Gut microbiome and metabolome of sea cucumber (Stichopus ocellatus) as putative markers for monitoring the marine sediment pollution in Pahang, Malaysia

Siew, Shing Wei; Yen, Choo Mei; Marshall, Ian P. G.; Hamid, Hazrulrizawati Abd; Kamal, Shamrulazhar Shamzir; Nielsen, Dennis Sandris; Ahmad, Hajar Fauzan

doi:10.1016/j.marpolbul.2022.114022

Cited by 19 publications

(7 citation statements)

References 68 publications

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“…This work confirms the high importance for bacterial pathogens detection due to their various uses, as reported before [ 1 , 2 , 7 , [25] , [26] , [27] , [28] , [29] , [30] , [31] ].…”

Section: Methods Detailssupporting

confidence: 91%

Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing

Mat-Hussin,

Siew,

Maghpor

et al. 2024

MethodsX

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“…This work confirms the high importance for bacterial pathogens detection due to their various uses, as reported before [ 1 , 2 , 7 , [25] , [26] , [27] , [28] , [29] , [30] , [31] ].…”

Section: Methods Detailssupporting

confidence: 91%

Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing

Mat-Hussin,

Siew,

Maghpor

et al. 2024

MethodsX

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“…Analysis of the intestines of South American white shrimp revealed the presence of sulfadiazine, ciprofloxacin, and norfloxacin in all samples, which belong to the sulfonamides and quinolones [ 81 ]. Moreover, antibiotics in the intestines of squid ginseng were detected, showing high levels of amikacin, gentamicin, ampicillin, and ribostamycin, which belong to the aminoglycoside and β-lactam antibiotic families [ 82 ]. Among them, the aminoglycoside amikacin was the most abundant antibiotic.…”

Section: The Presence Of Antibiotics Arb and Args In Aquaculture Envi...mentioning

confidence: 99%

“…Exogenous addition of antibiotics in aquaculture would induce one or a variety of resistance genes produced by bacteria in aquaculture organisms, leading to antibiotic resistance development. In aquaculture organisms, there are four major classes of ARGs, comprising those conferring resistance to quinolones, macrolides, tetracyclines, and sulfonamides ( Table 2 ), among which sul1, sul2, qnrA, qnrS, macB, tetA, and tetG were more likely to be detected [ 82 , 87 ]. Currently, metagenomics is increasingly used to detect ARGs in aquaculture organisms or an environmental medium, in addition to PCR assays or gene chip technology.…”

Section: The Presence Of Antibiotics Arb and Args In Aquaculture Envi...mentioning

confidence: 99%

A Review of Antibiotics, Antibiotic Resistant Bacteria, and Resistance Genes in Aquaculture: Occurrence, Contamination, and Transmission

Yuan

Zhang

et al. 2023

Toxics

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Antibiotics are commonly used to prevent and control diseases in aquaculture. However, long-term/overuse of antibiotics not only leaves residues but results in the development of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Antibiotics, ARB, and ARGs are widespread in aquaculture ecosystems. However, their impacts and interaction mechanisms in biotic and abiotic media remain to be clarified. In this paper, we summarized the detection methods, present status, and transfer mechanisms of antibiotics, ARB, and ARGs in water, sediment, and aquaculture organisms. Currently, the dominant methods of detecting antibiotics, ARB, and ARGs are UPLC−MS/MS, 16S rRNA sequencing, and metagenomics, respectively. Tetracyclines, macrolides, fluoroquinolones, and sulfonamides are most frequently detected in aquaculture. Generally, antibiotic concentrations and ARG abundance in sediment are much higher than those in water. Yet, no obvious patterns in the category of antibiotics or ARB are present in organisms or the environment. The key mechanisms of resistance to antibiotics in bacteria include reducing the cell membrane permeability, enhancing antibiotic efflux, and structural changes in antibiotic target proteins. Moreover, horizontal transfer is a major pathway for ARGs transfer, including conjugation, transformation, transduction, and vesiculation. Identifying, quantifying, and summarizing the interactions and transmission mechanisms of antibiotics, ARGs, and ARB would provide useful information for future disease diagnosis and scientific management in aquaculture.

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“…Statistical analysis of microbiome data was performed using MicrobiomeAnalyst 2.0 to pro le the bacterial community found in indoor air with adjustments [23,24]. The data was ltered at a minimum count of zero and interquartile range of 10%.…”

Section: Discussionmentioning

confidence: 99%

May the Pathogenic Microbes Not Be with You: Core Microbiome Profiling in Hospital Airspace

Hussin,

Tay,

Zainulabid

et al. 2024

Preprint

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The hospital indoor air microbiome, a diverse range of microorganisms, gains prominence amid the COVID-19 pandemic. Elevated awareness underscores implications for patient and staff well-being. Concerns about risks to indoor air quality persist due to prolonged indoor exposure, necessitating further research on specific threats within the hospital environment. In this study, an independent culture-based approach was used to analyze the baseline core microbiome present in hospital environments, utilizing amplicon sequencing on the next-generation sequencing technology to target the V3 region of the 16S rRNA gene. Firmicutes, Proteobacteria, and Actinobacteria were the main bacterial phyla that were most isolated from the wards and clinics with different orders of abundance; Firmicutes being associated more in clinics and Actinobacteriota in wards. The bacteria Niallia taxi, Methyloversatilis universalis, unclassified Rummeliibacillus, unclassified Clostridium, and unclassified Sphingomonadaceae dominated the clinic area while ward areas reported Pseudonocardia bannensis, Rubrobacter A aplysinae, unclassified Brachybacterium, unclassified Bradyrhizobium, and unclassified Mycobacterium to be the top five features. While the alpha-diversity index showed no significant differences, the beta-diversity analysis showed a significant differences between clinic and ward areas (p < 0.05). Certain bacterial species associated with opportunistic pathogens as well as normal skin flora such as Methylobacterium spp., Cutibacterium spp., unclassified Sphingomonadaceae, and Anoxybacillus B spp., were also identified across all samples. The methods described in this research aim to establish a rapid and sensitive screening process that could be valuable for disease surveillance within the healthcare setting, shedding light on the potential impacts of the hospital microbiome on human illness.

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Gut microbiome and metabolome of sea cucumber (Stichopus ocellatus) as putative markers for monitoring the marine sediment pollution in Pahang, Malaysia

Cited by 19 publications

References 68 publications

Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing

Method for detection of pathogenic bacteria from indoor air microbiome samples using high-throughput amplicon sequencing

A Review of Antibiotics, Antibiotic Resistant Bacteria, and Resistance Genes in Aquaculture: Occurrence, Contamination, and Transmission

May the Pathogenic Microbes Not Be with You: Core Microbiome Profiling in Hospital Airspace

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