Amplicon Sequencing Customer Publications

As the number of Covid-19 cases has increased, the production and use of face masks have also increased accordingly. This widespread use of face masks generates millions of tons of mask waste. This study analyzed the bacterial community composition of discarded masks from landfills (Piyungan, Jatibarang, Burangkeng); mangroves (Wanatirta, Tirang, Teluk Naga); and beaches (Parangtritis, Marina, Tanjung Pasir) in Yogyakarta, Semarang, Bekasi, and Tangerang, Java, Indonesia using 16S rRNA sequencing. Analyzing all samples from landfills, mangroves, and beaches revealed that the Proteobacteria phylum is the predominant. In addition, Firmicutes was the second-highest phylum in the samples from landfills and mangroves. In the meantime, Actinobacteria and Cyanobacteria dominated the phyla found in samples from beaches. Analyses at the genus level revealed that Bacillus members predominated in samples of discarded face masks from landfills. addition, the most prevalent genus found in samples from mangroves and beaches was Vibrio. According to the findings,the distribution of bacterial communities differed among the various regions. Dissimilar bacterial communities and gradient distributions were found among discarded face masks in landfills, mangroves, and beaches. It was the first examination of bacterial distribution in discarded disposable face masks from various locations.

This research aims to investigate the microbial diversity of Budu prepared from fresh and frozen fish from the Pariaman and Pasaman districts in West Sumatra Province, Indonesia, as well as provide basic information about Budu quality. To obtain the bacterial microbial composition, deoxyribonucleic acid extraction was carried out using amplicon-sequencing of the 16S-rRNA gene in the V3–V4 region from two types of Budu and carried out in duplicate. Budu prepared with fresh (Pariaman) or frozen (Pasaman) fish was dominated by Firmicutes (78.455%–92.37%) and Proteobacteria (6.477%–7.23%) phyla. The total microbial species in Budu from Pariaman were higher (227 species) than in Pasaman (153 species). The bacterial species found are Lentibacillus kimchi (1.878%–2.21%), Staphylococcus cohnii (0.597%–
0.70%), Peptostreptococcus russeli (0.00%–0.002%), Clostridium disporicum (0.073%–0.09%),
Clostridium novyi (0.00%–0.01%), Nioella sediminis (0.00%–0.001%), and Shewanella baltica
(0.00%–0.003%). Lentibacillus kimchi, S. cohnii, and C. disporicum are found in both Budu. Nioella
sediminis and S. baltica are found in Budu Pariaman. Peptostreptococcus russeli and C. novyi were found in Budu Pasaman. Metagenomic analysis of Budu from different fish, Pariaman (fresh fish) and Pasaman (frozen fish) showed that the biodiversity of bacteria was barely different. Both Budu found lactic acid bacteria from the Enterococcaceae family, genus Vagococcus, and pathogenic bacteria, such as S. cohnii, P. russeli, C. disporicum, and S. baltica. The discovery of various species of pathogenic bacteria indicates that development is still needed in the Budu production process to improve Budu quality.

Cemetery soils most likely contain degradative bacteria which possibly have beneficial potencies. However, the bacterial exploration in these potencies is still limitedly conducted in Indonesia. The raw sequence data of total bacteria in the cemetery soils through metagenomic analysis have been revealed. The data were obtained by collecting soil samples from six spots of two major Cemetery areas, which were Pracimaloyo (P) and Bonoloyo (B), in Surakarta City, Central Java, Indonesia. The six sample spots consisted of two samples from P area with respectively 20 cm and 140 cm depths and four samples of each two samples from B area with 20 and 40 cm depths. The total DNA was subsequently extracted from the collected soils using ZymoBIOMICS DNA Miniprep Kit. The total DNA then was amplified using a couple of 16S rRNA primers through Illumina HiSeq 2500 PE250 (Novogen, Korea) environment system. The raw sequence data has been submitted to the National Center for Biotechnology Information (NCBI) with project ID PRJNA997385. The archived sequence can be accessed in the NCBI website with the following URLs https://www.ncbi.nlm.nih.gov/sra/PRJNA997385. A brief analysis of the sequence data showed that the most common phyla in 20 cm-depths were Proteobacteria (29.5%), Actinobacteria (21.6%), and Firmicutes (19.2%), while Actinobacteria were the most found in 140 cm-depths with 34.2% followed by Proteobacteria (21.9%) and Firmicutes (16.6%). This data would be the first report of total bacterial sequence from cemetery soils in Indonesia.

Gut microbiota is pivotal in maintaining children’s health and well-being. The ingestion of enteric pathogens and dysbiosis lead to Environmental Enteric Dysfunction (EED), which is essential in stunting pathogenesis. The roles of gut microbiome and enteric infections have not been explored comprehensively in relation to childhood stunting in Indonesia. This study aimed to determine the correlation between gut microbiota composition, enteric infections, and growth biomarker, Insulin-like Growth Factor 1 (IGF-1), in stunted children from Pidie, Aceh, Indonesia.This study was a case–control study involving 42 subjects aged 24 to 59 months, comprising 21 stunted children for the case and 21 normal children for the control group. The IGF-1 serum level was quantified using ELISA. The gut microbiome profiling was conducted using 16S rDNA amplicon sequencing. The expression of enteric pathogens virulence genes was determined using quantitative PCR (qPCR) assay. The correlations of observed variables were analysed using suitable statistical analyses.The result showed that the IGF-1 sera levels in stunted were lower than those in normal children (p ≤ 0.001). The abundance of Firmicutes (50%) was higher than Bacteroidetes (34%) in stunted children. The gut microbiome profile of stunted children showed enriched genera such as Blautia, Dorea, Collinsella, Streptococcus, Clostridium sensu stricto 13, Asteroleplasma and Anaerostipes. Meanwhile the depleted genera comprised Prevotella, Lactococcus, Butyrivibrio, Muribaculaceae, Alloprevotella, Akkermansia, Enterococcus, Terrisporobacter and Turicibacter. The abundance of water biological contaminants such as Aeromonas, Stappiaceae, and Synechococcus was also higher in stunted children compared to normal children. The virulence genes expression of Enteroaggregative Escherichia coli (aaiC), Enterotoxigenic E. coli (estA), Enteropathogenic E. coli (eaeA), Shigella/Enteroinvasive E. coli (ipaH3) and Salmonella enterica (ompC) in stunted was higher than in normal children (p ≤ 0.001), which negatively correlated to height and level of IGF-1.The present study showed the distinctive gut microbiome profile of stunted and normal children from Pidie, Aceh, Indonesia. The gut microbiota of stunted children revealed dysbiosis, comprised several pro-inflammatory, metabolic abnormalities and high-fat/low-fiber diet-related taxa, and expressed virulence genes of enteric pathogens. These findings provide evidence that it is imperative to restore dysbiosis and preserve the balance of gut microbiota to support linear growth in children.

Aquaculture and industrial activities have been recognized for their detrimental impact on coastal environment, particularly through large-scale mangrove conversion. This study employs interdisciplinary spatial, geochemical, and metagenomic approaches to examine the environmental legacy of past aquaculture and industrial activities in mangrove rehabilitation areas. The land use change of mangrove, aquaculture, and industrial area was investigated from 1990 to 2020. Mangrove coverage increased in the study area from 49.12 ha in year 1990 to 95.93 ha in 2020. This growth can be attributed to increasing environmental awareness related to issues such as tidal flooding, seawater intrusion, and coastal abrasion. However, despite increasing mangrove coverage, we still identified fecal bacteria communities in both sites, dominated by Campylobacteria, Gammaproteobacteria, and Deltaproteobacteria. Additionally, our functional prediction analysis revealed the presence of genes associated with pathogenicity, multidrug/antibiotic resistance, and xenobiotic degradation. We observed high nitrate concentration associated with aquaculture waste that was persistent in porewater even after the activity ended years ago. Low to moderate heavy metal concentration was found in the study sites, likely due to the role of mangroves as a biofilter. We conclude that mangrove restoration contributes to the lower environmental impact of anthropogenic activities on our sites. Therefore, it should be included in future coastal management plans to improve coastal water quality and ecosystem function in environmentally threatened areas.

Arabica and robusta are the two major coffee beans being sold worldwide. It is well recognized that coffee quality is influenced by their origin and the microbiological activities that drive their fermentation. However, in many coffee plantations, information about the natural diversity of bacteria that inhabit the arabica and robusta coffee cherries is limited. Here, we sampled arabica and robusta coffee cherries from Malang, East Java, Indonesia, then sequenced and analysed their bacterial composition. We found that: (a) arabica cherries contained bacteria with less diversity and abundance compared with robusta; (b) both coffee cherries were heavily populated by extremophiles, presumably dispersed from volcanic activities; (c) groups known to be involved in coffee fermentation such as lactic acid bacteria, acetic acid bacteria, Enterobacteria, and soil-associated bacteria were present in both arabica and robusta coffee cherries, and (d) arabica cherries were dominated by Leuconostoc pseudomesenteroides. These findings highlight that coffee cherry bacteria are highly diverse, the majority of which might come from the environment, with some potentially beneficial or detrimental to coffee quality. Knowledge of the natural microbial diversity of coffee cherries may be useful for the development of coffee fermentation technologies to yield coffee beans with consistent quality.

Wilt disease caused by Fusarium oxysporum is one of the most serious plant diseases in the world. There is no effective contol for. This study investigated the potential of arbuscular mycorrhizal and bacterial antagonists to control F. oxysporum through in vitro and in vivo studies. In this study, the antagonistic bacteria Stenotrophomonas maltophilia was isolated from mycorrhizal propagation media. Antagonist bacteria S. maltophilia showed antagonistic ability against F. oxysporum with an inhibition zone of 17.9 cm. Antagonistic bacteria and mycorrhizae used in this study significantly reduced the incidence of fusarium wilt in in vivo experiments. It was found that mycorrhizal and S. maltophilia inoculation showed disease incidence rates at 40% and 47.6%. While in the control treatment the incidence of disease reached 90.3%. The biocontrol agents of S. maltophilia and mycorrhizae have a promising prospective strategy to protect garlic plants. These results are expected to provide new insights for sustainable crop protection systems.