Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteriaAbstract
Ten samples of tropical lichens collected from Doi Inthanon, Thailand, were explored for the diversity of their bacterial microbiomes through 16S rRNA-based metagenomics analysis. The five predominant lichen-associated bacteria belonged to the phyla Proteobacteria (31.84%), Planctomycetota (17.08%), Actinobacteriota (15.37%), Verrucomicrobiota (12.17%), and Acidobacteriota (7.87%). The diversity analysis metric showed that Heterodermia contained the highest bacterial species richness. Within the lichens, Ramalina conduplicans and Cladonia rappii showed a distinct bacterial community from the other lichen species. The community of lichen-associated actinobacteria was investigated as a potential source of synthesized biologically active compounds. From the total Operational Taxonomic Units (OTUs) found across the ten different lichen samples, 13.21% were identified as actinobacteria, including the rare actinobacterial genera that are not commonly found, such as Pseudonocardia, Kineosporia, Dactylosporangium, Amycolatopsis, Actinoplanes, and Streptosporangium. Evaluation of the pretreatment method (heat, air-drying, phenol, and flooding) and isolation media used for the culture-dependent actinobacterial isolation revealed that the different pretreatments combined with different isolation media were effective in obtaining several species of actinobacteria. However, metagenomics analyses revealed that there were still several strains, including rare actinobacterial species, that were not isolated. This research strongly suggests that lichens appear to be a promising source for obtaining actinobacteria.
Association between gut microbiota and prediabetes in people living with HIVAbstract
The prevalence of prediabetes is rapidly increasing in general population and in people living with HIV (PLWH). Gut microbiota play an important role in human health, and dysbiosis is associated with metabolic disorders and HIV infection. Here, we aimed to evaluate the association between gut microbiota and prediabetes in PLWH. A cross-sectional study enrolled 40 PLWH who were receiving antiretroviral therapy and had an undetectable plasma viral load. Twenty participants had prediabetes, and 20 were normoglycemic. Fecal samples were collected from all participants. The gut microbiome profiles were analyzed using 16S rRNA sequencing. Alpha-diversity was significantly lower in PLWH with prediabetes than in those with normoglycemia (p<0.05). A significant difference in beta-diversity was observed between PLWH with prediabetes and PLWH with normoglycemia (p<0.05). Relative abundances of two genera in Firmicutes (Streptococcus and Anaerostignum) were significantly higher in the prediabetes group. In contrast, relative abundances of 13 genera (e.g., Akkermansia spp., Christensenellaceae R7 group) were significantly higher in the normoglycemic group. In conclusion, the diversity of gut microbiota composition decreased in PLWH with prediabetes. The abundances of 15 bacterial taxa in the genus level differed between PLWH with prediabetes and those with normoglycemia. Further studies on the effect of these taxa on glucose metabolism are warranted.
Evaluation of nutrient characteristics and bacterial community in agricultural soil groups for sustainable land managementAbstract
The soil bacterial community is critical for understanding biological processes in soils and is used for agricultural soil management. The understanding of microorganisms and ecology in different soil groups classified based on soil properties (e.g., minerals, soil texture, location, nitrogen, phosphorus, organic carbon and pH, among others), is limited. To suggest soil management strategies using bacterial data, we classified soils into four groups based on physical–chemical characteristics and elucidated their relationships with soil nutrient characteristics and the bacterial community in agricultural fields in Saraburi Province, Thailand. Results show that soil groups with high bacterial diversity had positive correlations with total Kjeldahl nitrogen and available phosphorus but were negatively affected by total organic carbon and pH levels. Dominant bacterial genera included Lactobacillus, Phascolarctobacterium, Prevotella, Clostridium, Gaiellales and Blautia. Significant key biomarkers were found (p < 0.05). Nutrient-rich soil groups (high available P, acidic pH) were found with genus Agromyces, while low nutrient soil groups (low available P, basic pH) were found with Hydrogenispora, Ignavibacterium and Bauldia. Based on co-occurrence networks, organic degrading bacteria functioned with other bacteria at high degrees of interconnections, suggesting organic amendment, biostimulation and biodegradation using nutrient-rich organic substrates could be used for agricultural soil improvements.
Microbiome Fingerprint as Biomarker for Geographical Origin and Heredity in Crocus sativus: A Feasibility StudyAbstract
Host–microbiome interactions are specific and not random, making them defining entities for the host. The hypothesis proposed by various researchers earlier, that both plants and animals harbor specific inheritable core microbiome, is being augmented in the present study. Additionally, a case for using microbial fingerprint as a biomarker, not only for plant identification but also as a geographical indicator, has been investigated, taking Crocus sativus, saffron, as a study material. Crocus sativus, a monogenetic herb, on account of its male sterility and vegetative propagation, is reported to lack genome based molecular markers. Cormosphere microbiome (microbiome associated with corm) has been compared across three geographical locations, in two continents, to identify the core and unique microbiome, during the vegetative phase of its growth. Microbiome analysis done at phylum and genus level, using next generation sequencing technology, revealed that cormosphere at three locations harbored common phyla. At genus level, 24 genera were found common to all three geographical locations, indicating them to be part of the core microbiome of saffron. However, there were some bacterial genera unique to Kashmir, Kishtwar, and Morocco that can be used to develop microbial markers/geographical indicators for saffron grown in these regions. This is a preliminary study, indicating that the location specific bacterial community can be used to develop microbial barcodes but needs further augmentation with high coverage data from other saffron growing geographical regions.
Integrative approaches for unmasking hidden species in herbal dietary supplement products: What is in the capsule?Abstract
Herbal dietary supplement products are often marketed as herbal mixtures, which makes quality control processes
difficult. Herein, paired-end next-generation sequencing (NGS), microscopic examination and highperformance
thin layer chromatography (HPTLC) were integrated to unveil herbal ingredient compositions in
a selected herbal dietary supplement product. The product was labeled as containing capsicum, cactus, wheat,
white bean, Garcinia cambogia, psyllium husk and black pepper in each capsule. A laboratory-made sample was
prepared as a reference sample according to the product label. NGS indicated that six out of the seven herbal
species were detected in the laboratory-made sample, while 97.02 ± 0.15% of sequencing reads from the
commercial product belonged to Senna alexandrina. Microscopic examination also confirmed the presence of
Senna. Similar chemical constituents of the product and Senna powder were observed by HPTLC patterns. Surprisingly,
there was a distinct band difference between samples. After extraction and LC-MS/MS analysis, oleamide
was found as an adulterant in the product. None of the plants listed on the commercial product label were
detected by any of the methods. Therefore, the integrative approaches successfully unmasked nonlisted herbal
species in a selected herbal dietary supplement product. These approaches should be applied to other dietary
supplement products for registration and regulation processes.
Effect of Partial Replacement of Fish Meal by Bacillus sp-Fermented Soybean Meal on Growth Performance, Immunity, Hepatopancreas Microbiota and Disease Resistance in Pacific White Shrimp (Litopenaeus vannamei)Abstract
This study examined the effect of substituting a diet containing 20% fish meal (FM) and 10%
soy bean meal (SBM) with Bacillus-fermented soybean meal (FSBM) on growth, immune response,
microbial community in the hepatopancreas, and disease prevention in Pacific white shrimp. Shrimp
were fed diets with four levels of FSBM (0%, 15%, 20% and 25%) to replace FM and SBM. After 60
days of the feeding trial, no difference was found among treatments for specific growth rate (1.62-1.66 g),
survival rate (88.08-93.64 %), feed conversion ratio (FCR) (1.31-1.41), or protein efficiency ratio
(88.08-93.46). However, shrimp fed 25% FSBM showed a significant improvement in total hemocyte
count (THC), phagocytic activity, and phenoloxidase activity (PO) compared with other groups. In the
hepatopancreatic microbiota, we identified six phyla, of which Bacteroidetes was the most dominant
phylum in the three groups fed with FSBM. In contrast, Firmicutes was dominant in the control group.
After a challenge test with Vibrio parahaemolyticus, shrimp fed 25% FSBM had a significantly higher
average survival rate compared with other experimental groups infected with V. parahaemolyticus.
The histopathology of the hepatopancreas of shrimp from this group showed fewer signs of bacterial
infection than other groups infected with V. parahaemolyticus. This study indicates that FSBM at the
concentration of 25% can enhance immune response and tolerance to pathogenic V. parahaemolyticus
in the Pacific white shrimp.
DNA metabarcoding to unravel plant species composition in selected herbal medicines on the National List of Essential Medicines (NLEM) of ThailandAbstract
Traditional medicines are widely traded across the globe and have received considerable attention
in the recent past, with expectations of heightened demand in the future. However, there are
increasing global concerns over admixture, which can affect the quality, safety, and efficacy of herbal
medicinal products. In this study, we aimed to use DNA metabarcoding to identify 39 Thai herbal
products on the Thai National List of Essential Medicines (NLEM) and assess species composition and
admixture. Among the products, 24 samples were in-house-prepared formulations, and 15 samples
were registered formulations. In our study, DNA metabarcoding analysis using ITS2 and rbcL barcode
regions were employed to identify herbal ingredients mentioned in the products. The nuclear region,
ITS2, was able to identify herbal ingredients in the products at the genus- and family-levels in 55% and
63% of cases, respectively. The chloroplast gene, rbcL, enabled genus- and family-level identifications
in 58% and 73% of cases, respectively. In addition, plant species were detected in larger numbers
(Family identified, absolute %) in registered herbal products than in in-house-prepared formulations.
The level of fidelity increases concerns about the reliability of the products. This study highlights that
DNA metabarcoding is a useful analytical tool when combined with advanced chemical techniques for
the identification of plant species in highly processed, multi-ingredient herbal products.
Environmental DNA metabarcoding as a tool for biodiversity assessment and monitoring: reconstructing established fish communities of north-temperate lakes and riversAbstract
To evaluate the ability of precipitation-based environmental DNA (eDNA) sample collection and mitochondrial 12S metabarcoding sequencing to reconstruct well-studied fish communities in lakes and rivers. Specific objectives were to 1) determine correlations between eDNA species detections and known community composition based on conventional field sampling, 2) compare efficiency of eDNA to detect fish biodiversity among systems with variable morphologies and trophic states, and 3) determine if species habitat preferences predict eDNA detection.
Upper Great Lakes Region, North America.
Fish community composition was estimated for seven lakes and two Mississippi River navigation pools using sequence data from the mitochondrial 12S gene amplified from 10 to 50 water samples per waterbody collected in 50-mL centrifuge tubes at a single time point. Environmental DNA (eDNA) was concentrated without filtration by centrifuging samples to reduce per-sample handling time. Taxonomic detections from eDNA were compared to established community monitoring databases containing up to 40 years of sampling and a detailed habitat/substrate preference matrix to identify patterns of bias.
Mitochondrial 12S gene metabarcoding detected 15%–47% of the known species at each waterbody and 30%–76% of known genera. Non-metric multidimensional scaling (NMDS) assessment of the community structure indicated that eDNA-detected communities grouped in a similar pattern as known communities. Discriminant analysis of principal components indicated that there was a high degree of overlap in habitat/substrate preference of eDNA-detected and eDNA-undetected species suggesting limited habitat bias for eDNA sampling.
Large numbers of small volume samples sequenced at the mitochondrial 12S gene can describe the coarse community structure of freshwater systems. However, additional conventional sampling and environmental DNA sampling may be necessary for a complete diversity census.