containing compounds remained in the solid phase as aliphatic sulfur and sulfonic acid after carbon-EPT, thereby mitigating sulfide emission. While the pattern of sulfur distribution in sludge with titanium-EPT was dominated by sulfide, it was similar to the control sample. Reduction in bacteria associated with sulfide production (i.e., Lachnospiraceae) in CEPT sludge after carbon-EPT also contributed to sulfide elimination. This study demonstrates that EPT can be a superior option for simultaneously enhancing the dewaterability of CEPT sludge and mitigating its sulfide production.

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation

BACKGROUND

Spaceflight impacts astronauts in many ways but little is known on how spaceflight affects the salivary microbiome and the consequences of these changes on astronaut health, such as viral reactivation. In order to understand this, the salivary microbiome was analyzed with 16S rRNA gene amplicon sequencing, and saliva viral titers were analyzed with quantitative polymerase chain reaction (qPCR) with primers specific for Epstein-Barr virus (EBV), herpes simplex virus (HSV), and varicella zoster virus (VZV) from 10 astronauts pre-flight, in-flight, and post-flight.

RESULTS

Streptococcus was the most abundant organism in the saliva, making up 8% of the total organisms detected, and their diversity decreased during spaceflight. Other organisms that had statistically significant changes were Proteobacteria and Fusobacteria which increased during flight and Actinobacteria which decreased during flight. At the genus level, Catonella, Megasphera, and Actinobacillus were absent in more than half of saliva samples collected pre-flight but were then detected during flight. In those subjects that already had these genera pre-flight, their relative abundances increased during flight. Correlation analyses between the microbiome and viral titers revealed a positive correlation with Gracilibacteria, Absconditabacteria, and Abiotrophia and a negative correlation between Oribacterium, Veillonella, and Haemophilus. There was also a significant positive correlation between microbiome richness and EBV viral titers.

CONCLUSIONS

This is the first study to look at how the salivary microbiome changes as a result of spaceflight and the search for bacterial biomarkers for viral reactivation. Further studies examining the role of specific organisms that were shown to be correlative and predictive in viral reactivation, a serious problem in astronauts during spaceflight, could lead to mitigation strategies to help prevent disease during both short and long duration space missions. Video abstract.

Paenibacillus oralis sp. nov., Isolated from Human Subgingival Dental Plaque of Gingivitis Lesion

A Gram-stain-negative, facultative anaerobic, spore-forming, motile, and rod-shaped bacterium, strain ChDC PVNT-B20^T, was isolated from the human subgingival dental plaque of a gingivitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) showed that the strain belonged to the genus Paenibacillus. BLAST analysis of 16S rDNA sequence of the strain displayed high identity to those of Paenibacillus faecis DSM 23593^T (97.7% similarity) and Paenibacillus macerans ATCC 8244^T (97.6% similarity). Draft genome of strain ChDC PVNT-B20^T was composed of 8,112,407 bp. The DNA G+C content of the strain was 51.3 mol%. Average nucleotide identity values between strain ChDC PVNT-B20^T and P. faecis DSM 23593^T or P. macerans ATCC 8244^T were 75.71% and 91.5%, respectively. Genome-to-genome distance values between strain ChDC PVNT-B20^T and P. faecis DSM 23593^T or P. macerans ATCC 8244^T were 21.6% (19.3-24.0%) and 44.9% (42.3-47.4%), respectively. Major cellular fatty acids of strain ChDC PVNT-B20^T were anteiso-C_15:0 (43.4%), C_16:0 (16.6%), iso-C_16:0 (14.4%), and anteiso-C_17:0 (12.4%). The sole respiratory quinone of the strain was menaqinone-7. Major polar lipids of the strain were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and one unidentified glycolipid (GL). Minor polar lipids were one unidentified aminolipid (AL), one unidentified phospholipid (PL), and three unidentified lipids (L1-L3). Based on these results, strain ChDC PVNT-B20^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus oralis sp. nov. is proposed. Type strain is ChDC PVNT-B20^T (= KCOM 3021^T = JCM 33462 ^T).

Lachnoanaerobaculum gingivalis sp. nov., Isolated from Human Subgingival Dental Plaque of a Gingivitis Lesion

A novel Gram-stain-positive, obligately anaerobic, spore-forming rod, designated strain ChDC B114^T, was isolated from a human dental plaque of a gingivitis lesion. The strain was characterized by polyphasic taxonomic analysis to identify it at the species level. The 16S ribosomal RNA gene (16S rDNA) sequence analysis revealed that the strain belongs to the genus Lachnoanaerobaculum. The percent similarity of the 16S rDNA of the strain was closest to the homologous gene sequence of Lachnoanaerobaculum orale N1^T (98.5%) and Lachnoanaerobaculum saburreum CCUG 28089^T (97.6%). The major fatty acids of strain ChDC B114^T were C_16:0 (30.7%), C_14:0 (17.7%), iso-C_19:0 (14.9%), and C_17:0 2OH (12.0%). The draft genome of strain ChDC B114^T was 3,097,953 bp in length. The G+C content of the strain was 35.9 mol %. Average nucleotide identity values between strain ChDC B114^T and L. orale N1^T and L. saburreum CCUG 28089^T were 83.2% and 82.0%, respectively. Genome-to-genome distance values between strain ChDC B114^T and L. orale N1^T and L. saburreum CCUG 28089^T were 26.8% (24.5-29.3%) and 26.30% (24.0-28.8%), respectively. Based on these results, strain ChDC B114^T (= KCOM 2030^T = JCM 33452^T) should be classified as a novel species of genus Lachnoanaerobaculum, for which the name Lachnoanaerobaculum gingivalis sp. nov. is proposed.

Intra-oral single-site comparisons of periodontal and peri-implant microbiota in health and disease

OBJECTIVE

Periodontitis and peri-implantitis are oral infectious-inflammatory diseases that share similarities in their pathology and etiology. Our objective was to characterize the single-site subgingival and submucosal microbiomes of implant-rehabilitated, partially dentate Chinese subjects (n = 18) presenting with both periodontitis and peri-implantitis.

MATERIALS AND METHODS

Subgingival/submucosal plaque samples were collected from four clinically distinct sites in each subject: peri-implantitis submucosa (DI), periodontal pocket (DT), clinically healthy (unaffected) peri-implant submucosa (HI), and clinically healthy (unaffected) subgingival sulcus (HT). The bacterial microbiota present was analyzed using Illumina MiSeq sequencing.

RESULTS

Twenty-six phyla and 5,726 operational taxonomic units (OTUs, 97% sequence similarity cutoff) were identified. Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria, Synergistetes, TM7, and Spirochaetes comprised 99.6% of the total reads detected. Bacterial communities within the DI, DT, HI, and HT sites shared high levels of taxonomic similarity. Thirty-one "core species" were present in >90% sites, with Streptococcus infantis/mitis/oralis (HMT-070/HMT-071/HMT-638/HMT-677) and Fusobacterium sp. HMT-203/HMT-698 being particularly prevalent and abundant. Beta-diversity analyses (PERMANOVA test, weighted UniFrac) revealed the largest variance in the microbiota was at the subject level (46%), followed by periodontal health status (4%). Differing sets of OTUs were associated with periodontitis and peri-implantitis sites, respectively. This included putative "periodontopathogens," such as Prevotella, Porphyromonas, Tannerella, Bacteroidetes [G-5], and Treponema spp. Interaction network analysis identified several putative patterns underlying dysbiosis in periodontitis/peri-implantitis sites.

CONCLUSIONS

Species (OTU) composition of the periodontal and peri-implant microbiota varied widely between subjects. The inter-subject variations in subgingival/submucosal microbiome composition outweighed differences observed between implant vs. tooth sites, or between diseased vs. healthy (unaffected) peri-implant/periodontal sites.

Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows

In this study, differences in the ruminal bacterial community between high-yield and low-yield lactating dairy cows under the same dietary conditions were investigated. Sixteen lactating dairy cows with similar parity and days in milk were divided into high-yield (HY) and low-yield (LY) groups based on their milk yield. On day 21, rumen content samples were collected, and their microbiota compositions were determined using high-throughput sequencing of the 16S rRNA gene by the Illumina MiSeq platform. During the study period, dry matter intake (DMI) and milk yield were measured daily, and milk composition was assessed 3 times per week. The results showed that the milk of the LY group tended to have higher fat (P = 0.08), protein (P = 0.01) and total solid contents (P = 0.04) than that of the HY group, while the HY group had higher ruminal propionate (P = 0.08) proportion and volatile fatty acid (VFA) (P = 0.02) concentrations. Principal coordinate analysis indicated significant differences in ruminal bacterial community compositions and structures between the HY group and LY group. The abundances of Ruminococcus 2, Lachnospiraceae and Eubacterium coprostanoligenes were significantly higher in the HY group than in the LY group. In addition, Bacteroides, Ruminococcus 2 and Candidatus-Saccharimonas were positively correlated with ruminal propionate proportion (r>0.4, P<0.05). These findings enhance the understanding of bacterial synthesis within the rumen and reveal an important mechanism underlying differences in milk production in dairy cows.

Glycaemic status affects the subgingival microbiome of diabetic patients

AIM

Periodontitis is correlated with type 2 diabetes mellitus (T2DM), but little is known about glycaemic status effect on subgingival microbiota associated with periodontitis. This study evaluated if periodontal microbiome of T2DM patients is affected by glycaemic status.

MATERIALS AND METHODS

Twenty-one T2DM non-smoking patients with chronic periodontitis and body mass index ≤40 kg/m² were allocated into two groups according to systemic glycaemic status: inadequate (DMI- HbA1c ≥ 8%) and adequate (DMA- HbA1c <7.8%). Subgingival biofilm was collected from sites with moderate (PD = 4-6 mm) and severe disease (PD ≥ 7 mm) in two quadrants. The V5-V6 hypervariable region of the 16SrRNA was sequenced using the GS-FLX-454 Titanium platform. Sequences were compared with HOMD database using QIIME and PhyloToAST pipelines. Statistical comparisons were made using two-sample t-tests.

RESULTS

DMA microbiome presented higher diversity than DMI. Inadequate glycaemic control favoured fermenting species, especially those associated with propionate/succinate production, whereas those forming butyrate/pyruvate was decreased in DMI. Higher abundances of anginosus group and Streptococcus agalactiae in DMI may indicate that subgingival sites can be reservoir of potentially invasive pathogens. Altered subgingival microbiome in DMI may represent an additional challenge in the periodontal treatment of these patients and in the prevention of more invasive infections.

CONCLUSION

Glycaemic status in T2DM patients seems to modulate subgingival biofilm composition.

Influence of Intestinal Microbiota Transplantation and NleH Expression on Citrobacter rodentium Colonization of Mice

The intestinal microbiota plays an important role in regulating host resistance to enteric pathogens. The relative abundance of the microbiota is dependent upon both genetic and environmental factors. The attaching and effacing pathogens enteropathogenic Escherichia coli, enterohemorrhagic E. coli, and Citrobacter rodentium cause diarrheal disease and translocate type III secretion system effector proteins into host cells to inhibit pro-inflammatory host responses. Here we determined the influence of both the intestinal microbiota and the expression of the C. rodentium NleH effector on C. rodentium colonization in different mouse models. We performed fecal transplantation experiments between C57BL/6J and C57BL/10ScNJ mice and found that such microbiota transfers altered both the host resistance to C. rodentium infection as well as the benefit or detriment of expressing NleH to C. rodentium intestinal colonization.

Improving in vivo conversion of oleuropein into hydroxytyrosol by oral granules containing probiotic Lactobacillus plantarum 299v and an Olea europaea standardized extract

This study reports novel food-grade granules for co-delivery of L. plantarum 299v and a standardized extract of Olea europaea leaves (Phenolea®) as oral carrier of probiotics and hydroxytyrosol. Different granule formulations containing either L. plantarum 299v (Lac), or the olive leave extract (Phe) or their combination (Lac-Phe) have been successfully produced through wet granulation employing excipients generally regarded as safe as granulating/binding agents. L. plantarum cells withstood the manufacturing process and were stable upon storage at 4 °C for more than 6 months. In vitro dissolution studies in simulated gastro-intestinal fluids showed the capability of the granules to rapidly dissolve and deliver both olive leave phenols and living L. plantarum cells. In simulated digestion conditions, Lac and Lac-Phe granules protected L. plantarum against the harsh environment of the gastro-intestinal tract. Co-administration of Lac and Phe oral granules to healthy mice provided for higher amounts of hydroxytyrosol in urines as compared to Phe granules alone, suggesting that L. plantarum 299v boosted in vivo conversion of oleuropein to hydroxytyrosol. On the other hand, PCR-assisted profiling of the Lactobacillus population in faeces obtained from mice treated with Lac or Lac plus Phe confirmed that the probiotic arrived alive to colon and was there able to exert a sort of perturbing effect on the climax colonic microflora. Overall, these results pave the way towards the development of a nutraceutical useful for combined delivery of bioactive hydroxytyrosol and probiotics to colon site.

Association between metabolic profile and microbiomic changes in rats with functional dyspepsia

Functional dyspepsia (FD) is one of the most prevalent functional gastrointestinal disorders (FGIDs). Accumulated evidence has shown that FD is a metabolic disease that might relate to gut microbiota, but the relationship between microbiome and the host metabolic changes is still uncertain. To clarify the host–microbiota co-metabolism disorders related to FD, an integrated approach combining ¹H NMR-based metabolomics profiles, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA gene sequencing was used to investigate the relationship among FD, metabolism of gut microbiota and the host. 34 differential urinary metabolites and 19 differential fecal metabolites, which affected the metabolism of energy, amino acids, nucleotides and short chain fatty acids (SCFAs), were found to have associated with FD. Based on the receiver operating characteristic (ROC) analysis, 10 biomarkers were screened out as diagnostic markers of FD. Meanwhile, the concentrations of Flintibacter, Parasutterella, Eubacterium and Bacteroides significantly increased in the FD group, whereas Eisenbergiella, Butyrivibrio, Intestinimonas, Saccharofermentans, Acetivibrio, Lachnoanaerobaculum and Herbinix significantly decreased. Furthermore, the above altered microbiota revealed a strong correlation with the intermediate products of the tricarboxylic acid (TCA) cycle, amino acids and SCFAs. In our study, it suggested that the energy metabolism was mainly disturbed in FD rats. Our findings also demonstrated that FD might be the result of gut microbiota and metabolism disorders, which was potentially valuable to enrich our understanding of the pathogenesis of FD.

Functional dyspepsia (FD) is one of the most prevalent functional gastrointestinal disorders (FGIDs). The aim of our study was to evaluate the effects of FD on the microbiota and its metabolic profiles in feces and urine.

Immunopathology of childhood celiac disease-Key role of intestinal epithelial cells

BACKGROUND & AIMS

Celiac disease is a chronic inflammatory disease of the small intestine mucosa due to permanent intolerance to dietary gluten. The aim was to elucidate the role of small intestinal epithelial cells in the immunopathology of celiac disease in particular the influence of celiac disease-associated bacteria.

METHODS

Duodenal biopsies were collected from children with active celiac disease, treated celiac disease, and clinical controls. Intestinal epithelial cells were purified and analyzed for gene expression changes at the mRNA and protein levels. Two in vitro models for human intestinal epithelium, small intestinal enteroids and polarized tight monolayers, were utilized to assess how interferon-γ, interleukin-17A, celiac disease-associated bacteria and gluten influence intestinal epithelial cells.

RESULTS

More than 25 defense-related genes, including IRF1, SPINK4, ITLN1, OAS2, CIITA, HLA-DMB, HLA-DOB, PSMB9, TAP1, BTN3A1, and CX3CL1, were significantly upregulated in intestinal epithelial cells at active celiac disease. Of these genes, 70% were upregulated by interferon-γ via the IRF1 pathway. Most interestingly, IRF1 was also upregulated by celiac disease-associated bacteria. The NLRP6/8 inflammasome yielding CASP1 and biologically active interleukin-18, which induces interferon-γ in intraepithelial lymphocytes, was expressed in intestinal epithelial cells.

CONCLUSION

A key factor in the epithelial reaction in celiac disease appears to be over-expression of IRF1 that could be inherent and/or due to presence of undesirable microbes that act directly on IRF1. Dual activation of IRF1 and IRF1-regulated genes, both directly and via the interleukin-18 dependent inflammasome would drastically enhance the inflammatory response and lead to the pathological situation seen in active celiac disease.

Unraveling the human salivary microbiome diversity in Indian populations

The importance of studying the salivary microbiome has been highlighted for its connection to health and disease and as a potential tool for supplementing human genetic diversity studies. While the salivary microbiome has been studied in various world populations, Indian populations have not been examined. We therefore analyzed microbiome diversity in saliva samples from 92 volunteers from eight different sampling locations in India by amplifying and sequencing variable regions (V1 and V2) of the bacterial 16S rRNA gene. The results showed immense bacterial richness in Indian populations; we identified 165 bacterial genera and 785 unique Operational Taxonomic Units (OTUs), with substantial sharing among the populations. There were small, but significant correlations in the abundance of bacterial genera in sampling locations from the same geographic region. Most of the core OTUs detected were also observed previously in other populations, but Solobacterium spp., Lachnoanaerobaculum spp. and Alloprevotella spp. were observed to be a component of the saliva microbiome unique to Indian populations. Importantly, nine bacterial genera were observed that were not listed in the Human Oral Microbiome Database (HOMD). These results highlight the importance of analyzing underrepresented populations like those of India.

What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.

Murimonas intestini gen. nov., sp. nov., an acetate-producing bacterium of the family Lachnospiraceae isolated from the mouse gut

Three strains of an anaerobic, Gram-stain-positive coccobacillus were isolated from the intestines of mice. These strains shared 100 % similarity in their 16S rRNA gene sequences, but were distantly related to any described members of the family Lachnospiraceae (<94 %). The most closely related species with names that have standing in nomenclature were Robinsoniella peoriensis , Ruminococcus gnavus , Blautia producta and Clostridium xylanolyticum . Phylogenetic relationships based on 16S rRNA gene sequence analysis were confirmed by partial sequencing of hsp60 genes. The use of an in-house database search pipeline revealed that the new isolates are most prevalent in bovine gut samples when compared with human and mouse samples for Ruminococcus gnavus and B. producta . All three isolated strains shared similar cellular fatty acid patterns dominated by C16 : 0 methyl ester. Differences in the proportions of C12 : 0 methyl ester, C14 : 0 methyl ester and C18 : 1 cis-11 dimethyl acetal were observed when compared with phylogenetically neighbouring species. The major short-chain fatty acid produced by strain SRB-530-5-HT was acetic acid. This strain tested positive for utilization of d-fructose, d-galacturonic acid, d-malic acid, l-alanyl l-threonine and l-glutamic acid but was negative for utilization of amygdalin, arbutin, α-d-glucose, 3-methyl d-glucose and salicin, in contrast to the type strain of the closest related species Robinsoniella peoriensis . The isolates were not able to use mannitol for growth. Based on genotypic, phenotypic and chemotaxonomic characteristics, we propose to create the new genus and species Murimonas intestini gen. nov., sp. nov. to accommodate the three strains SRB-530-5-HT ( = DSM 26524T = CCUG 63391T) (the type strain of Murimonas intestini), SRB-509-4-S-H ( = DSM 27577 = CCUG 64595) and SRB-524-4-S-H ( = DSM 27578 = CCUG 64594).

Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association

Background

In spite of its association with gastroenteritis and inflammatory bowel diseases, the isolation of Campylobacter concisus from both diseased and healthy individuals has led to controversy regarding its role as an intestinal pathogen. One proposed reason for this is the presence of high genetic diversity among the genomes of C. concisus strains.

Results

In this study the genomes of six C. concisus strains were sequenced, assembled and annotated including two strains isolated from Crohn’s disease patients (UNSW2 and UNSW3), three from gastroenteritis patients (UNSW1, UNSWCS and ATCC 51562) and one from a healthy individual (ATCC 51561). The genomes of C. concisus BAA-1457 and UNSWCD, available from NCBI, were included in subsequent comparative genomic analyses. The Pan and Core genomes for the sequenced C. concisus strains consisted of 3254 and 1556 protein coding genes, respectively.

Conclusion

Genes were identified with specific conservation in C. concisus strains grouped by phenotypes such as invasiveness, adherence, motility and diseased states. Phylogenetic trees based on ribosomal RNA sequences and concatenated host-related pathways for the eight C. concisus strains were generated using the neighbor-joining method, of which the 16S rRNA gene and peptidoglycan biosynthesis grouped the C. concisus strains according to their pathogenic phenotypes. Furthermore, 25 non-synonymous amino acid changes with 14 affecting functional domains, were identified within proteins of conserved host-related pathways, which had possible associations with the pathogenic potential of C. concisus strains. Finally, the genomes of the eight C. concisus strains were compared to the nine available genomes of the well-established pathogen Campylobacter jejuni, which identified several important differences in the respiration pathways of these two species. Our findings indicate that C. concisus strains are genetically diverse, and suggest the genomes of this bacterium contain respiration pathways and modifications in the peptidoglycan layer that may play an important role in its virulence.

Prevotella jejuni sp. nov., isolated from the small intestine of a child with coeliac disease

Five obligately anaerobic, Gram-stain-negative, saccharolytic and proteolytic, non-spore-forming bacilli (strains CD3 : 27, CD3 : 28(T), CD3 : 33, CD3 : 32 and CD3 : 34) are described. All five strains were isolated from the small intestine of a female child with coeliac disease. Cells of the five strains were short rods or coccoid cells with longer filamentous forms seen sporadically. The organisms produced acetic acid and succinic acid as major metabolic end products. Phylogenetic analysis based on comparative 16S rRNA gene sequence analysis revealed close relationships between CD3 : 27, CD3 : 28(T) and CD3 : 33, between CD3 : 32 and Prevotella histicola CCUG 55407(T), and between CD3 : 34 and Prevotella melaninogenica CCUG 4944B(T). Strains CD3 : 27, CD3 : 28(T) and CD3 : 33 were clearly different from all recognized species within the genus Prevotella and related most closely to but distinct from P. melaninogenica. Based on 16S rRNA, RNA polymerase β-subunit (rpoB) and 60 kDa chaperonin protein subunit (cpn60) gene sequencing, and phenotypic, chemical and biochemical properties, strains CD3 : 27, CD3 : 28(T) and CD3 : 33 are considered to represent a novel species within the genus Prevotella, for which the name Prevotella jejuni sp. nov. is proposed. Strain CD3 : 28(T) ( = CCUG 60371(T) = DSM 26989(T)) is the type strain of the proposed novel species. All five strains were able to form homologous aggregates, in which tube-like structures were connecting individual bacteria cells. The five strains were able to bind to human intestinal carcinoma cell lines at 37 °C.

Intestinal T-cell responses in celiac disease - impact of celiac disease associated bacteria

A hallmark of active celiac disease (CD), an inflammatory small-bowel enteropathy caused by permanent intolerance to gluten, is cytokine production by intestinal T lymphocytes. Prerequisites for contracting CD are that the individual carries the MHC class II alleles HLA-DQ2 and/or HLA-DQ8 and is exposed to gluten in the diet. Dysbiosis in the resident microbiota has been suggested to be another risk factor for CD. In fact, rod shaped bacteria adhering to the small intestinal mucosa were frequently seen in patients with CD during the “Swedish CD epidemic” and bacterial candidates could later be isolated from patients born during the epidemic suggesting long-lasting changes in the gut microbiota. Interleukin-17A (IL-17A) plays a role in both inflammation and anti-bacterial responses. In active CD IL-17A was produced by both CD8⁺ T cells (Tc17) and CD4⁺ T cells (Th17), with intraepithelial Tc17 cells being the dominant producers. Gluten peptides as well as CD associated bacteria induced IL-17A responses in ex vivo challenged biopsies from patients with inactive CD. The IL-17A response was suppressed in patients born during the epidemic when a mixture of CD associated bacteria was added to gluten, while the reverse was the case in patients born after the epidemic. Under these conditions Th17 cells were the dominant producers. Thus Tc17 and Th17 responses to gluten and bacteria seem to pave the way for the chronic disease with interferon-γ-production by intraepithelial Tc1 cells and lamina propria Th1 cells. The CD associated bacteria and the dysbiosis they might cause in the resident microbiota may be a risk factor for CD either by directly influencing the immune responses in the mucosa or by enhancing inflammatory responses to gluten.

Suppression of Clostridium difficile in the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae

The indigenous microbial community of the gastrointestinal (GI) tract determines susceptibility to Clostridium difficile colonization and disease. Previous studies have demonstrated that antibiotic-treated mice challenged with C. difficile either developed rapidly lethal C. difficile infection or were stably colonized with mild disease. The GI microbial community of animals with mild disease was dominated by members of the bacterial family Lachnospiraceae, while the gut community in moribund animals had a predominance of Escherichia coli. We investigated the roles of murine Lachnospiraceae and E. coli strains in colonization resistance against C. difficile in germfree mice. Murine Lachnospiraceae and E. coli isolates were cultured from wild-type mice. The ability of each of these isolates to interfere with C. difficile colonization was tested by precolonizing germfree mice with these bacteria 4 days prior to experimental C. difficile challenge. Mice precolonized with a murine Lachnospiraceae isolate, but not those colonized with E. coli, had significantly decreased C. difficile colonization, lower intestinal cytotoxin levels and exhibited less severe clinical signs and colonic histopathology. Infection of germfree mice or mice precolonized with E. coli with C. difficile strain VPI 10463 was uniformly fatal by 48 h, but only 20% mortality was seen at 2 days in mice precolonized with the Lachnospiraceae isolate prior to challenge with VPI 10463. These findings confirm that a single component of the GI microbiota, a murine Lachnospiraceae isolate, could partially restore colonization resistance against C. difficile. Further study of the members within the Lachnospiraceae family could lead to a better understanding of mechanisms of colonization resistance against C. difficile and novel therapeutic approaches for the treatment and prevention of C. difficile infection.