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At least 19 recordsLinked to original sources

PubMed2026

Unlocking the unexplored AMPSphere in marine rare species.

BACKGROUND: Antimicrobial peptides (AMPs) have advantages over traditional antibiotics in fighting against drug-resistant bacterial infections. Natural microbial communities are considered as the priority targets for next-generation AMP bioprospecting initiatives. While progress has been made in characterizing AMPs from the dominant microbial taxa in natural ecosystems, current research largely overlooks the biosynthetic potential of rare species. Given their distinct evolutionary pressures, rare species likely produce AMPs with novel structures and unconventional mechanisms of action. RESULTS: In this study, enrichment cultivation of a marine biofilm was conducted in 138 carbon source- and oxygen level-based conditions, followed by metagenomic sequencing using both Illumina and Nanopore platforms. Analysis of 435 high-quality genomes derived from the metagenomes suggests that these bacterial strains are significantly underrepresented (< 0.01%) in global marine biofilm communities. Through multi-model prediction, we identified 3,054,472 candidate AMPs from the genomes, including 1048 high-confidence ones, thereby significantly expanding the previously known AMPSphere. Furthermore, AMPs derived from the rare bacterial species exhibit unique sequence characteristics, structural diversity, remarkable stability under diverse pH conditions and pepsin exposure, and strong therapeutic potential in animal models, reflecting their specialized adaptive and defensive strategies developed within ecological systems. CONCLUSIONS: The features of the underexplored AMPs from low-abundance bacteria in marine biofilms provide valuable resources and theoretical foundations for the development of highly effective antimicrobial agents. Video Abstract.

Biofilms↗

PubMed1979

Oerskovia species: rare opportunistic pathogens.

The second documented instance of opportunistic infection by member of the genus Oerskovia is reported. There is some evidence to suggest that this group of bacteria, which is extensively distributed in the soil, may be more closely associated with man than has hitherto been supposed.

Bacterial Infections↗

PubMed2024

Elucidating the roles of SOD3 correlated genes and reactive oxygen species in rare human diseases using a bioinformatic-ontology approach.

Superoxide Dismutase 3 (SOD3) scavenges extracellular superoxide giving a hydrogen peroxide metabolite. Both Reactive Oxygen Species diffuse through aquaporins causing oxidative stress and biomolecular damage. SOD3 is differentially expressed in cancer and this research utilises Gene Expression Omnibus data series GSE2109 with 2,158 cancer samples. Genome-wide expression correlation analysis was conducted with SOD3 as the seed gene. Categorical SOD3 Pearson Correlation gene lists incrementing in correlation strength by 0.01 from ρ≥|0.34| to ρ≥|0.41| were extracted from the data. Positively and negatively SOD3 correlated genes were separated for each list and checked for significance against disease overlapping genes in the ClinVar and Orphanet databases via Enrichr. Disease causal genes were added to the relevant gene list and checked against Gene Ontology, Phenotype Ontology, and Elsevier Pathways via Enrichr before the significant ontologies containing causal and non-overlapping genes were reviewed with a literature search for possible disease and oxidative stress associations. 12 significant individually discriminated disorders were identified: Autosomal Dominant Cutis Laxa (p = 6.05x10-7), Renal Tubular Dysgenesis of Genetic Origin (p = 6.05x10-7), Lethal Arteriopathy Syndrome due to Fibulin-4 Deficiency (p = 6.54x10-9), EMILIN-1-related Connective Tissue Disease (p = 6.54x10-9), Holt-Oram Syndrome (p = 7.72x10-10), Multisystemic Smooth Muscle Dysfunction Syndrome (p = 9.95x10-15), Distal Hereditary Motor Neuropathy type 2 (p = 4.48x10-7), Congenital Glaucoma (p = 5.24x210-9), Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome (p = 3.77x10-16), Classical-like Ehlers-Danlos Syndrome type 1 (p = 3.77x10-16), Retinoblastoma (p = 1.9x10-8), and Lynch Syndrome (p = 5.04x10-9). 35 novel (21 unique) genes across 12 disorders were identified: ADNP, AOC3, CDC42EP2, CHTOP, CNN1, DES, FOXF1, FXR1, HLTF, KCNMB1, MTF2, MYH11, PLN, PNPLA2, REST, SGCA, SORBS1, SYNPO2, TAGLN, WAPL, and ZMYM4. These genes are proffered as potential biomarkers or therapeutic targets for the corresponding rare diseases discussed.

Humans↗

PubMed2026

Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes.

Transposable elements have the potential to drive genome evolution by introducing mutations and causing structural instability and chromosomal rearrangements, particularly under conditions like environmental or genetic stress. In this study, we generated 18 new long-read-based metagenomically assembled reference genomes for lichenized fungi, which form obligate mutualistic symbioses with algae or cyanobacteria. We used the new genomes and 10 publicly available genomes to investigate the relationships between species traits (i.e. dominant reproductive mode, distribution size, and generation length) and the abundance and spatial distribution of transposable elements using a phylogenetic comparative framework. We found that species with smaller distribution sizes and longer generation lengths had a higher genomic DNA transposon load. Specifically, their genomes were enriched with Rolling Circle transposons, which contradict previous research that has identified high proportions of retrotransposons in rare species. Disproportionate distributions of transposable elements in rare and range-restricted species may disrupt genomic stability, decrease fitness, and be reflective of species experiencing a greater degree of stress. Conversely, greater transposable element activity may be an important source of novel genetic diversity in isolated populations with limited gene flow. Further research is needed to understand the potential mechanisms driving transposable element proliferation in rare species' genomes and if transposable element content is predictive of increased extinction risk.

DNA Transposable Elements↗

PubMed2025

Species distribution of nontuberculous mycobacteria isolated from respiratory specimens at a tertiary care hospital in South Korea, 2017-2022.

The clinical relevance and drug resistance patterns of nontuberculous mycobacteria (NTM) vary by species. This study investigated the species distribution of NTM isolated from respiratory specimens at a tertiary care hospital in South Korea from 2017 to 2022. A retrospective analysis was conducted on laboratory data from respiratory specimens submitted for acid-fast bacilli culture. NTM isolates were identified using a line probe assay, and those unidentifiable at the species or complex level underwent multigene sequencing of the 16S rRNA, rpoB, and hsp65 genes. Among all mycobacterial isolates, the proportion of NTM showed an increasing trend, rising from 87.4% in 2017 to 93.3% in 2022. The eight most common species were M. avium complex (61.9%), M. abscessus (14.2%), M. fortuitum complex (8.4%), M. gordonae (5.3%), M. simiae complex (3.4%), M. kansasii complex (1.9%), M. terrae complex (1.5%), and M. chelonae (1.2%), accounting for 97.7% of all NTM isolates. Among the remaining isolates (2.3%, n = 169), 161 were classified into 24 species and groups, the majority with proportions below 0.1%. Two of the eight isolates that could not be identified at the species or group level despite multigene sequencing underwent whole-genome sequencing, which suggested they likely represent novel Mycobacterium species. This study provides valuable insights into the distribution of NTM species, particularly rarely encountered species, isolated from respiratory specimens in South Korea. These findings may aid in optimizing diagnostic strategies and selecting appropriate treatment options.IMPORTANCEGiven the significant variations in clinical relevance and drug resistance patterns among nontuberculous mycobacteria (NTM) species, understanding their geographic distribution is essential for selecting appropriate treatment options and improving patient outcomes. This study investigated the distribution of NTM species isolated from respiratory specimens at a tertiary care hospital in South Korea from 2017 to 2022. Our findings revealed an increasing proportion of NTM, with M. avium complex and M. abscessus remaining predominant. Additionally, we identified 24 rarely encountered species and groups, along with two strains that likely represent novel Mycobacterium species. Our study advances the understanding of the evolving NTM epidemiology in South Korea, contributing to the optimization of diagnostic strategies and improvement of patient management.

Republic of Korea↗

PubMed1975

Skin-piercing blood-sucking moths I: ecological and ethological studies on Calpe eustrigata (Lepid., noctuidae).

The Noctuid Calpe [Calyptral] eustrigata Hmps. was reported as a skin-piercing blood-sucking moth for the first time in Malaya (Bänziger, 1968) and is so far the only lepidopteran proved to suck blood by means of a piercing act. A few field observations and the description of the piercing behaviour of caged moths were given. Apart from a taxonomic study of the genus Calpe (Berio, 1956), a single record (Büttiker, 1969) and some notes on the moth's proboscis and possible evolutionary pathway (Bänziger, 1970, 1971, 1972) to our knowledge no other data have been published on the moth after its description as a new species (Hampson, 1926). The life cycle is completely unknown. From the scanty museum specimens available, it appears that the species inhabits South and Southeast Asia. A closely related, though less rare species, the fruit-piercing C. thalictri Bkh., has been used for a detailed study of the piercing mechanism likely to be adopted by Calpe (Bänziger, 1970); the feeding turned out to be as unusual as the feeding habits. Little or nothing is known about other Calpe species. C. eustrigata is not the only adult lepidopterous parasite of mammals. Lachryphagous ("eye-frequenting") moths feed as "marginal" parasites upon eye-secretions of ungulates, elephants and occasionally man (Shannon, 1928; Reid, 1954; Büttiker, 1964, 1967; Bänziger, 1966). Arcyophora species and the eulachryphagous Noctuid Lobocraspis graseifusa Hmps. which apparently feeds exclusively upon eye discharges, are suspected as vectors of eye diseases (Guilbride et al., 1959, Büttiker, 1964; Bänziger, 1972). While no lachryphagous moth is able to suck blood by a piercing act, there are a number of facultative lachryphagous moths which lick up the blood freely present at wounds, or that excreted anally by mosquitoes (Bänziger, 1969, 1972). Because of the scientific interest in C. eustrigata, research has been carried out to investigate different biological aspects of the species in Malaysia, Thailand. Laos and Indonesia (May 1971-May 1973). The first account presented here will be continued with a paper (in prep.) on the piercing mechanism and soon, it is hoped, with more information on the physiology, life cycle and medical importance of the moth.

Adaptation, Biological↗

PubMed1979

[Occurrence and distribution of fruiting body-forming myxobacteria in Siebengebirge. Comparative studies with special reference to characteristic biotypes].

In the region of the "Siebengebirge" near Bonn, six characteristic biotopes were studied with respect to the occurrence of fruiting body forming myxobacteria. 23 different species, belonging to the 8 known genera, were found. The number of species in the respective biotopes varied between 6 and 17, the average numbers of species per sampling area were between 2.1 and 10.0. 15 species were found on dung pellets of wild living herbivorous mammals. Deciduous forest soils contained 13 species in spring, 17 species in autumn. Rock coverings contained 14, creek slopes 16, bark of living trees 9, and rotting wood 16 fruiting myxobacterial species. Myxococcus fulvus, Myxococcus coralloides and Archangium gephyra occurred in all biotops studied. The rare species were Melittangium boletus, Polyangium vitellinum, Stigmatella aurantiaca, and Chondramyces apiculatus. The composition of the myxobacterial flora depends on ecological factors (kind of dung pellets, rock, bark and pH). The ecological influences upon the distribution are discussed.

Altitude↗

PubMed1977

Attempts to induce mutations in Haemophilus influenzae with the base analogues 5-bromodeoxyuridine and 2-aminopurine.

Attempts were made to induce mutations in Haemophilus influenzae with the base analogues 5-bromodeoxyuridine and 2-aminopurine. These attempts were unsuccessful. Incorporation studies with BrdUrd showed, in agreement with earlier studies on Escherichia coli, that BrdUrd was discriminated against when dThd was also present but was incorporated to essentially the same extent as dThd when only BrdUrd was present. In this latter case, strands fully substituted with BrdUrd was produced, but survival data suggest that bacteria deriving their DNA by replication on such fully substituted templates were inviable. However, bacteria with about 20% of the thymine substituted with bromouracil were usually viable. No mutations could be detected in the descendants of such bacteria. The reasons for this are discussed and it is concluded that in all probability the replication system in species rarely if every treats incorporated bromouracil as anything except a thymine analogue. The alternative possibility, that the negative results are a consequence of the absence of the reclex (SOS) error-prone repair system in this species, is considered much less likely.

2-Aminopurine↗

PubMed2026

Genomic insights into Aeromonas infections in diarrheal patients: high diversity, emerging resistance, and potential outbreak in Beijing.

BACKGROUND: Aeromonas species are ubiquitous aquatic bacteria that have emerged as significant foodborne enteric pathogens worldwide, yet their genomic landscape in clinical settings remains poorly delineated, particularly in Beijing. METHODS: To address this gap, we performed active surveillance for Aeromonas among 691 consecutive diarrheal outpatients in a Beijing district from January to December 2024. Isolates were recovered using enrichment culture coupled with PCR screening and identified by MALDI-TOF MS. Antimicrobial susceptibility was tested against 17 agents. Whole-genome sequencing was conducted on all isolates, enabling average nucleotide identity (ANI) analysis, comprehensive annotation of antimicrobial resistance and virulence genes, multilocus sequence typing (MLST), and core-genome SNP (cgSNP)-based phylogenetics. RESULTS: Aeromonas was detected in 3.3% (23/691) of patients, with Aeromonas veronii (56.52%, 13/23) and Aeromonas caviae (26.09%, 6/23) predominating. Co-infections with other enteric pathogens occurred in 65.2% of positive cases. Resistance rates were notably high for ampicillin/ampicillin-sulbactam (78.26%), nalidixic acid (56.52%), and ertapenem (21.73%), and 65.21% of isolates were multidrug-resistant. Genotypic-phenotypic concordance was robust, with β-lactamase genes ampS (60.87%) and blaCEPH-A3 (47.83%) being most prevalent. Strikingly, mcr-3.25 and mcr-3.3, which belong to the mcr family (originally described as mobile colistin resistance genes), were identified in 8.70% of isolates, exhibiting perfect correlation with phenotypic resistance. Plasmer analysis suggested both mcr genes to be chromosomally encoded. Comparative genomic analysis of virulence-associated genes revealed striking species-specific specialization: A. veronii predominantly carried complete T3SS clusters (61.5%), A. caviae and Aeromonas enteropelogenes were enriched in T6SS genes, and a single A. dhakensis isolate possessed an extensive arsenal including T3SS, T6SS, and a full RTX toxin cluster. MLST resolved the 23 isolates into 22 sequence types, 18 of which were novel. Phylogenetic reconstruction identified a tight monophyletic cluster of three A. veronii isolates (9-27 SNP differences) recovered within a 96-h window, suggestive of a potential cluster that warrants further epidemiological investigation. Comparative genomic analysis of the rare species Aeromonas allosaccharophila demonstrated that the Beijing clinical isolate S14 differs from the U.S. clinical strain ATCC 35942 by 42,099 SNPs, confirming its distinct genetic lineage. CONCLUSION: Collectively, this study delineates high genetic diversity, emerging chromosomal colistin resistance, and species-specific virulence specialization among Aeromonas isolates from diarrheal patients in Beijing. The detection of a potential outbreak cluster and a rare clinical isolate underscores the power of genomics-based surveillance for detecting and mitigating foodborne pathogen threats.

Aeromonas↗

PubMed1977

Pulmonary disease caused by Candida species.

Candida species are often found in sputum specimens. Their role as a possible cause of pulmonary disease is a frequent consideration, particularly in patients receiving immunosuppressive or long-standing antimicrobial therapy. At Memorial Hospital and New York Hospital, 30 patients with histologic evidence of Candida pulmonary infection were identified over a two year period. These infections reached the lungs by hematogenous spread in 10 patients and by aspiration in 16 patients. Most the patients had malignant neoplastic disease. The Candida pulmonary disease appeared to be significant clinical factor in only three cases. Experience from our institutions and from the literature indicates that Candida species rarely cause significant pulmonary disease. When such involvement is extensive, the patient is usually terminally ill from multiple other factors.

Biopsy↗

PubMed1977

Unusual Pseudomonas corneal ulcers.

Two rare species of Pseudomonas were isolated from corneal ulcers in two patients. In the first case P. acidovorans was isolated and suspected as the primary pathogenic microorganism in human disease. In the second case P. stutzeri was isolated from ocular sources, but this is the first report of its role in causing corneal disease. The patient in the second case had a scarred cornea, possibly caused by a previous herpetic infection, and this may have been a predisposing factor to the development of the infection by P. stutzeri. Susceptibility studies of both organisms revealed sensitivity to a wide range of antibiotics but resistance to carbenicillin, a drug currently used in the treatment of infections from P. aeruginosa.

Abscess↗

PubMed2026

Genomic characterization of efflux pumps and putative small multidrug resistance (SMR)-like transporters in disinfectant-tolerant coagulase-negative staphylococci from a Vietnamese hospital.

Coagulase-negative staphylococci (CoNS) are common inhabitants of healthcare environments and can serve as reservoirs of antimicrobial resistance determinants. However, the relationship among disinfectant tolerance, efflux-associated phenotypes, and multidrug resistance in environmental CoNS remains incompletely defined. Here, 51 staphylococcal isolates were recovered from high-touch hospital surfaces in Hanoi, Vietnam, and 14 isolates showed elevated MICs to at least one disinfectant, including benzalkonium chloride, chlorhexidine gluconate, or hydrogen peroxide, relative to Staphylococcus aureus ATCC 25923. These isolates also displayed multidrug-resistant phenotypes. Moreover, ethidium bromide accumulation assays revealed a clear efflux-associated phenotype, and representative isolates exhibited biofilm-forming ability. Whole-genome sequencing of three representative isolates reclassified SDH.B1 and SDH.B3 as Staphylococcus nepalensis-a CoNS species rarely documented in hospital AMR surveillance-and confirmed SDH.B7 as Staphylococcus haemolyticus. To our knowledge, this is among the first reports of S. nepalensis carrying mecA together with the disinfectant efflux gene qacG, and a set of putative small multidrug resistance (SMR)-like transporters in a hospital environment from Southeast Asia. In addition, six putative SMR-like proteins were identified. Phylogenetic and structural analyses suggested relatedness to YkkC/YkkD-like systems, although their transport activity remains to be experimentally verified. These findings identify environmental CoNS as reservoirs of disinfectant tolerance and multidrug resistance in hospital settings and provide a basis for future functional investigation of putative SMR-like transporters.IMPORTANCEHospital environmental CoNS are often dismissed as low-priority contaminants, yet they may persist under disinfectant pressure and carry clinically relevant resistance determinants. Here, disinfectant-tolerant CoNS recovered from a Vietnamese hospital combined multidrug resistance, efflux-associated phenotypes, and biofilm-related traits. Genome analysis further revealed known qac genes and six putative SMR-like proteins that merit functional testing. These findings support inclusion of environmental CoNS in infection-prevention surveillance and disinfectant stewardship programs.

Staphylococcus haemolyticus↗

PubMed1979

Pulmonary disease caused by Mycobacterium xenopi in an Australian man.

A 63-year-old man with a history of increasing cough with sputum, weight loss, and lethargy was found to have pulmonary disease caused by Mycobacterium xenopi, a species rarely seen in Australia. Chemotherapy was successful. Apart from war service in Papua New Guinea, the patient had not travelled outside Australia.

Australia↗

PubMed1979

A preliminary key to the common calliphorid flies of peninsular Malaysia (Insecta: Diptera).

A key to the common Calliphorid flies of Peninsular Malaysia is presented. Illustrations of the genitalia of some rare species, list of new localities, altitudes and other ecological data are also presented. The following species were recorded for the first time from Peninsular Malaysia; Catapicephala sinica, C. kurahashii, Taninanina javanica, Hemipyrellia tagaliana, Lucilia sinensis, Blaesoxipha kasterni, Boettcherisca javanica, Parasarcophaga misera, P. orchidea, P. albicephs, Sarcosolomonia crinita, Thyrsocnema bornensis, Sarcorohdendorfia antilope and Lioproctia pattoni.

Animals↗

PubMed1979

Experimental reproduction of neonatal diarrhea in young gnotobiotic hares simultaneously associated with Clostridium difficile and other Clostridium strains.

Clostridium difficile, C. perfringens, and C. tertium are very often present simultaneously in the feces of conventional diarrheic young hares, whereas these three bacterial species are rarely encountered and never present simultaneously in the feces of healthy young hares. When a strain of each of the three bacterial species was monoassociated with axenic young hares, the appearance of pathological disorders was only observed in animals monoassociated with C. difficile, when the number of C. difficile exceeded 10(8) per g of fresh feces. When a strain of C. perfringens or a strain of C. tertium, or both, was associated with C. difficile, diarrhea and death occurred more rapidly than in hares monoassociated with C. difficile. C. difficile and C. perfringens became established more rapidly when disassociated than when monoassociated with axenic hares. The association of C. perfringens and C. tertium with axenic hares did not bring about any pathological disorders. It may be concluded that C. difficile is the causal agent of neonatal diarrhea in conventional and gnotobiotic young hares and that other strains of Clostridium enhance its pathogenic effect. C difficile alone or associated with C. perfringens or C. tertium does not play any pathogenic role in young rats, mice, or rabbits.

Animals↗

PubMed1979

Enterotoxigenic enteric bacteria in foods and outbreaks of food-borne diseases in Sweden.

All of 86 food routinely examined for potentially pathogenic enteric bacteria were found to harbour one or more coliform species. None of the strains isolated produced heat-labile enterotoxin (LT) or showed invasive properties. The suckling mouse test indicated that one strain of Escherichia coli produced heat-stable enterotoxin (ST). Twelve incidents of suspected food poisoning were also investigated. In two of them the foods examined contained LT-producing strains of E. coli and in two there were LT-producing strains of Klebsiella pneumoniae. The counts of viable enterotoxigenic micro-organisms in these foods were 3000-30,000 E. coli/g and 50,000 to 1 million K. pneumoniae/g. The dominant symptom in all the incidents was watery diarrhoea. These seem to be the first reported cases of foodborne enterotoxigenic enteric bacteria in Europe. Though enterotoxigenic E. coli and related gram-negative enterotoxin-producing species are rare in correctly handled food in Sweden, these micro-organisms should be searched for when outbreaks of food poisoning are investigated.

Enterotoxins↗

PubMed2026

How the social lives of bacteria affect their pangenome.

Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.

Bacteria↗

PubMed1979

[On the frequency of occurrence of salmonella species. An analysis of 1.5 millions trains of salmonellae isolated in 109 countries during the period 1934-1975 (author's transl)].

1 542 257 strains of Salmonellae isolated in 109 countries during the period 1934-75 were analysed to determine the relative frequency of the 1864 species currently recognized. In addition to the absolute numbers of strains isolated, the "age" of the species and the numbers of reports were used to compute a frequency quotient (QF). It is proposed, on the basis of occurrence, that species be classified as most frequent, frequent, uncommon, rare and very rare. The Salmonella species most frequently isolated from man, food animals, other animals, foods, feeding stuffs, and water including sewage are listed in tables.

Animals↗