Chemical and Microbial Characteristics of Blackening Disease in Lotus (Nelumbo nucifera Gaertn.) Caused by Hirschmanniella diversa Sher

The lotus (Nelumbo nucifera Gaertn.) is widely cultivated in Asia, but a blackening disease in the lotus tuber, called “kurokawa-senchu-byo”, is a serious problem caused by the Hirschmanniella diversa Sher plant-parasitic nematode. To effectively control the disease, we must elucidate the blackening mechanisms; therefore, in this study, we performed a soil chemical analysis and an evaluation of the disease level in the lotus cultivation fields, identified the chemical components of the black spots on the lotus surface, and performed a 16S rRNA gene-based microbial community analysis of the black spots. Using linear regression analysis, a positive linear relationship with a strong correlation between the damage index values and fertilizer components such as P2O5 was observed. As a result of scanning electron microscopy and energy-dispersive X-ray spectroscopy analysis, phosphorus (P) and iron (Fe) were found to be concentrated in the black spots of the lotus tubers. Furthermore, we found that the concentrations of P and Fe in the black spots were 1.5- and 2.7-fold higher, respectively, than those found in the healthy parts of the lotus tubers. A 16S rRNA gene analysis revealed that dissimilatory Fe(III)-reducing bacteria (DIRB) were predominant in the black spots, suggesting that these bacteria are important to the formation of P and Fe compounds in the black spots.

Download Full-text

Microbiome of Odontogenic Abscesses

Microorganisms ◽

10.3390/microorganisms9061307 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1307

Author(s):

Sebastian Böttger ◽

Silke Zechel-Gran ◽

Daniel Schmermund ◽

Philipp Streckbein ◽

Jan-Falco Wilbrand ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Oral Microbiome ◽

Minor Role ◽

Rrna Gene ◽

Sequencing Analysis ◽

Bacterial Strains ◽

16S Rrna Gene Analysis ◽

Odontogenic Infections ◽

Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

Download Full-text

Human Isolates of Large Colony-Forming β Hemolytic Group G Streptococci form a Distinct Clade upon 16S rRNA Gene Analysis

Streptococci and the Host - Advances in Experimental Medicine and Biology ◽

10.1007/978-1-4899-1825-3_87 ◽

1997 ◽

pp. 363-365 ◽

Cited By ~ 3

Author(s):

Norbert Schnitzler ◽

Gerhard Haase ◽

Andreas Podbielski ◽

Achim Kaufhold ◽

Christoph Lämmler ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Analysis ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Group G Streptococci ◽

Large Colony

Download Full-text

Resource Development and Investigation of Novel Species from Unidentified Pathogens in NCCP using MALDI-TOF MS and 16S rRNA Gene Analysis

Journal of Bacteriology and Virology ◽

10.4167/jbv.2016.46.4.201 ◽

2016 ◽

Vol 46 (4) ◽

pp. 201

Author(s):

Won Seon Yu ◽

Kyeong Min Lee ◽

Kyu Jam Hwang

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Novel Species ◽

Resource Development ◽

Gene Analysis ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Maldi Tof Ms ◽

Maldi Tof ◽

Tof Ms

Download Full-text

Clinical Relevance of the Microbiome in Odontogenic Abscesses

Biology ◽

10.3390/biology10090916 ◽

2021 ◽

Vol 10 (9) ◽

pp. 916

Author(s):

Sebastian Böttger ◽

Silke Zechel-Gran ◽

Daniel Schmermund ◽

Philipp Streckbein ◽

Jan-Falco Wilbrand ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Oral Microbiome ◽

Molecular Methods ◽

Gene Analysis ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Cultural Methods ◽

Odontogenic Abscess ◽

Polymicrobial Infections

Odontogenic abscesses are usually caused by bacteria of the oral microbiome. However, the diagnostic culture of these bacteria is often prone to errors and sometimes fails completely due to the fastidiousness of the relevant bacterial species. The question arises whether additional pathogen diagnostics using molecular methods provide additional benefits for diagnostics and therapy. Experimental 16S rRNA gene analysis with next-generation sequencing (NGS) and bioinformatics was used to identify the microbiome of the pus in patients with severe odontogenic infections and was compared to the result of standard diagnostic culture. The pus microbiome was determined in 48 hospitalized patients with a severe odontogenic abscess in addition to standard cultural pathogen detection. Cultural detection was possible in 41 (85.42%) of 48 patients, while a pus-microbiome could be determined in all cases. The microbiomes showed polymicrobial infections in 46 (95.83%) cases, while the picture of a mono-infection occurred only twice (4.17%). In most cases, a predominantly anaerobic spectrum with an abundance of bacteria was found in the pus-microbiome, while culture detected mainly Streptococcus, Staphylococcus, and Prevotella spp. The determination of the microbiome of odontogenic abscesses clearly shows a higher number of bacteria and a significantly higher proportion of anaerobes than classical cultural methods. The 16S rRNA gene analysis detects considerably more bacteria than conventional cultural methods, even in culture-negative samples. Molecular methods should be implemented as standards in medical microbiology diagnostics, particularly for the detection of polymicrobial infections with a predominance of anaerobic bacteria.

Download Full-text

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004879 ◽

2021 ◽

Vol 71 (7) ◽

Author(s):

Priya Lakra ◽

Helianthous Verma ◽

Chandni Talwar ◽

Durgesh Narain Singh ◽

Nirjara Singhvi ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Sequence Similarity ◽

Rrna Gene ◽

Species Delineation ◽

16S Rrna Gene Analysis ◽

Content Type ◽

Link Type ◽

The 16S Rrna Gene

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .

Download Full-text

Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor

Canadian Journal of Microbiology ◽

10.1139/cjm-2020-0012 ◽

2020 ◽

Vol 66 (9) ◽

pp. 495-504

Author(s):

Yan Zheng ◽

Xiaolong Hu ◽

Zhongjun Jia ◽

Paul L.E. Bodelier ◽

Zhiying Guo ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Illumina Miseq ◽

Rrna Gene ◽

Prokaryotic Community ◽

16S Rrna Gene Analysis ◽

Pit Mud ◽

Niche Competition ◽

Occurrence Patterns ◽

The 16S Rrna Gene

It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in different-aged pit mud (1, 6, and 10 years old) were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. Analysis of the 16S rRNA gene indicated that the prokaryotic community was significantly altered with pit mud age. There was a significant increase in the genera Methanosarcina, Methanobacterium, and Aminobacterium with increased age of pit mud, while the genus Lactobacillus showed a significant decreasing trend. Network analysis demonstrated that both synergetic co-occurrence and niche competition were dominated by 68 prokaryotic genera. These genera formed 10 hubs of co-occurrence patterns, mainly under the phyla Firmicutes, Euryarchaeota, and Bacteroidetes, playing important roles on ecosystem stability of the pit mud. Environmental variables (pH, NH4+, available P, available K, and Ca2+) correlated significantly with prokaryotic community assembly. The interaction of prokaryotic communities in the pit mud ecosystem and the relationship among prokaryotic communities and environmental factors contribute to the higher quality of the pit mud in older fermentation pits.

Download Full-text

Spoilage potential of spore-forming bacteria from refrigerated raw milk

Semina Ciências Agrárias ◽

10.5433/1679-0359.2018v39n5p2049 ◽

2018 ◽

Vol 39 (5) ◽

pp. 2049 ◽

Cited By ~ 2

Author(s):

José Carlos Ribeiro Júnior ◽

Ronaldo Tamanini ◽

André Luís Martinez de Oliveira ◽

Juliane Ribeiro ◽

Vanerli Beloti

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Shelf Life ◽

Lipolytic Activity ◽

Raw Milk ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Pasteurized Milk ◽

Bacillus Spp ◽

Aerobic Spores

Aerobic bacterial spores are an important group of microorganisms in raw milk. These microbes are thermoduric, whereas the vegetative forms are thermophilic, thermoduric and psychrotrophic and reduce the shelf life of pasteurized milk. In Brazil, there are a lack of studies on the load of aerobic spores in raw milk; thus, little is known about the spoilage activity of these organisms. The aim the present study was to quantify the aerobic spores in Brazilian refrigerated raw milk of dairy region of Castro, Paraná state, assess the potential proteolytic and/or lipolytic isolates and identify the microorganisms derived from the germination. Twenty milk samples were evaluated, and the aerobic spore count was performed after plating the samples following heat treatment at 80°C for 12 min. The activity proteolytic and lipolytic isolates were evaluated through subculture on milk agar and tributyrin agar, respectively, and these microorganisms were identified using partial 16S rRNA gene sequences that were compared through GenBank. The aerobic spore counts ranged from 1 to 3.7 log CFU.mL-1, with a mean of 1.75 (± 0.59) log CFU.mL-1. After spore germination, 137 aerobic bacterial isolates were obtained, 40 of which (29.2%) showed milk spoilage activity. Among these, 31 isolates (77.5%) were proteolytic and lipolytic, seven isolates (17.5%) were exclusively lipolytic and two isolates (5%) were only proteolytic. Based on the 16S rRNA gene analysis, Bacillus licheniformis (55%), Bacillus spp. (27.5%), Paenibacillus spp. (7.5%), Bacillus pumilus (5%), Bacillus circulans (2.5%) and Brevibacillus spp. (2.5%) were identified. Studies of Brazilian raw milk microbiota have not yet described B. circulans which are frequently detected in milk from other countries. Among the 22 B. licheniformis isolates, 21 microbes (95.5%) showed proteolytic and lipolytic activity, and one isolate (4.5%) exhibited only proteolytic activity. The two B. pumilus isolates were proteolytic and lipolytic, whereas the B. circulans isolate was only lipolytic. Among the 11 Bacillus spp. isolates, eight isolates (72.7%) were proteolytic and lipolytic, one isolate (9.1%) was proteolytic and the other two isolates (18.2%) were lipolytic. The three Paenibacillus spp. and Brevibacillus spp. isolates were primarily lipolytic. Therefore, to extend the shelf life of pasteurized milk, preventive measures must be adopted to reduce contamination with spores because one-third of these microorganisms exhibited proteolytic and/or lipolytic activity.

Download Full-text

Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02741-0 ◽

2004 ◽

Vol 54 (5) ◽

pp. 1669-1676 ◽

Cited By ~ 105

Author(s):

Yi-Chueh Lin ◽

Kazunori Uemori ◽

Dominique A. de Briel ◽

Vallapa Arunpairojana ◽

Akira Yokota

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Novel Species ◽

Rrna Gene ◽

Hexadecanoic Acid ◽

16S Rrna Gene Analysis ◽

Separate Branch ◽

The Family ◽

Diamino Acid

Seven strains of actinobacteria, isolated from soil, wounds, urine, cow faeces, human blood and butter, were characterized by a polyphasic approach to clarify their taxonomic position. On the basis of chemotaxonomy, 16S rRNA gene analysis and DNA relatedness, strain IAM 14851T can be classified within the cluster of the genus Leucobacter and is proposed as a novel species, Leucobacter albus sp. nov., with strain IAM 14851T (=TISTR 1515T) as the type strain. The other six strains formed a phylogenetically separate branch in the family Microbacteriaceae, having the following characteristics: the major menaquinones are MK-8 to MK-10, the DNA G+C content ranges from 62 to 68 mol%, the diamino acid in the cell wall is diaminobutyric acid and the muramic acid in the peptidoglycan is of the acetyl type. The major fatty acids are 12-methyltetradecanoic acid (anteiso-C15 : 0), hexadecanoic acid (C16 : 0), 14-methyl-pentadecanoic acid (iso-C16 : 0) and 14-methyl-hexadecanoic acid (anteiso-C17 : 0). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA hybridization and 16S rRNA gene sequence comparison, the novel genus Zimmermannella gen. nov. is proposed for these six strains. Four novel species are proposed: Zimmermannella helvola sp. nov. (type species; type strain IAM 14726T=NBRC 15775T=DSM 20419T=TISTR 1509T), Zimmermannella alba sp. nov. (type strain IAM 14724T=NBRC 15616T=TISTR 1510T), Zimmermannella bifida sp. nov. (type strain IAM 14848T=TISTR 1511T) and Zimmermannella faecalis sp. nov. (type strain IAM 15030T=NBRC 15706T=ATCC 13722T=TISTR 1514T).

Download Full-text