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Volume 71 (2022): Issue 3 (September 2022)

Volume 71 (2022): Issue 2 (June 2022)

Volume 71 (2022): Issue 1 (March 2022)

Volume 70 (2021): Issue 4 (December 2021)

Volume 70 (2021): Issue 3 (September 2021)

Volume 70 (2021): Issue 2 (June 2021)

Volume 70 (2021): Issue 1 (March 2021)

Volume 69 (2020): Issue 4 (December 2020)

Volume 69 (2020): Issue 3 (September 2020)

Volume 69 (2020): Issue 2 (June 2020)

Volume 69 (2020): Issue 1 (March 2020)

Volume 68 (2019): Issue 4 (January 2019)

Volume 68 (2019): Issue 3 (September 2019)

Volume 68 (2019): Issue 2 (June 2019)

Volume 68 (2019): Issue 1 (March 2019)

Volume 67 (2018): Issue 4 (December 2018)

Volume 67 (2018): Issue 3 (September 2018)

Volume 67 (2018): Issue 2 (June 2018)

Volume 67 (2018): Issue 1 (January 2018)

Volume 66 (2017): Issue 4 (December 2017)

Volume 66 (2017): Issue 3 (September 2017)

Volume 66 (2017): Issue 2 (June 2017)

Volume 66 (2017): Issue 1 (March 2017)

Volume 65 (2016): Issue 4 (December 2016)

Volume 65 (2016): Issue 3 (August 2016)

Volume 65 (2016): Issue 2 (June 2016)

Volume 65 (2016): Issue 1 (March 2016)

Journal Details
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English

Search

Volume 70 (2021): Issue 2 (June 2021)

Journal Details
Format
Journal
eISSN
2544-4646
First Published
04 Mar 1952
Publication timeframe
4 times per year
Languages
English

Search

12 Articles

original-paper

Open Access

First Description of Various Bacteria Resistant to Heavy Metals and Antibiotics Isolated from Polluted Sites in Tunisia

Published Online: 06 Dec 2021
Page range: 161 - 174

Abstract

Abstract

Environmental bacteria belonging to various families were isolated from polluted water collected from ten different sites in Tunisia. Sites were chosen near industrial and urban areas known for their high degree of pollution. The aim of this study was to investigate cross-resistance between heavy metals (HM), i.e., silver, mercury and copper (Ag, Hg, and Cu), and antibiotics. In an initial screening, 80 isolates were selected on ampicillin, and 39 isolates, retained for further analysis, could grow on a Tris-buffered mineral medium with gluconate as carbon source. Isolates were identified based on their 16S rRNA gene sequence. Results showed the prevalence of antibiotic resistance genes, especially all isolates harbored the blaTEM gene. Some of them (15.38%) harbored blaSHV. Moreover, several were even ESBLs and MBLs-producers, which can threaten the human health. On the other hand, 92.30%, 56.41%, and 51.28% of the isolates harbored the heavy metals resistance genes silE, cusA, and merA, respectively. These genes confer resistance to silver, copper, and mercury. A cross-resistance between antibiotics and heavy metals was detected in 97.43% of our isolates.

Keywords

  • contaminated water
  • environmental bacteria
  • heavy metals (HM)
  • antibiotics (AB)
  • cross-resistance
Open Access

Comparative Analysis of the Microbiota Between Rumen and Duodenum of Twin Lambs Based on Diets of Ceratoides or Alfalfa

Published Online: 06 Dec 2021
Page range: 175 - 187

Abstract

Abstract

In our previous study, diet directly impacted the microbiota of the rumen in twin lambs. The duodenum is the first part of the small intestine, so we seek to determine whether there is a difference in the digesta between the two feed groups HFLP (high fiber, low protein) and LFHP (low fiber, high protein), and its impact on the biodiversity and metabolism of the duodenum. Results showed that the number of Operational Taxonomic Units (OTUs) in the duodenum (2,373 OTUs) was more than those in the rumen (1,230 OTUs), and 143 OTUs were significantly different in the duodenum between the two groups. The two most predominant phyla were Bacteriodetes and Firmicutes, but this ratio was reversed between the rumen and duodenum of lambs fed different feedstuffs. The difference in the digesta that greatly changed the biodiversity of the rumen and duodenum could affect the microbial community in the gastrointestinal tract (GIT). Sixteen metabolites were significantly different in the duodenum between the two groups based on the metabolome analysis. The relationships were built between the microbiome and the metabolome based on the correlation analysis. Some metabolites have a potential role in influencing meat quality, which indicated that the diet could affect the microbiota community and finally change meat quality. This study could explain how the diet affects the rumen and duodenum’s microbiota, lay a theoretical basis for controlling feed intake, and determine the relationship between the duodenum’s microbiota and metabolism.

Keywords

  • correlation analysis
  • digesta
  • metabolome
  • 16S rRNA sequencing
  • sheep
Open Access

Genomic Analysis of the Mycoparasite Pestalotiopsis sp. PG52

Published Online: 06 Dec 2021
Page range: 189 - 199

Abstract

Abstract

Pestalotiopsis sp. is a mycoparasite of the plant pathogen Aecidium wenshanense. To further understand the mycoparasitism mechanism of Pestalotiopsis sp., we assembled and analyzed its genome. The genome of Pestalotiopsis sp. strain PG52 was assembled into 335 scaffolds and had a size of 58.01 Mb. A total of 20,023 predicted genes and proteins were annotated. This study compared PG52 with the mycoparasites Trichoderma harzianum, Trichoderma atroviride, and Trichoderma virens. This study reveals the entirely different mycoparasitism mechanism of Pestalotiopsis compared to Trichoderma and reveals this mycoparasite’s strong ability to produce secondary metabolites.

Keywords

  • genome
  • DNA sequencing
  • sp.
  • mycoparasite
Open Access

Screening of Human Immunodeficiency Virus (HIV) among Newly Diagnosed Tuberculosis Patients in Eastern Sudan

Published Online: 06 Dec 2021
Page range: 201 - 206

Abstract

Abstract

Tuberculosis (TB) is a leading cause of death in patients infected with Human Immunodeficiency Virus (HIV), and HIV infection is the most potent risk factor for the development of active TB disease from a latent TB infection. This study aims to determine the seroprevalence of HIV among newly diagnosed TB patients in Kassala state eastern Sudan. This was a descriptive, hospital-based, cross-sectional study of 251 active and newly diagnosed TB patients, selected by simple random sampling. Blood samples and demographic data were collected from each patient. TB was diagnosed by direct ZN smear and molecular detection by Xpert MTB/RIF. The serum samples were tested for HIV using 4th generation enzyme-linked immunosorbent assay (ELISA). The prevalence of HIV was 13.9% (35/251), the infection rate among pulmonary TB was 17%, whereas that in extrapulmonary TB was 4.8%, the prevalence was (18.2%) in the males, and (7.2%) in the females. In conclusion: TB/HIV co-infection in the Eastern part of Sudan was high compared with the global prevalence, all TB patients should therefore be assessed for HIV risk factors and advised to undergo HIV testing.

Keywords

  • Tuberculosis
  • ELISA
  • HIV
  • ZN
  • Xpert MTB/RIF
Open Access

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for Identification of Microorganisms in Clinical Urine Specimens after Two Pretreatments

Published Online: 06 Dec 2021
Page range: 207 - 213

Abstract

Abstract

Rapid identification of microorganisms in urine is essential for patients with urinary tract infections (UTIs). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed as a method for the direct identification of urinary pathogens. Our purpose was to compare centrifugation-based MALDI-TOF MS and short-term culture combined with MALDI-TOF MS for the direct identification of pathogens in urine specimens. We collected 965 urine specimens from patients with suspected UTIs, 211/965 isolates were identified as positive by conventional urine culture. Compared with the conventional method, the results of centrifugation-based MALDI-TOF MS were consistent in 159/211 cases (75.4%), of which 135/159 (84.9%) had scores ≥ 2.00; 182/211 cases (86.3%) were detected using short-term culture combined with MALDI-TOF MS, of which 153/182 (84.1%) had scores ≥ 2.00. There were no apparent differences among the three methods (p = 0.135). MALDI-TOF MS appears to accelerate the microbial identification speed in urine and saves at least 24 to 48 hours compared with the routine urine culture. Centrifugation-based MALDI-TOF MS is characterized by faster identification speed; however, it is substantially affected by the number of bacterial colonies. In contrast, short-term culture combined with MALDI-TOF MS has a higher detection rate but a relatively slow identification speed. Combining these characteristics, the two methods may be effective and reliable alternatives to traditional urine culture.

Keywords

  • Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS)
  • rapid identification
  • urinary tract infection
Open Access

Environmental Factors Associated with the Eukaryotic Microbial Community and Microalgal Groups in the Mountain Marshes of South Korea

Published Online: 06 Dec 2021
Page range: 215 - 233

Abstract

Abstract

The diversity indices of eukaryotic microalgal groups in the Jeonglyeongchi, Waegok, and Wangdeungjae marshes of Mount Jiri, Korea, were measured using Illumina MiSeq and culture-based analyses. Waegok marsh had the highest species richness, with a Chao1 value of 828.00, and the highest levels of species diversity, with Shannon and Simpson index values of 6.36 and 0.94, respectively, while Wangdeungjae marsh had the lowest values at 2.97 and 0.75, respectively. The predominant species in all communities were Phagocata sibirica (Jeonglyeongchi, 68.64%), Aedes albopictus (Waegok, 34.77%), Chaetonotus cf. (Waegok, 24.43%), Eimeria sp. (Wangdeungjae, 26.17%), and Eumonhystera cf. (Wangdeungjae, 22.27%). Relative abundances of the microalgal groups Bacillariophyta (diatoms) and Chlorophyta (green algae) in each marsh were respectively: Jeonglyeongchi 1.38% and 0.49%, Waegok 7.0% and 0.3%, and Wangdeungjae 10.41% and 4.72%. Illumina MiSeq analyses revealed 34 types of diatoms and 13 types of green algae. Only one diatom (Nitzschia dissipata) and five green algae (Neochloris sp., Chlamydomonas sp., Chlorococcum sp., Chlorella vulgaris, Scenedesmus sp.) were identified by a culture-based analysis. Thus, Illumina MiSeq analysis can be considered an efficient tool for analyzing microbial communities. Overall, our results described the environmental factors associated with geographically isolated mountain marshes and their respective microbial and microalgal communities.

Keywords

  • environmental sample
  • Illumina MiSeq
  • Mount Jiri marshes
  • microbial community
  • microalgal community
Open Access

The Effect of Lactobacillus plantarum BW2013 on The Gut Microbiota in Mice Analyzed by 16S rRNA Amplicon Sequencing

Published Online: 06 Dec 2021
Page range: 235 - 243

Abstract

Abstract

Lactobacillus plantarum BW2013 was isolated from the fermented Chinese cabbage. This study aimed to test the effect of this strain on the gut microbiota in BALB/c mice by 16S rRNA amplicon sequencing. The mice were randomly allocated to the control group and three treatment groups of L. plantarum BW2013 (a low-dose group of 108 CFU/ml, a medium-dose group of 109 CFU/ml, and a high-dose group of 1010 CFU/ml). The weight of mice was recorded once a week, and the fecal samples were collected for 16S rRNA amplicon sequencing after 28 days of continuous treatment. Compared with the control group, the body weight gain in the treatment groups was not significant. The 16S rRNA amplicon sequencing analysis showed that both the Chao1 and ACE indexes increased slightly in the medium-dose group compared to the control group, but the difference was not significant. Based on PCoA results, there was no significant difference in β diversity between the treatment groups. Compared to the control group, the abundance of Bacteroidetes increased in the low-dose group. The abundance of Firmicutes increased in the medium-dose group. At the genus level, the abundance of Alloprevotella increased in the low-dose group compared to the control group. The increased abundance of Ruminococcaceae and decreased abundance of Candidatus_Saccharimonas was observed in the medium-dose group. Additionally, the abundance of Bacteroides increased, and Alistipes and Candidatus_Saccharimonas decreased in the high-dose group. These results indicated that L. plantarum BW2013 could ameliorate gut microbiota composition, but its effects vary with the dose.

Keywords

  • composition
  • gut microbiota
  • 16S rRNA amplicon sequencing
  • BALB/c mice
Open Access

Isolation, Identification, Biocontrol Activity, and Plant Growth Promoting Capability of a Superior Streptomyces tricolor Strain HM10

Published Online: 06 Dec 2021
Page range: 245 - 256

Abstract

Abstract

Streptomyces is a genus with known biocontrol activity, producing a broad range of biologically active substances. Our goal was to isolate local Streptomyces species, evaluate their capacity to biocontrol the selected phytopathogens, and promote the plant growth via siderophore and indole acetic acid (IAA) production and phosphate solubilization. Eleven isolates were obtained from local soil samples in Saudi Arabia via the standard serial dilution method and identified morphologically by scanning electron microscope (SEM) and 16S rRNA amplicon sequencing. The biocontrol of phytopathogens was screened against known soil-borne fungi and bacteria. Plant growth promotion capacity was evaluated based on siderophore and IAA production and phosphate solubilization capacity. From eleven isolates obtained, one showed 99.77% homology with the type strain Streptomyces tricolor AS 4.1867, and was designated S. tricolor strain HM10. It showed aerial hyphae in SEM, growth inhibition of ten known phytopathogens in in vitro experiments, and the production of plant growth promoting compounds such as siderophores, IAA, and phosphate solubilization capacity. S. tricolor strain HM10 exhibited high antagonism against the fungi tested (i.e., Colletotrichum gloeosporides with an inhibition zone exceeding 18 mm), whereas the lowest antagonistic effect was against Alternaria solani (an inhibition zone equal to 8 mm). Furthermore, the most efficient siderophore production was recorded to strain HM8, followed by strain HM10 with 64 and 22.56 h/c (halo zone area/colony area), respectively. Concerning IAA production, Streptomyces strain HM10 was the most effective producer with a value of 273.02 μg/ml. An autochthonous strain S. tricolor HM10 should be an important biological agent to control phytopathogens and promote plant growth.

Keywords

  • HM10
  • plant growth-promoting
  • biocontrol
  • soil-borne disease
Open Access

Enhancing the Efficiency of Soybean Inoculant for Nodulation under Multi-Environmental Stress Conditions

Published Online: 06 Dec 2021
Page range: 257 - 271

Abstract

Abstract

The development of rhizobial inoculants with increased resistance to abiotic stress is critical to mitigating the challenges related to climate change. This study aims at developing a soybean stress-tolerant Bradyrhizobium inoculant to be used under the mixed stress conditions of acidity, high temperature, and drought. Six isolates of Bradyrhizobium with high symbiotic performance on soybean were tested to determine their growth or survival abilities under in vitro conditions. The representative stress-tolerant Bradyrhizobium isolates 184, 188, and 194 were selected to test their ability to promote soybean growth under stress conditions compared to the type strain Bradyrhizobium diazoefficiens USDA110. The plant experiment indicated that isolate 194 performed better in symbiosis with soybean than other Bradyrhizobium strains under stress conditions. Based on the stress tolerance index, soybeans inoculated with isolate 194 showed a high growth performance and significantly better nodulation competition ability than USDA110 under several stress conditions. Interestingly, supplementation of sucrose in the culture medium significantly enhances the survival of the isolate and leads to improved plant biomass under various stress conditions. Analysis of the intra-cellular sugars of isolate 194 supplemented with sucrose showed the accumulation of compatible solutes, such as trehalose and glycerol, that may act as osmoprotectants. This study indicates that inoculation of stress-tolerant Bradyrhizobium together with sucrose supplementation in a medium could enhance bacterial survival and symbiosis efficiency under stress conditions. Although it can be applied for inoculant production, this strategy requires validation of its performance in field conditions before adopting this technology.

Keywords

  • nodulation competition
  • stress conditions
  • compatible solutes
  • osmoprotectant
Open Access

Diversity of Endophytic Fungal Community in Leaves of Artemisia argyi Based on High-throughput Amplicon Sequencing

Published Online: 06 Dec 2021
Page range: 273 - 281

Abstract

Abstract

To investigate the community structure and diversity of endophytic fungi in the leaves of Artemisia argyi, leaf samples were collected from five A. argyi varieties grown in different cultivation areas in China, namely, Tangyin Beiai in Henan (BA), Qichun Qiai in Hubei (QA), Wanai in Nanyang in Henan (WA), Haiai in Ningbo in Zhejiang (HA), and Anguo Qiai in Anguo in Hebei (AQA), and analyzed using Illumina high-throughput sequencing technology. A total of 365,919 pairs of reads were obtained, and the number of operational taxonomic units for each sample was between 165 and 285. The alpha diversity of the QA and BA samples was higher, and a total of two phyla, eight classes, 12 orders, 15 families, and 16 genera were detected. At the genus level, significant differences were noted in the dominant genera among the samples, with three genera being shared in all the samples. The dominant genus in QA was Erythrobasidium, while that in AQA, HA, and BA was Sporobolomyces, and that in WA was Alternaria, reaching a proportion of 16.50%. These results showed that the fungal community structure and diversity in QA and BA were high. The endophytes are of great importance to the plants, especially for protection, phytohormone and other phytochemical production, and nutrition. Therefore, this study may be significant with the industrial perspective of Artemisia species.

Keywords

  • endophytic fungus
  • leaf
  • Illumina
  • next-generation sequencing

mini-review

Open Access

Emerging Applications of Bacteriocins as Antimicrobials, Anticancer Drugs, and Modulators of The Gastrointestinal Microbiota

Published Online: 06 Dec 2021
Page range: 143 - 159

Abstract

Abstract

The use of bacteriocins holds great promise in different areas such as health, food, nutrition, veterinary, nanotechnology, among others. Many research groups worldwide continue to advance the knowledge to unravel a novel range of therapeutic agents and food preservatives. This review addresses the advances of bacteriocins and their producer organisms as biocontrol agents for applications in the medical industry and agriculture. Furthermore, the bacteriocin mechanism of action and structural characteristics will be reviewed. Finally, the potential role of bacteriocins to modulate the signaling in host-associated microbial communities will be discussed.

Keywords

  • bacteriocin
  • bio-preservatives
  • agriculture
  • biomedical
  • microbial communities

short-communication

Open Access

Occurrence of Beta-Lactamases in Colistin-Resistant Enterobacterales Strains in Poland – a Pilot Study

Published Online: 06 Dec 2021
Page range: 283 - 288

Abstract

Abstract

Sixty-five colistin-resistant Enterobacterales isolates recovered from different clinical specimens were analyzed. The strains were collected in 12 hospitals all over Poland within a period of nine months. Strains were analyzed for eight genes from the mcr family. The presence of mcr-1 gene was detected in three Escherichia coli strains. The 45/65 isolates were identified as ESBL producers. CTX-M-1-like enzymes were the most common ESBLs (n = 40). One E. coli and seven Klebsiella pneumoniae strains produced carbapenemases, with the NDM being produced by five isolates. Among all the strains tested, four and five were resistant to new drugs meropenem/vaborbactam and ceftazidime/avibactam, respectively.

Keywords

  • Enterobacterales
  • colistin-resistance
  • ESBLs
  • carbapenemases
12 Articles

original-paper

Open Access

First Description of Various Bacteria Resistant to Heavy Metals and Antibiotics Isolated from Polluted Sites in Tunisia

Published Online: 06 Dec 2021
Page range: 161 - 174

Abstract

Abstract

Environmental bacteria belonging to various families were isolated from polluted water collected from ten different sites in Tunisia. Sites were chosen near industrial and urban areas known for their high degree of pollution. The aim of this study was to investigate cross-resistance between heavy metals (HM), i.e., silver, mercury and copper (Ag, Hg, and Cu), and antibiotics. In an initial screening, 80 isolates were selected on ampicillin, and 39 isolates, retained for further analysis, could grow on a Tris-buffered mineral medium with gluconate as carbon source. Isolates were identified based on their 16S rRNA gene sequence. Results showed the prevalence of antibiotic resistance genes, especially all isolates harbored the blaTEM gene. Some of them (15.38%) harbored blaSHV. Moreover, several were even ESBLs and MBLs-producers, which can threaten the human health. On the other hand, 92.30%, 56.41%, and 51.28% of the isolates harbored the heavy metals resistance genes silE, cusA, and merA, respectively. These genes confer resistance to silver, copper, and mercury. A cross-resistance between antibiotics and heavy metals was detected in 97.43% of our isolates.

Keywords

  • contaminated water
  • environmental bacteria
  • heavy metals (HM)
  • antibiotics (AB)
  • cross-resistance
Open Access

Comparative Analysis of the Microbiota Between Rumen and Duodenum of Twin Lambs Based on Diets of Ceratoides or Alfalfa

Published Online: 06 Dec 2021
Page range: 175 - 187

Abstract

Abstract

In our previous study, diet directly impacted the microbiota of the rumen in twin lambs. The duodenum is the first part of the small intestine, so we seek to determine whether there is a difference in the digesta between the two feed groups HFLP (high fiber, low protein) and LFHP (low fiber, high protein), and its impact on the biodiversity and metabolism of the duodenum. Results showed that the number of Operational Taxonomic Units (OTUs) in the duodenum (2,373 OTUs) was more than those in the rumen (1,230 OTUs), and 143 OTUs were significantly different in the duodenum between the two groups. The two most predominant phyla were Bacteriodetes and Firmicutes, but this ratio was reversed between the rumen and duodenum of lambs fed different feedstuffs. The difference in the digesta that greatly changed the biodiversity of the rumen and duodenum could affect the microbial community in the gastrointestinal tract (GIT). Sixteen metabolites were significantly different in the duodenum between the two groups based on the metabolome analysis. The relationships were built between the microbiome and the metabolome based on the correlation analysis. Some metabolites have a potential role in influencing meat quality, which indicated that the diet could affect the microbiota community and finally change meat quality. This study could explain how the diet affects the rumen and duodenum’s microbiota, lay a theoretical basis for controlling feed intake, and determine the relationship between the duodenum’s microbiota and metabolism.

Keywords

  • correlation analysis
  • digesta
  • metabolome
  • 16S rRNA sequencing
  • sheep
Open Access

Genomic Analysis of the Mycoparasite Pestalotiopsis sp. PG52

Published Online: 06 Dec 2021
Page range: 189 - 199

Abstract

Abstract

Pestalotiopsis sp. is a mycoparasite of the plant pathogen Aecidium wenshanense. To further understand the mycoparasitism mechanism of Pestalotiopsis sp., we assembled and analyzed its genome. The genome of Pestalotiopsis sp. strain PG52 was assembled into 335 scaffolds and had a size of 58.01 Mb. A total of 20,023 predicted genes and proteins were annotated. This study compared PG52 with the mycoparasites Trichoderma harzianum, Trichoderma atroviride, and Trichoderma virens. This study reveals the entirely different mycoparasitism mechanism of Pestalotiopsis compared to Trichoderma and reveals this mycoparasite’s strong ability to produce secondary metabolites.

Keywords

  • genome
  • DNA sequencing
  • sp.
  • mycoparasite
Open Access

Screening of Human Immunodeficiency Virus (HIV) among Newly Diagnosed Tuberculosis Patients in Eastern Sudan

Published Online: 06 Dec 2021
Page range: 201 - 206

Abstract

Abstract

Tuberculosis (TB) is a leading cause of death in patients infected with Human Immunodeficiency Virus (HIV), and HIV infection is the most potent risk factor for the development of active TB disease from a latent TB infection. This study aims to determine the seroprevalence of HIV among newly diagnosed TB patients in Kassala state eastern Sudan. This was a descriptive, hospital-based, cross-sectional study of 251 active and newly diagnosed TB patients, selected by simple random sampling. Blood samples and demographic data were collected from each patient. TB was diagnosed by direct ZN smear and molecular detection by Xpert MTB/RIF. The serum samples were tested for HIV using 4th generation enzyme-linked immunosorbent assay (ELISA). The prevalence of HIV was 13.9% (35/251), the infection rate among pulmonary TB was 17%, whereas that in extrapulmonary TB was 4.8%, the prevalence was (18.2%) in the males, and (7.2%) in the females. In conclusion: TB/HIV co-infection in the Eastern part of Sudan was high compared with the global prevalence, all TB patients should therefore be assessed for HIV risk factors and advised to undergo HIV testing.

Keywords

  • Tuberculosis
  • ELISA
  • HIV
  • ZN
  • Xpert MTB/RIF
Open Access

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for Identification of Microorganisms in Clinical Urine Specimens after Two Pretreatments

Published Online: 06 Dec 2021
Page range: 207 - 213

Abstract

Abstract

Rapid identification of microorganisms in urine is essential for patients with urinary tract infections (UTIs). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed as a method for the direct identification of urinary pathogens. Our purpose was to compare centrifugation-based MALDI-TOF MS and short-term culture combined with MALDI-TOF MS for the direct identification of pathogens in urine specimens. We collected 965 urine specimens from patients with suspected UTIs, 211/965 isolates were identified as positive by conventional urine culture. Compared with the conventional method, the results of centrifugation-based MALDI-TOF MS were consistent in 159/211 cases (75.4%), of which 135/159 (84.9%) had scores ≥ 2.00; 182/211 cases (86.3%) were detected using short-term culture combined with MALDI-TOF MS, of which 153/182 (84.1%) had scores ≥ 2.00. There were no apparent differences among the three methods (p = 0.135). MALDI-TOF MS appears to accelerate the microbial identification speed in urine and saves at least 24 to 48 hours compared with the routine urine culture. Centrifugation-based MALDI-TOF MS is characterized by faster identification speed; however, it is substantially affected by the number of bacterial colonies. In contrast, short-term culture combined with MALDI-TOF MS has a higher detection rate but a relatively slow identification speed. Combining these characteristics, the two methods may be effective and reliable alternatives to traditional urine culture.

Keywords

  • Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS)
  • rapid identification
  • urinary tract infection
Open Access

Environmental Factors Associated with the Eukaryotic Microbial Community and Microalgal Groups in the Mountain Marshes of South Korea

Published Online: 06 Dec 2021
Page range: 215 - 233

Abstract

Abstract

The diversity indices of eukaryotic microalgal groups in the Jeonglyeongchi, Waegok, and Wangdeungjae marshes of Mount Jiri, Korea, were measured using Illumina MiSeq and culture-based analyses. Waegok marsh had the highest species richness, with a Chao1 value of 828.00, and the highest levels of species diversity, with Shannon and Simpson index values of 6.36 and 0.94, respectively, while Wangdeungjae marsh had the lowest values at 2.97 and 0.75, respectively. The predominant species in all communities were Phagocata sibirica (Jeonglyeongchi, 68.64%), Aedes albopictus (Waegok, 34.77%), Chaetonotus cf. (Waegok, 24.43%), Eimeria sp. (Wangdeungjae, 26.17%), and Eumonhystera cf. (Wangdeungjae, 22.27%). Relative abundances of the microalgal groups Bacillariophyta (diatoms) and Chlorophyta (green algae) in each marsh were respectively: Jeonglyeongchi 1.38% and 0.49%, Waegok 7.0% and 0.3%, and Wangdeungjae 10.41% and 4.72%. Illumina MiSeq analyses revealed 34 types of diatoms and 13 types of green algae. Only one diatom (Nitzschia dissipata) and five green algae (Neochloris sp., Chlamydomonas sp., Chlorococcum sp., Chlorella vulgaris, Scenedesmus sp.) were identified by a culture-based analysis. Thus, Illumina MiSeq analysis can be considered an efficient tool for analyzing microbial communities. Overall, our results described the environmental factors associated with geographically isolated mountain marshes and their respective microbial and microalgal communities.

Keywords

  • environmental sample
  • Illumina MiSeq
  • Mount Jiri marshes
  • microbial community
  • microalgal community
Open Access

The Effect of Lactobacillus plantarum BW2013 on The Gut Microbiota in Mice Analyzed by 16S rRNA Amplicon Sequencing

Published Online: 06 Dec 2021
Page range: 235 - 243

Abstract

Abstract

Lactobacillus plantarum BW2013 was isolated from the fermented Chinese cabbage. This study aimed to test the effect of this strain on the gut microbiota in BALB/c mice by 16S rRNA amplicon sequencing. The mice were randomly allocated to the control group and three treatment groups of L. plantarum BW2013 (a low-dose group of 108 CFU/ml, a medium-dose group of 109 CFU/ml, and a high-dose group of 1010 CFU/ml). The weight of mice was recorded once a week, and the fecal samples were collected for 16S rRNA amplicon sequencing after 28 days of continuous treatment. Compared with the control group, the body weight gain in the treatment groups was not significant. The 16S rRNA amplicon sequencing analysis showed that both the Chao1 and ACE indexes increased slightly in the medium-dose group compared to the control group, but the difference was not significant. Based on PCoA results, there was no significant difference in β diversity between the treatment groups. Compared to the control group, the abundance of Bacteroidetes increased in the low-dose group. The abundance of Firmicutes increased in the medium-dose group. At the genus level, the abundance of Alloprevotella increased in the low-dose group compared to the control group. The increased abundance of Ruminococcaceae and decreased abundance of Candidatus_Saccharimonas was observed in the medium-dose group. Additionally, the abundance of Bacteroides increased, and Alistipes and Candidatus_Saccharimonas decreased in the high-dose group. These results indicated that L. plantarum BW2013 could ameliorate gut microbiota composition, but its effects vary with the dose.

Keywords

  • composition
  • gut microbiota
  • 16S rRNA amplicon sequencing
  • BALB/c mice
Open Access

Isolation, Identification, Biocontrol Activity, and Plant Growth Promoting Capability of a Superior Streptomyces tricolor Strain HM10

Published Online: 06 Dec 2021
Page range: 245 - 256

Abstract

Abstract

Streptomyces is a genus with known biocontrol activity, producing a broad range of biologically active substances. Our goal was to isolate local Streptomyces species, evaluate their capacity to biocontrol the selected phytopathogens, and promote the plant growth via siderophore and indole acetic acid (IAA) production and phosphate solubilization. Eleven isolates were obtained from local soil samples in Saudi Arabia via the standard serial dilution method and identified morphologically by scanning electron microscope (SEM) and 16S rRNA amplicon sequencing. The biocontrol of phytopathogens was screened against known soil-borne fungi and bacteria. Plant growth promotion capacity was evaluated based on siderophore and IAA production and phosphate solubilization capacity. From eleven isolates obtained, one showed 99.77% homology with the type strain Streptomyces tricolor AS 4.1867, and was designated S. tricolor strain HM10. It showed aerial hyphae in SEM, growth inhibition of ten known phytopathogens in in vitro experiments, and the production of plant growth promoting compounds such as siderophores, IAA, and phosphate solubilization capacity. S. tricolor strain HM10 exhibited high antagonism against the fungi tested (i.e., Colletotrichum gloeosporides with an inhibition zone exceeding 18 mm), whereas the lowest antagonistic effect was against Alternaria solani (an inhibition zone equal to 8 mm). Furthermore, the most efficient siderophore production was recorded to strain HM8, followed by strain HM10 with 64 and 22.56 h/c (halo zone area/colony area), respectively. Concerning IAA production, Streptomyces strain HM10 was the most effective producer with a value of 273.02 μg/ml. An autochthonous strain S. tricolor HM10 should be an important biological agent to control phytopathogens and promote plant growth.

Keywords

  • HM10
  • plant growth-promoting
  • biocontrol
  • soil-borne disease
Open Access

Enhancing the Efficiency of Soybean Inoculant for Nodulation under Multi-Environmental Stress Conditions

Published Online: 06 Dec 2021
Page range: 257 - 271

Abstract

Abstract

The development of rhizobial inoculants with increased resistance to abiotic stress is critical to mitigating the challenges related to climate change. This study aims at developing a soybean stress-tolerant Bradyrhizobium inoculant to be used under the mixed stress conditions of acidity, high temperature, and drought. Six isolates of Bradyrhizobium with high symbiotic performance on soybean were tested to determine their growth or survival abilities under in vitro conditions. The representative stress-tolerant Bradyrhizobium isolates 184, 188, and 194 were selected to test their ability to promote soybean growth under stress conditions compared to the type strain Bradyrhizobium diazoefficiens USDA110. The plant experiment indicated that isolate 194 performed better in symbiosis with soybean than other Bradyrhizobium strains under stress conditions. Based on the stress tolerance index, soybeans inoculated with isolate 194 showed a high growth performance and significantly better nodulation competition ability than USDA110 under several stress conditions. Interestingly, supplementation of sucrose in the culture medium significantly enhances the survival of the isolate and leads to improved plant biomass under various stress conditions. Analysis of the intra-cellular sugars of isolate 194 supplemented with sucrose showed the accumulation of compatible solutes, such as trehalose and glycerol, that may act as osmoprotectants. This study indicates that inoculation of stress-tolerant Bradyrhizobium together with sucrose supplementation in a medium could enhance bacterial survival and symbiosis efficiency under stress conditions. Although it can be applied for inoculant production, this strategy requires validation of its performance in field conditions before adopting this technology.

Keywords

  • nodulation competition
  • stress conditions
  • compatible solutes
  • osmoprotectant
Open Access

Diversity of Endophytic Fungal Community in Leaves of Artemisia argyi Based on High-throughput Amplicon Sequencing

Published Online: 06 Dec 2021
Page range: 273 - 281

Abstract

Abstract

To investigate the community structure and diversity of endophytic fungi in the leaves of Artemisia argyi, leaf samples were collected from five A. argyi varieties grown in different cultivation areas in China, namely, Tangyin Beiai in Henan (BA), Qichun Qiai in Hubei (QA), Wanai in Nanyang in Henan (WA), Haiai in Ningbo in Zhejiang (HA), and Anguo Qiai in Anguo in Hebei (AQA), and analyzed using Illumina high-throughput sequencing technology. A total of 365,919 pairs of reads were obtained, and the number of operational taxonomic units for each sample was between 165 and 285. The alpha diversity of the QA and BA samples was higher, and a total of two phyla, eight classes, 12 orders, 15 families, and 16 genera were detected. At the genus level, significant differences were noted in the dominant genera among the samples, with three genera being shared in all the samples. The dominant genus in QA was Erythrobasidium, while that in AQA, HA, and BA was Sporobolomyces, and that in WA was Alternaria, reaching a proportion of 16.50%. These results showed that the fungal community structure and diversity in QA and BA were high. The endophytes are of great importance to the plants, especially for protection, phytohormone and other phytochemical production, and nutrition. Therefore, this study may be significant with the industrial perspective of Artemisia species.

Keywords

  • endophytic fungus
  • leaf
  • Illumina
  • next-generation sequencing

mini-review

Open Access

Emerging Applications of Bacteriocins as Antimicrobials, Anticancer Drugs, and Modulators of The Gastrointestinal Microbiota

Published Online: 06 Dec 2021
Page range: 143 - 159

Abstract

Abstract

The use of bacteriocins holds great promise in different areas such as health, food, nutrition, veterinary, nanotechnology, among others. Many research groups worldwide continue to advance the knowledge to unravel a novel range of therapeutic agents and food preservatives. This review addresses the advances of bacteriocins and their producer organisms as biocontrol agents for applications in the medical industry and agriculture. Furthermore, the bacteriocin mechanism of action and structural characteristics will be reviewed. Finally, the potential role of bacteriocins to modulate the signaling in host-associated microbial communities will be discussed.

Keywords

  • bacteriocin
  • bio-preservatives
  • agriculture
  • biomedical
  • microbial communities

short-communication

Open Access

Occurrence of Beta-Lactamases in Colistin-Resistant Enterobacterales Strains in Poland – a Pilot Study

Published Online: 06 Dec 2021
Page range: 283 - 288

Abstract

Abstract

Sixty-five colistin-resistant Enterobacterales isolates recovered from different clinical specimens were analyzed. The strains were collected in 12 hospitals all over Poland within a period of nine months. Strains were analyzed for eight genes from the mcr family. The presence of mcr-1 gene was detected in three Escherichia coli strains. The 45/65 isolates were identified as ESBL producers. CTX-M-1-like enzymes were the most common ESBLs (n = 40). One E. coli and seven Klebsiella pneumoniae strains produced carbapenemases, with the NDM being produced by five isolates. Among all the strains tested, four and five were resistant to new drugs meropenem/vaborbactam and ceftazidime/avibactam, respectively.

Keywords

  • Enterobacterales
  • colistin-resistance
  • ESBLs
  • carbapenemases

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