Metagenomic Analysis Of Microbial Community Research Articles

Metagenomic Analysis of Microbial Communities from Coal Waste

Coal waste contains few macro-and micronutrients, which makes it less likely to become a growth site for microorganisms. One way to screen coal waste resources is to identify the diversity of microbes in them to study the relationship between these microbial communities in contributing to improving environmental pollution using metagenomics to determine microbial diversity. The purpose of this research is to study the diversity of microorganisms in areas contaminated with heavy metals using a metagenomic method. This study was performed using next-generation sequencing techniques, including DNA extraction, 16S rRNA amplification, and gene sequencing analysis. The results of this research found that the 10 most commonly found species were Baekduia soli, Nocardiodes iriomotensis, Nocardioides mesophilus, Nocardioides pakistanensis, Propionibacterium cyclohexanicum, Solirubrobacter ginsenosidimutans, Gemmatirosa kalamazoonensis, Roseisolibacter agri, Kosakonia saccahri, and Dickeya fangzhongdai. Based on this research, it can be concluded that most of the microbial communities from coal waste are dominated by the phylum Actinobaceria. The results of this study can be used as an adaptive microbial germplasm for industrial waste management strategies.

Metagenomic analysis of microbial communities and antibiotic resistant genes in the Tijuana river, and potential sources

The Tijuana River is a transborder river that flows northwest across the border from Baja California in Mexico into Southern California before discharging into the Pacific Ocean. The river is frequently contaminated with raw sewage due to inadequate sanitary infrastructure in Tijuana. To assess the type and degree of microbial contamination, water samples were collected monthly from a near-border and an estuarine site from August 2020 until May 2021. A portion of each sample was used for epifluorescent microscopy and DNA was extracted directly from the rest for shotgun metagenomic sequencing. After sequence quality checking and processing, we used the rapid taxonomic identifier tool Kaiju to characterize the microbial diversity of the metagenomes and matched the sequences against the Comprehensive Antibiotic Resistance Database (CARD) to examine antimicrobial resistance genes (ARGs). Bacterial and viral-like particle (VLP) abundance was consistently higher in the near-border samples than in the estuarine samples, while alpha diversity (within sample biodiversity) was higher in estuarine samples. Beta-diversity analysis found clear compositional separation between samples from the two sites, and the near-border samples were more dissimilar to one another than were the estuarine sites. Near-border samples were dominated by fecal-associated bacteria and bacteria associated with sewage sludge, while estuarine sites were dominated by marine bacteria. ARGs were more abundant at the near-border site, but were also readily detectable in the estuarine samples, and the most abundant ARGs had multi-resistance to beta-lactam antibiotics. SourceTracker analysis identified human feces and sewage sludge to be the largest contributors to the near-border samples, while marine waters dominated estuarine samples except for two sewage overflow dates with high fecal contamination. Overall, our research determined human sewage microbes to be common in the Tijuana River, and the prevalence of ARGs confirms the importance of planned infrastructure treatment upgrades for environmental health.

Metagenomic Analysis of Microbial Communities in Indoor Water Cultures: a Case Study in an Educational Building

Metagenomic Analysis of Microbial Communities in Indoor Water Cultures: a Case Study in an Educational Building

In Silico Comparative Metagenomic Analysis of Microbial Communities of Chromium Contaminated Sites

Chromium is one of the highly toxic and carcinogenic heavy metals. Due to increased anthropogenic activities, high concentration of chromium is found in many areas. Many microorganisms have the ability to detoxify chromium. Metagenomics allow us to comprehensively study microbial communities present at different sites without culturing them. The objective of this study was to analyze the abundance of microbial groups in different environments contaminated with chromium. For this purpose, chromium contaminated soil, anaerobic sludge and reactor samples were chosen. 16S rRNA data of these samples was retrieved from NCBI SRA database. The sequences were analyzed by Mothur software accessed via Galaxy server, and were classified using SILVA database. Venn diagram, phylogenetic tree, heatmap, relative abundance graphs and Krona pie charts were generated. Statistical analysis was also performed in the form of AMOVA and HOMOVA tests. According to results of our study, Proteobacteria, Leucobacter, Actinomycetales, Actinobacteria, Arthrobacter, Rhizobiales, Sphingomonas, Bradyrizobium and Nucardioidaceae were present in all the samples. Firmicutes, Planctomycetes, Verrucomicrobia and Bacteroidetes were more abundant in chromium contaminated samples as compared to control samples. The results were also found to be statistically significant. The above-mentioned bacteria can be targeted and studied to discover their roles in bioremediation of chromium contaminated sites.

Metagenomic analysis of microbial community and gene function of anodic biofilm for nonylphenol removal in microbial fuel cells

Nonylphenol as a high priority control of persistent toxic contaminant has been frequently detected in environment. In this study, Dual-chamber microbial fuel cells (MFCs) were constructed for simultaneous nonylphenol degradation and electricity generation; and microbial community and gene function of anodic biofilm were analyzed through metagenomic sequencing. The results showed that nonylphenol removal rate reached 82% within 60 h in MFCs, and the maximum voltage achieved 0.60 V when the external resistance was 1000 Ω. Metagenomics analysis showed that Proteobacteria and Actinobacteria were dominant phyla in biofilm attached to anode. At genus level, the relative abundance of Streptomyces (21.45%), Microbacterium (11.96%), Burkholderia (10.90%), Pusillimonas (7.59%), Stenotrophomonas (6.62%), Pseudomonas (4.44%), Nitrospirillum (3.75%), Nocardia (1.73%), Arthrobacter (1.71%) and Bacillus (1.21%) were remarkably higher than those of control groups. In terms of functional genes annotation, a relatively high gene number was focus on various metabolic pathways (such as carbon metabolism, riboflavin metabolism, and nitrogen metabolism) during MFCs operated. The metabolic pathways of nonylphenol were suggested to divide into the oxidation of aromatic ring (route-1) and the fission of alkyl chain (route-2) based on KEEG analysis.

Metagenomic analysis of microbial community and metabolic pathway of simultaneous sulfide and nitrite removal process exposed to divergent hydraulic retention times

The role of hydraulic retention time (HRT) on S0 production was assessed through metagenomics analyses. Considering comprehensive performance for the tested HRTs (0.25–13.33 h), the optimal HRT was 1 h, while respective sulfide and nitrite loading rate could reach 6.84 kg S/(m3·d) and 1.95 kg N/(m3·d), and total S0 yield was 0.36 kg S/(kg (VSS)·d). Bacterial community richness decreased along the shortening of HRT. Microbacterium, Sulfurimonas, Sulfurovum, Paracoccus and Thauera were highly abundant bacteria. During sulfur metabolism, high expression of sqr gene was the main reason of maintaining high desulfurization load, while lacking soxB caused the continuous increase of S0. Regarding nitrogen metabolism, the rapid decrease of nitrite transporter prevented nitrite to enter in cells, which caused a rapid decrease of nitrite removal under extreme HRT. Adjusting HRT is an effective way to enhance S0 production for the application of the simultaneous sulfide and nitrite removal process.

New insight on Fe-bioavailability: Bio-uptake, utilization and induce in optimizing methane production in anaerobic digestion

Fe-bioavailability is an essential factor affecting CH4 production from anaerobic digestion (AD). However, the actual uptake and utilization process of iron in complex microbial communities remains unclear. In this study, the effects of Fe-bioavailability in six iron dosages on CH4 production were compared. The results showed that CH4 production increased to 144.37 mL CH4/g COD (154.1% higher than the control group) when dosing is 50 mg/L with the best Fe-bioavailability (3.125 mg Fe/g TS). Flow cytometry and enzyme analysis further demonstrated that the reactor with the highest Fe-bioavailability had the protective mechanism of ferroptosis and the highest living cell and DNA content. Metagenomic analysis of microbial communities and metabolic pathways revealed the potential pathways of iron bio-utilization in pyruvate metabolism dominant by Candidatus Cloacamonas Acidaminovorans and methane metabolism dominant by acetophilic methanogens were improved. In view of the significant improvement of lipopolysaccharide biosynthesis, the two-component system, ABC transporter, quorum-sensing, and ribosome metabolic pathways, it can propose that iron-induced signaling molecule accelerates matter and energy exchange on the membrane, thus enhancing the microbial function of the anaerobic system. This study revealed the process of iron uptake and utilization by microbial communities and the potential mechanism of promoting interspecific iron uptake, improving the carbon conversion efficiency of organic matter in AD.

Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals

Numerous attempts have been utilized to unveil the occurrences of antibiotic resistance genes (ARGs) in human-associated and non-human-associated samples. However, spoiled household chemicals, which are usually neglected by the public, may be also a reservoir of ARGs because of the excessive and inappropriate uses of industrial drugs. Based upon the Comprehensive Antibiotic Research Database, a metagenomic sequencing method was utilized to detect and quantify Antibiotic Resistance Ontology (AROs) in six spoiled household chemicals, including hair conditioner, dishwashing detergent, bath shampoo, hand sanitizer, and laundry detergent. Proteobacteria was found to be the dominant phylum in all the samples. Functional annotation of the unigenes obtained against the KEGG pathway, eggNOG and CAZy databases demonstrated a diversity of their functions. Moreover, 186 types of AROs that were members of 72 drug classes were identified. Multidrug resistance genes were the most dominant types, and there were 17 AROs whose resistance mechanisms were categorized into the resistance-nodulation-cell division antibiotic efflux pump among the top 20 AROs. Moreover, Proteobacteria was the dominant carrier of AROs with the primary resistance mechanism of antibiotic efflux. The maximum temperature of the months of collection significantly affected the distributions of AROs. Additionally, the isolated individual bacterium from spoiled household chemicals and artificial mixed communities of isolated bacteria demonstrated diverse resistant abilities to different biocides. This study demonstrated that there are abundant microorganisms and a broad spectrum profile of AROs in spoiled household chemicals that might induce a severe threat to public healthy securities and merit particular attention.

Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica.

Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value=<.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.

Metagenomic analysis of microbial communities in the sediments of a semi-intensive penaeid shrimp culture system

The present study reports metagenomic sequencing and microbial diversity analysis of the sediment samples of a semi-intensive penaeid shrimp culture system. 16S rRNA gene-based high-throughput sequencing revealed distinct and diverse microbial communities in the analyzed sample. Analysis of the results showed a high abundance of Proteobacteria followed by Verrucomicrobia, Bacteroidetes, Planctomycetes, Firmicutes, Cyanobacteria, and Actinobacteria in the metagenome retrieved from the sediment sample. Unclassified bacteria also contributed a significant portion of the metagenome. Two potential shrimp pathogens viz Vibrio harveyi and Acinetobacter lwoffii detected in the sediment sample show the risk associated with the pond. Microbes that play essential roles in nutrient cycling and mineralization of organic compounds such as Bacteroidetes, Planctomycetes, Gammaproteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria could also be identified. The present study provides preliminary data with respect to the microbial community present in the sediments of a shrimp culture system and emphasizes the application of metagenomics in exploring the microbial diversity of aquaculture systems, which might help in the early detection of pathogens within the system and helps to develop pathogen control strategies in semi-intensive aquaculture systems.

Metagenomic analysis of microbial communities continuously exposed to Bisphenol A in mangrove rhizosphere and non-rhizosphere soils

Bisphenol A (BPA) is widely distributed in littoral zones and may cause adverse impacts on mangrove ecosystem. Biodegradation and phytoremediation are two primary processes for BPA dissipation in mangrove soils. However, the rhizosphere effects of different mangrove species on BPA elimination are still unresolved. In this study, three typical mangrove seedlings, namely Avicennia marina, Bruguiera gymnorrhiza (L.) and Aegiceras corniculatum, were cultivated in soil microcosms for four months and then subjected to 28-day continuous BPA amendment. Un-planted soil microcosms (as control) were also set up. The BPA residual rates and root exudates were monitored, and the metabolic pathways as well as functional microbial communities were also investigated to decipher the rhizosphere effects based on metagenomic analysis. The BPA residual rates in all planted soils were significantly lower than that in un-planted soil on day 7. Both plantation and BPA dosage had significant effects on bacterial abundance. A distinct separation of microbial structure was found between planted and un-planted soil microcosms. Genera Pseudomonas and Lutibacter got enriched with BPA addition and may play important roles in BPA biodegradation. The shifts in bacterial community structure upon BPA addition were different among the microcosms with different mangrove species. Genus Novosphingobium increased in Avicennia marina and Bruguiera gymnorrhiza (L.) rhizosphere soils but decreased in Aegiceras corniculatum rhizosphere soil. Based on KEGG annotation and binning analysis, the proposal of BPA degradation pathways and the quantification of relevant functional genes were achieved. The roles of Pseudomonas and Novosphingobium may differ in lower BPA degradation pathways. The quantity variation patterns of functional genes during the 28-day BPA amendment were different among soil microcosms and bacterial genera.

Metagenomic Analysis of Microbial Community Affiliated with Termitarium Reveals High Lignocellulolytic Potential.

Termitarium (nest of termites) is a rich source of microbial populations whose resources remain untapped to date. Using the metagenomic sequencing approach, we generated 38GB sequences comprising 808,386 contigs (896MB) with a maximum contig size of 470kb. The taxonomic profile obtained by BLAST against the NCBI NR database and annotation by MEGAN showed that the termitarium microbial community was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Functional annotation using the CAZY database revealed a huge diversity of glycosyl hydrolase genes from 104 families, some of which appeared to be part of polysaccharide utilization systems (PUL). Strikingly, Actinobacteria was the main contributor of the cellulolytic and hemicellulolytic GHs. Genes involving in lignin degradation were also abundantly identified in this metagenome. Comparative analysis of COG profiles of termitarium with those of other lignocellulolytic microbial communities showed a distant clustering pattern resulting from the dietary differences in carbohydrate compositions. Altogether, this study revealed that termitarium hosts a unique microbial community, which can efficiently degrade lignocelluloses.

Metagenomic analysis of microbial community and its role in bioelectrokinetic remediation of tannery contaminated soil

Tanneries create a serious threat to the environment by generating a significant amount of toxic metal-containing solid waste. This study deals with the application of bio-electrokinetic remediation (Bio-EK) of tannery effluent contaminated soil (TECS). Metagenomes representing the TECS sample were sequenced using the Illumina HiSeq platform. The bioreduction of hexavalent chromium Cr(VI)to trivalent chromium Cr (III) was achieved by BIO-EK techniques. NGS-data (Next Generation Sequencing) analysis was revealed that Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Planctomycetes were identified in the bio-electrokinetic system. Proteobacteria are responsible for the bioreduction of chromium hexavalent by the formation of FeS particles. The bio-generated FeS particles can be reduced the toxic chromium (VI) to non–toxic chromium (III) in soil. Simultaneously total chromium and organic content were significantly removed in BIO-EK (40 and 290 mg kg−1) when compared to control soil (182 and 240 mg kg−1). The presence of pollutant degrading microbes such as Desulfovibrio, Pseudomonas, Bacillus, Clostridium, Halanaerobium enhanced the bioreduction of the chromium during the electrokinetic remediation. This study can be claimed that the microbial cultures assisted electrokinetic remediation of total chromium, organic and iron in the tannery effluent contaminated soil was one of the suitable efficient techniques. In addition, the viability of the new combination technology developed (Electrokinetic + Bio) to treat low-permeability polluted soils was demonstrated.

Microbiota composition data for wild and captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839).

The Labroides dimidiatus is known as the “doctor fish” because of its role in removing parasites and infectious pathogens from the body of other fishes. This important role played both in wild and captive conditions could represent a novel form of parasitic transmission process mediated by the cleaning activity of the fish. Yet, there is a paucity of data on the microflora associated with this fish which is important for tracking disease infection and generally monitoring the health status of the fish. This article, therefore, represents the first dataset for the microbiota composition of wild and captive L. dimidiatus. Wild fish samples and carriage water were gotten in Terengganu Malaysia around the corals of the Karah Island. The captive sample, however, was obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Thereafter, bacteria present on the skin, in the stomach and the aquarium water were enumerated using culture-independent approaches and Next Generation Sequencing (NGS) technology. Data obtained from the three metagenomic libraries using NGS analysis gave 1,426,740 amplicon sequence reads which are composed of 508 operational taxonomic units (OTUs) for wild samples and 3,238,564 valid reads and 828 OTUs for captive samples. All sequence reads were deposited in the GeneBank (Accession numbers SAMN14260247, SAMN14260248, SAMN14260249, SAMN14260250, SAMN14260251, and SAMN14260252). The dataset presented is associated with the research article “16S rDNA-Based Metagenomic Analysis of Microbial Communities Associated with Wild Labroides dimidiatus From Karah Island, Terengganu, Malaysia” [1]. The microbiota data presented in this article can be used to monitor the health and wellbeing of the ornamental fish, especially under captivity, hence preventing possible cross-infection.

Exploring Elimination Kinetics of Four 5-Nitrofuran Derivatives by Microbes Present in Rural and Municipal Activated Sludge

The wastewater treatment plants (WWTPs) are the biggest reservoirs of pharmaceutical residues discharged into the environment. Among many pharmaceuticals, derivatives of 5-nitrofuran, whose cytotoxicity and neurotoxicity have been proved, are widely used. The ability of such compounds to accumulate in water and sediments motivated us to analyze the ability of microbial communities of rural and municipal WWTPs to eliminate nitrofurantoin (NFT), nitrofurazone (NFZ), furaltadone (FTD), and furazolidone (FZD). Metagenomic analysis of microbial communities in rural and municipal activated sludge has provided information about the bacterial biodiversity in the WWTPs. In both samples, the most dominant phylum in terms of abundance was Proteobacteria followed by Bacteroidetes; however, microbial community of the municipal WWTP exhibited greater biodiversity than the one of the rural WWTP. The results of high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis of the samples and elimination kinetic calculations allowed the determination of FZD, FTD, NFT, and NFZ elimination half-time varying from 104 to 327 h and test system first-order half-lives in the examined WWTP samples (from 31 to 231 h). Moreover, a comparison of the effectiveness of the microbials from two treatment plants, a rural one and a municipal one, revealed the poorer performance of the microbial communities from the smaller, rural WWTP in disposal of the analyzed pharmaceuticals, as after 24 days, the rural WWTP community was able to eliminate from 20 to 62% of 5-nitrofuran derivatives, while the municipal consortium removed over 85% of the compounds from the cultures.

Metagenomic analysis of microbial community and function reveals the response of soil respiration to the conversion of cropland to plantations in the Loess Plateau of China

As an effective method to control soil erosion and increase vegetation coverage in the Loess Plateau of China, the conversion of cropland to plantations also influences soil respiration (Rs). A lot of research work has been performed on the response of Rs to land use change in this region. Nevertheless, the microbiological mechanism on the response of Rs to land use change has not been elucidated. In this study, Rs was measured during the conversion of cropland to plantations. Moreover, soil microbial community and metabolic function were analyzed by metagenomic sequencing. When the conversion of cropland to plantations was implemented, Rs significantly increased. Metagenomic analysis indicated that the conversion of cropland to plantations had a stronger impact on microbial abundance than microbial composition, which was reflected in the abundance of dominant phyla, such as Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Cyanobacteria, Gemmatimonadetes, Planctomycetes and Verrucomicrobia. Carbon metabolic pathways and genes also had a remarkable response to land use change. Although the abundance of some carbon metabolic genes decreased with the conversion of cropland to plantations, the abundance of CAZy (Carbohydrate-Active Enzymes) genes increased. Moreover, carbon metabolic genes with significant differences affiliated to above dominant phyla. All results indicated that the conversion of cropland to plantations changed microbial abundance, which in turn affected abundance of carbon metabolic and CAZy genes. The increase in the storage of organic matter caused by the above changes promoted microbial catabolism for producing a large amount of CO2 in plantations soil, which was reflected by high Rs. Our study provides insights into the microbiological mechanism on the response of Rs to land use change during the conversion of cropland to plantations in the Loess Plateau of China.

Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

BackgroundCurrently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).MethodsShotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.ResultsThe three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.ConclusionThis Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades.

Metagenomic analysis of microbial community associated with coral mucus from the Gulf of Aqaba

Coral-associated microbial communities contribute to a wide variety of useful roles regarding the their host, and therefore, the arrangement of the general microbiome network can emphatically impact coral wellbeing and survival. Various pollution sources can interfere and disrupt the microbial relationship with corals. Here, we adopted the bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP®) technique to investigate the shift of microbial communities associated with the mucus of the coral Stylophora pistillata collected from five sites (Marine Science Station, Industrial Complex, Oil Terminal, Public Beach, and Phosphate Port) along the Gulf of Aqaba (Red Sea). Our results revealed a high diversity in bacterial populations associated with coral mucus. Proteobacteria were observed to be the dominating phylum among all sampling sites. The identified bacterial taxa belong to the pathogenic bacteria from the genus Vibrio was presented in varying abundances at all sampling sites. Diversity and similarity analysis of microbial communists based on rarefaction curve and UniFrac cluster respectively demonstrated that there are variances in microbial groups associated with coral mucus along sites. The pollution sources among different locations along the Gulf of Aqaba seem to affect the coral-associated holobiont leading to changes in bacterial populations due to increasing human activities.

Feeding reduced lignin alfalfa hay modulates the horse fecal microbiome in an individualized manner

The Labroides dimidiatus is known as the “doctor fish” because of its role in removing parasites and infectious pathogens from the body of other fishes. This important role played both in wild and captive conditions could represent a novel form of parasitic transmission process mediated by the cleaning activity of the fish. Yet, there is a paucity of data on the microflora associated with this fish which is important for tracking disease infection and generally monitoring the health status of the fish. This article, therefore, represents the first dataset for the microbiota composition of wild and captive L. dimidiatus. Wild fish samples and carriage water were gotten in Terengganu Malaysia around the corals of the Karah Island. The captive sample, however, was obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Thereafter, bacteria present on the skin, in the stomach and the aquarium water were enumerated using culture-independent approaches and Next Generation Sequencing (NGS) technology. Data obtained from the three metagenomic libraries using NGS analysis gave 1,426,740 amplicon sequence reads which are composed of 508 operational taxonomic units (OTUs) for wild samples and 3,238,564 valid reads and 828 OTUs for captive samples. All sequence reads were deposited in the GeneBank (Accession numbers SAMN14260247, SAMN14260248, SAMN14260249, SAMN14260250, SAMN14260251, and SAMN14260252). The dataset presented is associated with the research article “16S rDNA-Based Metagenomic Analysis of Microbial Communities Associated with Wild Labroides dimidiatus From Karah Island, Terengganu, Malaysia” [1]. The microbiota data presented in this article can be used to monitor the health and wellbeing of the ornamental fish, especially under captivity, hence preventing possible cross-infection.

Metagenomic analysis of microbial community in over-fermented tempeh

Abstract. Pangastuti A, Alfisah RK, Istiana NI, Sari SLA, Setyaningsih R, Susilowati A, Purwoko T. 2019. Metagenomic analysis of microbial community in over-fermented tempeh. Biodiversitas 20: 1106-1114. Tempeh is a traditional Indonesian food which is made from soybeans through a fermentation process using Rhizopus as a starter culture. Tempeh is now considered as a functional food with many beneficial effects to human health beyond its nutritional value. The microbial community during the further fermentation process of tempeh give typical characteristic taste and flavor. Therefore the over-fermented tempeh is used as a flavoring in some dishes. Metagenomic analysis needed to know the involvement of microbial communities since most of the microbes involved in further fermentation process are unculturable. This research aimed to study the diversity of the microbial community in the over-fermented tempeh (72 hours) using the metagenomic analysis. Seventeen OTUs of fungi in over-fermented tempeh were detected. Among them, 9 OTUs had significant abundance: six species were identified as Tryblidiopsis sichuanensis, Candida sp.2_1., Kluyveromyces marxianus, Trichosporon asahii, Trichosporon gracile, and Trichosporon ovoides, one species was identified in the order level Mucorales, and two fungi species could not be determined. Species of the order Mucorales was the dominant species in over-fermented tempeh (72 hours) with a relative abundance of 62.46%, followed by Kluyveromyces marxianus with a relative abundance of 3698%. Meanwhile, 132 OTUs of the bacterial community was detected, the predominant 10 genera were Chryseobacterium, Lactococcus, Lactobacillus, Streptococcus, Acetobacter, Novosphingobium, Comamonas, Escherichia, Klebsiella, and Stenotrophomonas, in which Lactobacillus agilis, Lactococcus sp., and Klebsiella sp., were most abundant with relative abundance of 27%, 26.3%, and 13% respectively.