Parvimonas micra a new potential pathogen in hospitalized patients: a case series from 2015-2022.

Parvimonas micra isolations are usually part of polymicrobial infections and the pathogenic role of this microrganism is still debated. We describe here a large series of hospitalized patients diagnosed with Parvimonas micra infections and discuss the clinical and therapeutic management and the outcome of these infections.

Parvimonas micra activates the Ras/ERK/c-Fos pathway by upregulating miR-218-5p to promote colorectal cancer progression.

BACKGROUND: Colorectal cancer (CRC) is the third most common cancer in the world, and a strong relationship exists between CRC and gut microbiota, which affects the occurrence, development, and metastasis of cancer. Bioinformatics-based analyses revealed that the abundance of Parvimonas micra (P. micra) in the feces of patients with cancer is significantly higher than that in healthy people. Therefore, an important relationship may exist between P. micra and CRC. METHODS: We first confirmed that P. micra can promote the proliferation of cell lines through cell experiments and mouse models. Then we selected the signaling pathways and content of exosomes to promote the development of CRC by transcriptomics and microRNA sequencing. Finally, we confirmed that P. micra promoted CRC development through miR-218-5p/Ras/ERK/c-Fos pathway through the in vivo and in vitro experiments. RESULTS: First, it was confirmed by in vitro and in vivo experiments that P. micra can promote the development of CRC. Transcriptome analysis after the coincubation of bacteria and cells revealed that P. micra promoted cell proliferation by activating the Ras/ERK/c-Fos pathway. Furthermore, microRNA sequencing analysis of the cells and exosomes showed that miR-218-5p and protein tyrosine phosphatase receptor R (PTPRR) were the key factors involved in activating the Ras/ERK/c-Fos pathway, and the miR-218-5p inhibitor was used to confirm the role of microRNA in xenograft mice. CONCLUSION: This experiment confirmed that P. micra promoted the development of CRC by upregulating miR-218-5p expression in cells and exosomes, inhibiting PTPRR expression, and ultimately activating the Ras/ERK/c-Fos signaling pathway.

PLSDB: advancing a comprehensive database of bacterial plasmids.

Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb.

Microbial community of soda Lake Van as obtained from direct and enriched water, sediment and fish samples.

Soda lakes are saline and alkaline ecosystems that are considered to have existed since the first geological records of the world. These lakes support the growth of ecologically and economically important microorganisms due to their unique geochemistry. Microbiota members of lakes are valuable models to study the link between community structure and abiotic parameters such as pH and salinity. Lake Van is the largest endroheic lake and in this study, bacterial diversity of lake water, sediment, and pearl mullet (inci kefali; Alburnus tarichi), an endemic species of fish which are collected from different points of the lake, are studied directly and investigated meticulously using a metabarcoding approach after pre-enrichment. Bacterial community structures were identified using Next Generation Sequencing of the 16S rRNA gene. The analysis revealed that the samples of Lake Van contain high level of bacterial diversity. Direct water samples were dominated by Proteobacteria, Cyanobacteria, and Bacteroidota, on the other hand, pre-enriched water samples were dominated by Proteobacteria and Firmicutes at phylum-level. In direct sediment samples Proteobacteria, whereas in pre-enriched sediment samples Firmicutes and Proteobacteria were determined at highest level. Pre-enriched fish samples were dominated by Proteobacteria and Firmicutes at phylum-level. In this study, microbiota members of Lake Van were identified by taxonomic analysis.

Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.

Traditional sampling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative sampling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive samples (excreta, litter and poultry dust) are representative of invasive samples (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene amplicon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive samples were detected in non-invasive samples, the relative abundance of members of the microbial communities of these groups were different, as shown by beta diversity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes, and excreta as a proxy of caecal contents for the detection of Tenericutes. Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes. However, none of the non-invasive samples could be used to infer the overall abundance of OTUs observed in invasive samples. In conclusion, non-invasive samples could be used to detect the presence and absence of the majority of the OTUs found in invasive samples, but could not accurately reflect the microbial community structure of invasive samples.

Severe pneumonia caused by Parvimonas micra: a case report.

BACKGROUND: Parvimonas micra (P. micra) is a gram-positive anaerobic coccus that is detected widely on the skin, in the oral mucosa and in the gastrointestinal tract. In certain circumstances, P. micra can cause abdominal abscesses, bacteraemia and other infections. To the best of our knowledge, there have been no case reports describing the biological characteristics of P. micra-related pneumonia. These bacteria do not always multiply in an aerobic organ, such as the lung, and they could be easily overlooked because of the clinical mindset. CASE PRESENTATION: A 35-year-old pregnant woman was admitted to the emergency department 4 weeks prior to her due date who was exhibiting 5 points on the Glasgow coma scale. A computed tomography (CT) scan showed a massive haemorrhage in her left basal ganglia. She underwent a caesarean section and brain surgery before being admitted to the ICU. She soon developed severe pneumonia and hypoxemia. Given that multiple sputum cultures were negative, the patient's bronchoalveolar lavage fluid was submitted for next-generation sequencing (NGS) to determine the pathogen responsible for the pneumonia; as a result, P. micra was determined to be the causative pathogen. Accordingly the antibiotic therapy was altered and the pneumonia improved. CONCLUSION: In this case, we demonstrated severe pneumonia caused by the anaerobic organism P. micra, and the patient benefited from receiving the correct antibiotic. NGS was used as a method of quick diagnosis when sputum culture failed to distinguish the pathogen.

Severe deep neck space infection caused by Eggerthia catenaformis.

A 64-year-old woman was acutely referred to the Department of Otorhinolaryngology, Head and Neck Surgery, Aalborg University Hospital due to rapidly progressing neck swelling, fever and dysphagia. Clinical examination revealed submental swelling, trismus and laryngeal inflammation. A contrast-enhanced CT scan showed infection in the deep neck spaces with multiple abscesses. The patient underwent acute surgery and antimicrobial therapy was initiated and she was transferred to an intensive care unit. Three additional surgical procedures were needed before sufficient drainage was achieved. There was growth of different oral commensals from four separate pus aspirates, while Eggerthia catenaformis was cultured in all samples. Due to the extent of the infection, the patient stayed in the intensive care unit for 16 days, but recovered completely due to adequate surgery and antimicrobial therapy for 4 weeks. Here we present the third reported case of a severe deep neck space infection with multiple abscesses due to E. catenaformis.

A Case of Brain Abscess Caused by Actinomyces Cardiffensis and Parvimonas Micra.

Brain abscesses occur in 0.3-1.3 per 100,000 worldwide each year with 0.4-0.9 in Japan alone. Most of the causes are direct infection from a nearby infectious lesion and are rarely caused by an odontogenic infection. Here, we reported a case of brain abscess suspected to be associated with odontogenic infection. The patient was a 55-year-old woman. Blurred eyes and pain in the left eye noted, for which she consulted an ophthalmologist, but her eyes were normal. She was conscious and was able to converse clearly, but she could not read the letters and had difficulty in writing at the time of admission. A brain abscess was diagnosed based on the head magnetic resonance imaging (MRI) and clinical course, and a small craniotomy abscess drainage was performed. A. cardiffensis and P. micra were detected in the abscess, suggesting the involvement of periodontal disease bacteria. After the surgery, antimicrobial treatment was performed for about 2 months. At the same time, perioperative treatment was performed. On the 70th day after the surgery, tooth extraction, which was considered as the source of infection, was performed. The patient was discharged 74 days after surgery. A good turning point was obtained without relapse of symptoms.

Six cases of Solobacterium moorei isolated alone or in mixed culture in Hungary and comparison with previously published cases.

Solobacterium moorei is a strict anaerobic gram-positive rod. It is found in the human microbiota in different parts of the body, but it also appears to be an opportunistic pathogen in some infectious processes. We describe six cases of severe infections identified in 2016 in which S. moorei was isolated alone or in mixed culture involving other anaerobes or both aerobic and anaerobic bacteria. Three cases were associated with the oral cavity, including a middle ear infection, a wound infection after total laryngectomy, and a mandibular abscess as a result of bisphosphonate therapy. In the other three patients, the sites of infection had no connections with the oral cavity and included chronic osteomyelitis of the tibia, a superinfection of cutaneous tuberculosis associated with hidradenitis suppurativa, and the isolation of S. moorei from the blood culture of a cachectic man with several comorbidities. Based on our findings, S. moorei does not appear to be that virulent of a bacterium; except for the case with bacteraemia, S. moorei was recovered as a co-pathogen in patients with several immunosuppressive predisposing factors. We highlight the finding that the routine use of MALDI-TOF MS in microbiology laboratories can in a timely and detailed manner identify members of mixed infections involving different anaerobic bacteria that may be rare and difficult-to-culture and identify species, such as S. moorei.

Role of the oral microbiota in cancer evolution and progression.

Bacteria identified in the oral cavity are highly complicated. They include approximately 1000 species with a diverse variety of commensal microbes that play crucial roles in the health status of individuals. Epidemiological studies related to molecular pathology have revealed that there is a close relationship between oral microbiota and tumor occurrence. Oral microbiota has attracted considerable attention for its role in in-situ or distant tumor progression. Anaerobic oral bacteria with potential pathogenic abilities, especially Fusobacterium nucleatum and Porphyromonas gingivalis, are well studied and have close relationships with various types of carcinomas. Some aerobic bacteria such as Parvimonas are also linked to tumorigenesis. Moreover, human papillomavirus, oral fungi, and parasites are closely associated with oropharyngeal carcinoma. Microbial dysbiosis, colonization, and translocation of oral microbiota are necessary for implementation of carcinogenic functions. Various underlying mechanisms of oral microbiota-induced carcinogenesis have been reported including excessive inflammatory reaction, immunosuppression of host, promotion of malignant transformation, antiapoptotic activity, and secretion of carcinogens. In this review, we have systemically described the impact of oral microbial abnormalities on carcinogenesis and the future directions in this field for bringing in new ideas for effective prevention of tumors.

Parvimonas micra as a rare cause of spondylodiscitis - case series from a single centre.

BACKGROUND: The anaerobe Parvimonas micra is usually recovered as part of the normal flora or in polymicrobial infections of odontogenic or gastrointestinal origin. P. micra has rarely been described as the causative organism of pyogenic spondylodiscitis. Here we report multiple cases of spondylodiscitis caused by this organism and compare their clinical features with the published literature. METHODS: We performed a retrospective review of all institutional cases with P. micra spondylodiscitis between 01 June 2012 and 31 May 2019. For comparison, the literature was searched for studies reporting vertebral infections with P. micra in adult patients. RESULTS: Over 7 years, six cases were identified: one with a polymicrobial infection (with P. micra and Fusobacterium nucleatum) and five with P. micra as the only pathogen isolated. The six patients with P. micra infections were between 63 and 82 years old (median 72 years) and presented with persistent lower back pain. Common findings were infection of the lumbar spine region (in 6/6 cases) and recent dental inflammation (4/6 cases). 3/6 patients had previously undergone decompressive spinal surgery due to spinal stenosis (2 to 11 years before). In 4/6 cases the organism was detected in blood cultures drawn at admission. Treatment consisted of antibiotics for all patients and additional decompressive surgery due to abscess formation in half the cases. Outcomes were mostly favourable, but persistent pain was a common complaint after resolution of infection. CONCLUSIONS: P. micra is a rare cause of spondylodiscitis. Nevertheless, recent dental procedures with subsequent back pain should lead to the consideration of possible anaerobic causes of spondylodiscitis. Heightened awareness of this pathogen and improvements in diagnostic methods might lead to higher detection rates.

Sanguinarine modulate gut microbiome and intestinal morphology to enhance growth performance in broilers.

Sanguinarine is a bioactive compound as a quaternary benzophenanthridine alkaloid from plant of the Macleaya cordata, Papaveraceae family. The present study was conducted to investigate the effects of dietary sanguinarine supplementation on growth performance, serum biochemistry parameters, intestinal mucosal morphology and gut microbiome in yellow feathered broilers. Two hundred and seventy 1-d-old female broilers were randomly assigned to 3 treatments ① Basal diet (NG); ② Basal diet containing bacitracin methylene disalicylate (50mg/Kg diet) (ANT); ③ Basal diet containing sanguinarine (0.7 mg/ kg of feed) (SAG). The statistical results showed that dietary sanguinarine supplementation enhanced growth performance and decreased glucose, uric acid as well as urea nitrogen levels of broilers at 28d of age (P<0.05). The 16S rRNA gene sequence analysis revealed that sanguinarine significantly decreased the species from the phyla Bacteroidetes, and increased the species from phyla Firmicutes. Moreover, dietary sanguinarine supplementation improved mucosal morphology to achieve higher ratio of intestinal villus height to crypt depth (P < 0.05), and decreased the concentrations of TNF-α and IL-4 in jejunum mucosal. This study demonstrated that sanguinarine supplementation in the diet of yellow feathered broilers improved intestinal morphology and microbiota community structure to promote growth performance on 1-28d.

Study of the gut Microbiome Profile in Children with Autism Spectrum Disorder: a Single Tertiary Hospital Experience.

The role of gut microbiome was recently raised in the pathogenesis of neurodevelopmental disorders including autism spectrum disorder (ASD). The aim of this study was to elucidate changes in gut microbiome in Egyptian autistic children and its possible correlation with the severity of autism and gastrointestinal (GI) symptoms. The gut bacterial microbiome of 41 ASD children, 45 siblings, and 45 healthy controls were analyzed using quantitative SYBR Green real-time PCR technique targeting 16S rRNA of selected bacteria. The gut microbiome of ASD children and their siblings contained a higher relative abundance of Bacteroides as well as Ruminococcus than controls. Prevotella/Bacteroides (P/B) ratio and Firmicutes/Bacteroidetes (F/B) were significantly lower in both ASD cases and their siblings. The only difference between the autistic cases and their siblings was the significantly higher level of Bifidobacterium in siblings, which appears to offer them a protective role. There was no correlation between the altered gut microbiome and the severity of autism or GI symptoms. The current study showed an evidence of changes in the gut microbiome of autistic children compared to the unrelated control. However, the microbiome profile of siblings was more like that of autistic children than that of unrelated controls indicating that gut microbiota is affected by dietary habits, living conditions together with host genetic factors.

Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes.

We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.

Peptoniphilus asaccharolyticus - Commensal, pathogen or synergist? Two case reports on invasive Peptoniphilus asaccharolyticus infection.

Peptoniphilus asaccharolyticus are gram-positive anaerobic cocci (GPAC) usually found as commensals of the skin or in the setting of polymicrobial colonisation of chronic wounds and ulcers. However, its pathogenic potential in more severe, invasive infections such as bone, joint or blood stream infections remains unclear, with studies on underlying virulence factors still pending. In this case report we present two cases of P. asaccharolyticus-associated infections of the bone and joint as well as a review of the literature. The cases cast a new light on possible synergistic interactions between P. asaccharolyticus and more virulent aerobic bacteria as well as on its role as pathogen in severe mono-infection.

Septic pulmonary embolism associated with periodontal disease: a case report and literature review.

BACKGROUND: Periodontal disease, including periodontitis, has been reported to be a rare cause of septic pulmonary embolism (SPE). It is however extremely difficult to isolate the causative pathogen of periodontal disease-associated SPE from blood cultures of these patients. CASE PRESENTATION: In this study, an 85-year-old Japanese man was admitted with fever and worsening malaise. He was later noted to have multiple bilateral subpleural pulmonary nodules on chest computed tomography scan. After admission, Parvimonas micra (P. micra) was isolated from his blood culture. This was followed by a meticulous search for the primary source of SPE, focusing on the head and neck areas. Consequently, apical periodontitis and infratemporal fossa abscess were identified as the primary sources of SPE. Although P. micra is one of the most frequently detected bacteria in the infected root canals of teeth with chronic apical periodontitis, it has rarely been proven as a causative pathogen of periodontal disease-associated SPE. CONCLUSIONS: This case study demonstrated that periodontal disease is an important primary source of SPE and P. micra could be a causative pathogen of SPE.

Lung inflammation and disease: A perspective on microbial homeostasis and metabolism.

It is now well appreciated that the human microbiome plays a significant role in a number of processes in the body, significantly affecting its metabolic, inflammatory, and immune homeostasis. Recent research has revealed that almost every mucosal surface in the human body is associated with a resident commensal microbiome of its own. While the gut microbiome and its role in regulation of host metabolism along with its alteration in a disease state has been well studied, there is a lacuna in understanding the resident microbiota of other mucosal surfaces. Among these, the scientific information on the role of lung microbiota in pulmonary diseases is currently severely limited. Historically, lungs have been considered to be sterile and lung diseases have only been studied in the context of bacterial pathogenesis. Recently however, studies have revealed a resilient microbiome in the upper and lower respiratory tracts and there is increased evidence on its central role in respiratory diseases. Knowledge of lung microbiome and its metabolic fallout (local and systemic) is still in its nascent stages and attracting immense interest in recent times. In this review, we will provide a perspective on lung-associated metabolic disorders defined for lung diseases (e.g., chronic obstructive pulmonary disease, asthma, and respiratory depression due to infection) and correlate it with lung microbial perturbation. Such perturbations may be due to altered biochemical or metabolic stress as well. Finally, we will draw evidence from microbiome and classical microbiology literature to demonstrate how specific lung morbidities associate with specific metabolic characteristics of the disease, and with the role of microbiome in this context. © 2018 IUBMB Life, 71(1):152-165, 2019.

The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.

BACKGROUND: The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate. RESULTS: Two hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome. CONCLUSIONS: Diet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.

Decrease of Staphylococcus aureus Virulence by Helcococcus kunzii in a Caenorhabditis elegans Model.

Social bacterial interactions are considered essential in numerous infectious diseases, particularly in wounds. Foot ulcers are a common complication in diabetic patients and these ulcers become frequently infected. This infection is usually polymicrobial promoting cell-to-cell communications. Staphylococcus aureus is the most prevalent pathogen isolated. Its association with Helcococcus kunzii, commensal Gram-positive cocci, is frequently described. The aim of this study was to assess the impact of co-infection on virulence of both H. kunzii and S. aureus strains in a Caenorhabditis elegans model. To study the host response, qRT-PCRs targeting host defense genes were performed. We observed that H. kunzii strains harbored a very low (LT50: 5.7 days ± 0.4) or an absence of virulence (LT50: 6.9 days ± 0.5). In contrast, S. aureus strains (LT50: 2.9 days ± 0.4) were significantly more virulent than all H. kunzii (P < 0.001). When H. kunzii and S. aureus strains were associated, H. kunzii significantly reduced the virulence of the S. aureus strain in nematodes (LT50 between 4.4 and 5.2 days; P < 0.001). To evaluate the impact of these strains on host response, transcriptomic analysis showed that the ingestion of S. aureus led to a strong induction of defense genes (lys-5, sodh-1, and cyp-37B1) while H. kunzii did not. No statistical difference of host response genes expression was observed when C. elegans were infected with either S. aureus alone or with S. aureus + H. kunzii. Moreover, two well-characterized virulence factors (hla and agr) present in S. aureus were down-regulated when S. aureus were co-infected with H. kunzii. This study showed that H. kunzii decreased the virulence of S. aureus without modifying directly the host defense response. Factor(s) produced by this bacterium modulating the staphylococci virulence must be investigated.