scholarly journals Bacterial Distribution, Biogenic Amine Contents, and Functionalities of Traditionally Made Doenjang, a Long-Term Fermented Soybean Food, from Different Areas of Korea

2021 ◽  
Vol 9 (7) ◽  
pp. 1348
Author(s):  
Su-Ji Jeong ◽  
Myeong-Seon Ryu ◽  
Hee-Jong Yang ◽  
Xuan-Hao Wu ◽  
Do-Youn Jeong ◽  
...  
Keyword(s):  
Biogenic Amine ◽  
Fibrinolytic Activity ◽  
Diversity Index ◽  
Arachidonic Acid Metabolism ◽  
Shannon Index ◽  
Β Diversity ◽  
Metabolic Functions ◽  
Α Diversity ◽  
Bacillus Spp ◽  
Soybean Food

Since doenjang quality depends on the bacterial composition, which ambient bacteria in the environment and production conditions influence, a complete understanding of the bacteria community in traditionally madetraditionally made doenjang (TMD) from different regions is needed. We aimed to investigate the bacteria composition and quality of TMD in the following areas: Chonbuk (CB), Chonnam (CN), Kyungsang (KS), Kangwon (KW), Chungchung (CC) provinces, and Jeju island (JJ) of Korea. Twenty-nine TMD samples from different regions were used to assess biogenic amine contents, bacteria composition using next-generation methods, and metabolic functions of the bacteria using Picrust2. Bacillus spp. were isolated, and their antioxidant and fibrinolytic activities were determined. Most TMD contained high amounts of beneficial bacteria (Bacillus, Lactobacillus, Pediococcus and Weissella). However, some KS samples contained harmful bacteria (Cronobacter, Proteus and Acinetobacter) and less beneficial B. velezensis bacteria. There was no similarity among the regional groups, and each TMD showed a different bacteria composition. Shannon index, α-diversity index, was lower in TMD from JJ and CB than the other areas, but there was no β-diversity among TMD from the six area groups. Picrust2 analysis revealed that the functional potential for arachidonic acid metabolism was lowest in JJ and CN, that for supporting insulin action was highest in KS and JJ, and that for carbohydrate digestion and absorption was lowest in CB and JJ among all groups (p < 0.05) according to the Kyoto Encyclopedia of Genes and Genomes Orthology. Histamine contents were lower in CN and CC, and tyramine contents did not differ significantly. B. velezensis, B. subtilis, B. licheniformis, B. siamensis, and B. amyloliquefaciens were isolated from TMD. None of the isolated Bacillus spp. contained the B. cereus gene. B. subtilis from CN had the highest fibrinolytic activity, and B. velezensis from CB had the highest antioxidant activity. In conclusion, TMD mainly contained various Bacillus spp., and the predominant one was B. velezensis, which had antioxidant and fibrinolytic activity regardless of the regional origin.

scholarly journals Diversity of scorpions (Arachnida: Scorpiones) in Polonnaruwa Archaeological Reserve, Sri Lanka

2020 ◽  
Vol 12 (15) ◽  
pp. 17121-17128
Author(s):  
Kumudu B. Wijesooriya ◽  
Lakshani S. Weerasekara ◽  
Kithsiri B. Ranawana
Keyword(s):  
Sri Lanka ◽  
Diversity Index ◽  
Species Abundance ◽  
Abundant Species ◽  
Shannon Index ◽  
Habitat Modification ◽  
Future Research ◽  
Α Diversity ◽  
Distribution And Ecology ◽  
The Impact

Sri Lanka harbours 20 scorpion species belonging to four families, of which 15 are endemic.  The distribution and ecology of scorpion fauna in Sri Lanka is poorly known.  In this study, we surveyed the diversity of scorpions in the Polonnaruwa Archaeological Reserve in the dry zone of Sri Lanka.  Microhabitats were thoroughly observed using the direct visual encounter method and UV lights from July to November 2018 for about seven hours (19.00–02.00 h) by two to three observers.  Species, abundance, age/sex, and microhabitat features were recorded.  Diversity indices, including α-diversity and β-diversity, were calculated. Heterometrus swammerdami was the most abundant species recorded, while Isometrus thwaitesi was the rarest.  Reddyanus loebli and R. besucheti were common in both open and forest habitat types.  Charmus laneus was recorded for the first time in Polonnaruwa.  The highest Shannon Index and Margalef Diversity Index values were recorded in open habitats, but species evenness was low compared to forest habitats.  Sørensen index values showed a 58% species similarity between two habitats.  The results presented here contribute to the knowledge of the diversity of scorpions in these historically significant sites.  This can serve as a basis for future research on the impact of habitat modification and fragmentation on populations, distribution and ecology of scorpions.

scholarly journals The Dynamics of Respiratory Microbiota during Mechanical Ventilation in Patients with Pneumonia

2020 ◽  
Vol 9 (3) ◽  
pp. 638 ◽  
Author(s):  
Seongji Woo ◽  
So-Yeong Park ◽  
Youngmi Kim ◽  
Jin Pyeong Jeon ◽  
Jae Jun Lee ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Intensive Care ◽  
Clinical Outcomes ◽  
Extubation Failure ◽  
Shannon Index ◽  
Β Diversity ◽  
Α Diversity ◽  
Significant Difference ◽  
Respiratory Microbiome ◽  
Successful Extubation

Bacterial pneumonia is a major cause of mechanical ventilation in intensive care units. We hypothesized that the presence of particular microbiota in endotracheal tube aspirates during the course of intubation was associated with clinical outcomes such as extubation failure or 28-day mortality. Sixty mechanically ventilated ICU (intensive care unit) patients (41 patients with pneumonia and 19 patients without pneumonia) were included, and tracheal aspirates were obtained on days 1, 3, and 7. Gene sequencing of 16S rRNA was used to measure the composition of the respiratory microbiome. A total of 216 endotracheal aspirates were obtained from 60 patients. A total of 22 patients were successfully extubatedwithin3 weeks, and 12 patients died within 28days. Microbiota profiles differed significantly between the pneumonia group and the non-pneumonia group (Adonis, p < 0.01). While α diversity (Shannon index) significantly decreased between day 1 and day 7 in the successful extubation group, it did not decrease in the failed extubation group among intubated patients with pneumonia. There was a significant difference in the change of βdiversity between the successful extubation group and the failed extubation group for Bray-Curtis distances (p < 0.001). At the genus level, Rothia, Streptococcus, and Prevotella correlated with the change of β diversity. A low relative abundance of Streptococci at the time of intubation was strongly associated with 28-day mortality. The dynamics of respiratory microbiome were associated with clinical outcomes such as extubation failure and mortality. Further large prospective studies are needed to test the predictive value of endotracheal aspirates in intubated patients.

scholarly journals Sulfamethoxazole and Enrofloxacin Antibiotics Affect Primary Productivity of Phytoplankton in Fishery Environment

2021 ◽  
Vol 9 ◽  
Author(s):  
Xiangbao Shan ◽  
Yulu Shi ◽  
Longxiang Fang ◽  
Yuan Gui ◽  
Luchang Xing ◽  
...  
Keyword(s):  
Primary Productivity ◽  
Aquatic Ecosystems ◽  
Phytoplankton Community ◽  
Diversity Index ◽  
Promoting Effect ◽  
Β Diversity ◽  
Low Concentrations ◽  
Α Diversity ◽  
High Concentrations ◽  
Safety And Stability

The antibiotics sulfamethoxazole (SMZ) and enrofloxacin (ENF) are commonly used in aquaculture in China, but their effects on the primary productivity of phytoplankton are unclear. On the basis of the fishery drug use standards (SMZ, 100 mg kg−1 d−1; ENF, 15 mg kg−1 d−1), these antibiotics were put into culture ponds to observe their effects on the phytoplankton community and primary productivity. The results showed that the changes in phytoplankton species at SMZ and ENF sites were different. At the ENF sites, Bacillariophyta species increased from 7 to 9, euglenophyta from 8 to 12 and cyanophyta from 11 to 9. Chlorophyta species at the SMZ sites increased from 10 to 15 and euglenophyta from 7 to 4. SMZ and ENF significantly promoted the number of cyanophyta (p &lt; 0.05). The promoting effect of SMZ was more obvious than that of ENF. SMZ was more effective than ENF in promoting cyanophyta. The maximum number of cyanophyta at SMZ sites was 52.39 million L−1, and the concentration of SMZ was positively correlated with the number of cyanophyta. The maximum number of cyanophyta at ENF sites was 33.13 million L−1, and the promoting effect of low concentrations was more significant than that of high concentrations. Both SMZ and ENF promoted increased phytoplankton biomass, consistent with the residual time of the antibiotics in the aquaculture environment. The greatest biomass at the SMZ sites was 129.31 g m−³, and that at the ENF sites was 117.85 g m−³. The changes in the α diversity index showed that both SMZ and ENF led to a decrease in phytoplankton biodiversity, and that SMZ was more harmful to it. There were significant differences in the Shannon–Wiener, Pielou and Simpson indexes of the SMZ sites within groups (p &lt; 0.05). The β diversity index showed that both antibiotics could change the phytoplankton habitat, but the effect of ENF on the habitat was recoverable, while that of SMZ prevented its restoration. These data will be valuable in protecting the ecological environment of fisheries and ensuring the safety and stability of fishery aquatic ecosystems.

scholarly journals Pulmonary Microbiome of Patients Receiving Mechanical Ventilation: Changes Over Time

2021 ◽  
Vol 30 (2) ◽  
pp. 128-132
Author(s):  
Mary Lou Sole ◽  
Shibu Yooseph ◽  
Steven Talbert ◽  
Bassam Abomoelak ◽  
Chirajyoti Deb ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Prolonged Mechanical Ventilation ◽  
Intervention Group ◽  
Shannon Index ◽  
Control Group ◽  
Rrna Gene ◽  
Bacterial Taxonomy ◽  
Β Diversity ◽  
Α Diversity ◽  
Over Time

Background Interest in the pulmonary microbiome is growing, particularly in patients undergoing mechanical ventilation. Objectives To explore the pulmonary microbiome over time in patients undergoing prolonged mechanical ventilation and to evaluate the effect of an oral suctioning intervention on the microbiome. Methods This descriptive subanalysis from a clinical trial involved a random sample of 16 participants (7 intervention, 9 control) who received mechanical ventilation for at least 5 days. Five paired oral and tracheal specimens were evaluated for each participant over time. Bacterial DNA from the paired specimens was evaluated using 16S rRNA gene sequencing. Bacterial taxonomy composition, α-diversity (Shannon index), and β-diversity (Morisita-Horn index) were calculated and compared within and between participants. Results Participants were predominantly male (69%) and White (63%), with a mean age of 58 years, and underwent mechanical ventilation for a mean of 9.36 days. Abundant bacterial taxa included Prevotella, Staphylococcus, Streptococcus, Stenotrophomonas, and Veillonella. Mean tracheal α-diversity decreased over time for the total group (P = .002) and the control group (P = .02). β-Diversity was lower (P = .04) in the control group (1.905) than in the intervention group (2.607). Conclusions Prolonged mechanical ventilation was associated with changes in the pulmonary microbiome, with the control group having less diversity. The oral suctioning intervention may have reduced oral-tracheal bacterial transmission.

scholarly journals Salivary microbiome profiling reveals a dysbiotic schizophrenia-associated microbiota

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Ying Qing ◽  
Lihua Xu ◽  
Gaoping Cui ◽  
Liya Sun ◽  
Xiaowen Hu ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Oral Microbiome ◽  
Disease Stage ◽  
First Episode ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Β Diversity ◽  
Metabolic Functions ◽  
Α Diversity ◽  
Rrna Gene Sequencing

AbstractSchizophrenia is a debilitating mental disorder and often has a prodromal period, referred to as clinical high risk (CHR) for psychosis, prior to the first episode. The etiology and pathogenesis of schizophrenia remain unclear. Despite the human gut microbiome being associated with schizophrenia, the role of the oral microbiome, which is a vital player in the mouth–body connection, is not well understood. To address this, we performed 16S rRNA gene sequencing to investigate the salivary microbiome in 85 patients with drug-naïve first-episode schizophrenia (FES), 43 individuals at CHR, and 80 healthy controls (HCs). The salivary microbiome of FES patients was characterized by higher α-diversity and lower β-diversity heterogeneity than those of CHR subjects and HCs. Proteobacteria, the predominant phylum, was depleted, while Firmicutes and the Firmicutes/Proteobacteria ratio was enriched, in a stepwise manner from HC to CHR to FES. H2S-producing bacteria exhibited disease-stage-specific enrichment and could be potential diagnostic biomarkers for FES and CHR. Certain salivary microbiota exhibited disease-specific correlation patterns with symptomatic severities, peripheral pro-inflammatory cytokines, thioredoxin, and S100B in FES. Furthermore, the metabolic functions from inferred metagenomes of the salivary microbiome were disrupted in FES, especially amino acid metabolism, carbohydrate metabolism, and xenobiotic degradation. This study has established a link between salivary microbiome alterations and disease initiation and provided the hypothesis of how the oral microbiota could influence schizophrenia.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

scholarly journals Inhibitory Effects of Breast Milk-Derived Lactobacillus rhamnosus Probio-M9 on Colitis-Associated Carcinogenesis by Restoration of the Gut Microbiota in a Mouse Model

Nutrients ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 1143
Author(s):  
Haiyan Xu ◽  
Keizo Hiraishi ◽  
Lin-Hai Kurahara ◽  
Yuko Nakano-Narusawa ◽  
Xiaodong Li ◽  
...  
Keyword(s):  
Therapeutic Potential ◽  
Lactobacillus Rhamnosus ◽  
Tumor Model ◽  
Intestinal Bacteria ◽  
Inflammatory Cells ◽  
Shannon Index ◽  
Tumor Formation ◽  
Intestinal Bacterium ◽  
Α Diversity ◽  
Inflammatory Bowel

Chronic inflammation is a risk factor for colorectal cancer, and inflammatory cytokines secreted from inflammatory cells and active oxygen facilitate tumorigenesis. Intestinal bacteria are thought to regulate tumorigenesis. The longer the breastfeeding period, the lower is the risk of inflammatory bowel disease. Here, we investigated preventive effects of the probiotic Lactobacillus rhamnosus M9 (Probio-M9) on colitis-associated tumorigenesis. An inflammatory colorectal tumor model was established using a 6-week-old male C57BL/6NCrSlc mouse, which was intraperitoneally administered with azoxymethane (AOM: 12 mg/kg body weight). On weeks 2 and 4, 2% dextran sulfate sodium (DSS) was administered to mice for 7 days through drinking water. On weeks 8 and 10, Probio-M9 (2 × 109/day) was orally administered for 7 days. Animals were sacrificed at 20 weeks after AOM administration and immunohistochemical staining and Western blotting was performed. The α-diversity of microflora (Shannon index), principal coordinate analysis, and distribution of intestinal bacterium genera and metabolic pathways were compared. The AOM/DSS group showed weight loss, diarrhea, intestinal shortening, increased number of colon tumors, proliferating tumorigenesis, increased inflammation score, fibrosis, increased CD68+, or CD163+ macrophage cells in the subserosal layer of non-tumor areas. Inflammation and tumorigenesis ameliorated after Probio-M9 treatment. Fecal microbial functions were altered by AOM/DSS treatment. Probio-M9 significantly upregulated the fecal microbial diversity and reversed fecal microbial functions. Thus, Probio-M9 could suppress tumor formation in the large intestine by regulating the intestinal environment and ameliorating inflammation, suggesting its therapeutic potential for treatment of inflammation and colitis-associated tumorigenesis.

Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Robert Lavallée ◽  
Claude Guertin
Keyword(s):  
Population Density ◽  
Gut Microbiome ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Economic Damage ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Local Conditions ◽  
Β Diversity ◽  
Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

scholarly journals Arthropod community structure in pastures of an island archipelago (Azores): looking for local–regional species richness patterns at fine-scales

2004 ◽  
Vol 94 (2) ◽  
pp. 111-121 ◽  
Author(s):  
P.A.V. Borges ◽  
V.K. Brown
Keyword(s):  
Species Richness ◽  
Regional Scale ◽  
Local Scale ◽  
Local Species Richness ◽  
Β Diversity ◽  
Arthropod Species ◽  
Α Diversity ◽  
Local Species ◽  
Richness Patterns

AbstractThe arthropod species richness of pastures in three Azorean islands was used to examine the relationship between local and regional species richness over two years. Two groups of arthropods, spiders and sucking insects, representing two functionally different but common groups of pasture invertebrates were investigated. The local–regional species richness relationship was assessed over relatively fine scales: quadrats (= local scale) and within pastures (= regional scale). Mean plot species richness was used as a measure of local species richness (= α diversity) and regional species richness was estimated at the pasture level (= γ diversity) with the ‘first-order-Jackknife’ estimator. Three related issues were addressed: (i) the role of estimated regional species richness and variables operating at the local scale (vegetation structure and diversity) in determining local species richness; (ii) quantification of the relative contributions of α and β diversity to regional diversity using additive partitioning; and (iii) the occurrence of consistent patterns in different years by analysing independently between-year data. Species assemblages of spiders were saturated at the local scale (similar local species richness and increasing β-diversity in richer regions) and were more dependent on vegetational structure than regional species richness. Sucking insect herbivores, by contrast, exhibited a linear relationship between local and regional species richness, consistent with the proportional sampling model. The patterns were consistent between years. These results imply that for spiders local processes are important, with assemblages in a particular patch being constrained by habitat structure. In contrast, for sucking insects, local processes may be insignificant in structuring communities.

Diversity metrics, species turnovers and nestedness of bird assemblages in a deep karst sinkhole

2017 ◽  
Vol 63 (2) ◽  
pp. 8-16 ◽  
Author(s):  
Corrado Battisti ◽  
Marco Giardini ◽  
Francesca Marini ◽  
Lorena Di Rocco ◽  
Giuseppe Dodaro ◽  
...  
Keyword(s):  
Species Richness ◽  
Random Distribution ◽  
Diversity Index ◽  
Species Turnover ◽  
Floristic Composition ◽  
Bird Assemblages ◽  
Β Diversity ◽  
Stick Model ◽  
Karst Sinkhole

We reported a study on breeding birds occurring inside an 80 m-deep karst sinkhole, with the characterization of the assemblages recorded along its semi-vertical slopes from the upper edge until the bottom. The internal sides of the sinkhole have been vertically subdivided in four belts about 20 m high. The highest belt (at the upper edge of the cenote) showed the highest values in mean number of bird detections, mean and normalized species richness, and Shannon diversity index. The averaged values of number of detections and species richness significantly differ among belts. Species turnover (Cody’s β-diversity) was maximum between the highest belts. Whittaker plots showed a marked difference among assemblages shaping from broken-stick model to geometric series, and explicited a spatial progressive stress with a disruption in evenness towards the deepest belts. Bird assemblages evidenced a nested subset structure with deeper belts containing successive subsets of the species occurring in the upper belts. We hypothesize that, at least during the daytime in breeding season, the observed non-random distribution of species along the vertical stratification is likely due to (i) the progressive simplification both of the floristic composition and vegetation structure, and (ii) the paucity of sunlight as resources from the upper edge to the inner side of the cenote.

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