The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes

Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru

Background

The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where pediatric antibiotic consumption is exceptionally common. We characterized the effects of antibiotics commonly used by Peruvian children (i.e., amoxicillin, azithromycin, cefalexin, sulfa-trimethoprim) on gut diversity, genera, and antibiotic resistance gene (ARG) abundance from 3-16 months.

Methods

This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-2019. Stool collected at 3, 6, 7, 9, 12, and 16 months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40,662 observations) to tabulate the number of antibiotic courses consumed in the 30 days prior to stool sampling. Using linear mixed models, the association of recent antibiotic use with species richness, diversity, gut genera, and ARG abundance over time was examined.

Results

Most children were vaginally delivered (73%), received breastmilk almost daily over the study period, and belonged to socioeconomically diverse households. Amoxicillin, azithromycin, cefalexin, and sulfa-trimethoprim did not impact gut diversity or genera abundance. Azithromycin use significantly impacted ARGs from the macrolide, aminoglycoside, and folate pathway antagonist classes. Amoxicillin use significantly increased total ARGs. Antibiotics' effects on ARGs appeared to be independent of gut microbiome changes.

Conclusion

Common antibiotics like amoxicillin and azithromycin may be key drivers of the gut resistome but not the microbiome during early childhood in this setting with frequent breastfeeding.

Sampling fish gut microbiota - A genome-resolved metagenomic approach

Despite a surge in microbiota-focused studies in teleosts, few have reported functional data on whole metagenomes as it has proven difficult to extract high biomass microbial DNA from fish intestinal samples. The zebrafish is a promising model organism in functional microbiota research, yet studies on the functional landscape of the zebrafish gut microbiota through shotgun based metagenomics remain scarce. Thus, a consensus on an appropriate sampling method accurately representing the zebrafish gut microbiota, or any fish species is lacking. Addressing this, we systematically tested four methods of sampling the zebrafish gut microbiota: collection of faeces from the tank, the whole gut, intestinal content, and the application of ventral pressure to facilitate extrusion of gut material. Additionally, we included water samples as an environmental control to address the potential influence of the environmental microbiota on each sample type. To compare these sampling methods, we employed a combination of genome-resolved metagenomics and 16S metabarcoding techniques. We observed differences among sample types on all levels including sampling, bioinformatic processing, metagenome co-assemblies, generation of metagenome-assembled genomes (MAGs), functional potential, MAG coverage, and population level microdiversity. Comparison to the environmental control highlighted the potential impact of the environmental contamination on data interpretation. While all sample types tested are informative about the zebrafish gut microbiota, the results show that optimal sample type for studying fish microbiomes depends on the specific objectives of the study, and here we provide a guide on what factors to consider for designing functional metagenome-based studies on teleost microbiomes.

The Marine Fish Gut Microbiome as a Source of Novel Bacteriocins

The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due to the unique environmental pressures these microbial communities experience, the bioactive molecules they produce often evolve unique adaptations that give them diverse structures and activities, differentiating them from terrestrial homologues. Of particular interest, due to their structural and functional diversity, are the ribosomally-synthesized antimicrobial peptides (bacteriocins). With increasing pressure from emerging antibiotic-resistant disease and industrial demand for novel therapeutics, the marine fish gut microbiome represents a relatively untapped resource of novel bacteriocins that could prove beneficial to human health and aquaculture. This review presents an overview of the marine fish gut microbiome and explores its potential as a source of bacteriocins for human health with considerations for applications and future research in this area.

Nanopore-Enabled Microbiome Analysis: Investigating Environmental and Host-Associated Samples in Rainbow Trout Aquaculture

Microbiome sequencing is at the forefront of health management development, and as such, it is becoming of great interest to monitor the microbiome in the aquaculture industry as well. Oxford Nanopore Technologies (ONT) platforms are gaining popularity to study microbial communities, enabling faster sequencing, extended read length, and therefore, improved taxonomic resolution. Despite this, there is a lack of clear guidelines to perform a metabarcoding study, especially when dealing with samples from non-mammalian species, such as aquaculture-related samples. In this article, we provide general guidelines for sampling, nucleic acid extraction, and ONT-based library preparation for both environmental (water, sediment) and host-associated (gill or skin mucus, skin, gut content, or gut mucosa) microbiome analysis. Our procedures focus specifically on rainbow trout (Oncorhynchus mykiss) reared in experimental facilities. However, these protocols can also be transferred to alternative types of samples, such as environmental DNA (eDNA) monitoring from alternative water sources, or to different fish species. The additional challenge posed by the low biomass and limited bacterial diversity inherent in fish-associated microbiomes is addressed through the implementation of troubleshooting solutions. Furthermore, we describe a bioinformatic pipeline starting from raw reads and leading to taxonomic abundance tables using currently available tools and software. Finally, we provide a set of specific guidelines and considerations related to the strategic planning of a microbiome study within the context of aquaculture. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Environmental sample collection Basic Protocol 2: Host-associated sample collection Alternate Protocol: Host-associated sample collection: Alternative sample types Basic Protocol 3: Sample pre-treatment and nucleic acid extraction Basic Protocol 4: Quality control and preparation for 16S rRNA gene sequencing Support Protocol 1: Assessment of inhibition by quantitative PCR Support Protocol 2: Bioinformatic analysis from raw files to taxonomic abundance tables.

A Mini-Review of Anti-Listerial Compounds from Marine Actinobacteria (1990-2023)

Among the foodborne illnesses, listeriosis has the third highest case mortality rate (20-30% or higher). Emerging drug-resistant strains of Listeria monocytogenes, a causative bacterium of listeriosis, exacerbate the seriousness of this public health concern. Novel anti-Listerial compounds are therefore needed to combat this challenge. In recent years, marine actinobacteria have come to be regarded as a promising source of novel antimicrobials. Hence, our aim was to provide a narrative of the available literature and discuss trends regarding bioprospecting marine actinobacteria for new anti-Listerial compounds. Four databases were searched for the review: Academic Search Ultimate, Google Scholar, ScienceDirect, and South African Thesis and Dissertations. The search was restricted to peer-reviewed full-text manuscripts that discussed marine actinobacteria as a source of antimicrobials and were written in English from 1990 to December 2023. In total, for the past three decades (1990-December 2023), only 23 compounds from marine actinobacteria have been tested for their anti-Listerial potential. Out of the 23 reported compounds, only 2-allyoxyphenol, adipostatins E-G, 4-bromophenol, and ansamycins (seco-geldanamycin B, 4.5-dihydro-17-O-demethylgeldanamycin, and seco-geldanamycin) have been found to possess anti-Listerial activity. Thus, our literature survey reveals the scarcity of published assays testing the anti-Listerial capacity of bioactive compounds sourced from marine actinobacteria during this period.

Planococcus notacanthi sp. nov., isolated from the skin of a deep-sea snub-nosed spiny eel

A novel bacterial strain, APC 4016T, was previously isolated from the skin of a snub-nosed spiny eel, Notacanthus chemnitzii, from a depth of 1000 m in the northern Atlantic Ocean. Cells were aerobic, cocci, motile, Gram-positive to Gram-variable staining, and gave rise to orange-pigmented colonies. Growth occurred at 4-40 °C (optimum, 25-28 °C), pH 5.5-12 (optimum, pH 7-7.5), and 0-12 % (w/v) NaCl (optimum, 1 %). 16S rRNA gene phylogenetic analysis confirmed that strain APC 4016T belonged to the genus Planococcus and was most closely related to Planococcus okeanokoites IFO 12536T (98.98 % 16S similarity). However, digital DNA-DNA hybridization and average nucleotide identity values between these two strains were low, at 20.1 and 83.8 %, respectively. Major (>10 %) cellular fatty acids of strain APC 4016T were iso-C14 : 0, anteiso-C15 : 0 and C16 : 1-ω-Alc. The predominant respiratory quinones were menaquinones 5, 6, 7 and 8. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, and three unknown lipids were also present. The draft genome sequence is 3.6 Mb with a G+C content of 45.25 mol%. This strain was previously shown to have antimicrobial activity and to encode bacteriocin and secondary metabolite biosynthetic gene clusters. Based on the phylogenetic analysis and its distinct phenotypic characteristics, strain APC 4016T is deemed to represent a novel species of the genus Planococcus, and for which the name Planococcus notacanthi sp. nov. is proposed. The type strain of this species is APC 4016T (=DSM 115753T=NCIMB 15463T).

Cyanobacterial extracellular antibacterial substances could promote the spread of antibiotic resistance: impacts and reasons

Many studies have shown that antibiotic resistance genes (ARGs) can be facilitated by a variety of antibacterial substances. Cyanobacteria are photosynthetic bacteria that are widely distributed in the ocean. Some extracellular substances produced by marine cyanobacteria have been found to possess antibacterial activity. However, the impact of these extracellular substances on ARGs is unclear. Therefore, we established groups of seawater microcosms that contained different concentrations (1000, 100, 10, 1, 0.1, 0.01, and 0 μg mL-1) of cyanobacterial extracellular substances (CES), and tracked the changes of 17 types of ARGs, the integron gene (intI1), as well as the bacterial community at different time points. The results showed that CES could enrich most ARGs (15/17) in the initial stage, particularly at low concentrations (10 and 100 μg mL-1). The correlation analysis showed a positive correlation between several ARGs and intI1. It is suggested that the abundance of intI1 increased with CES may contribute to the changes of these ARGs, and co-resistance of CES may be the underlying reason for the similar variation pattern of some ARGs. Moreover, the results of qPCR and high-throughput sequencing of 16S rRNA showed that CES had an inhibitory impact on the growth of bacterial communities. High concentrations of CES were found to alter the structure of bacterial communities. Co-occurrence networks showed that bacteria elevated in the high concentration group of CES and might serve as the potential hosts for a variety of ARGs. In general, marine cyanobacteria could play an important role in the global dissemination of ARGs and antibiotic-resistant bacteria (ARBs).

Winogradskyella bathintestinalis sp. nov., isolated from the intestine of the deep-sea loosejaw dragonfish, Malacosteus niger

A novel bacterial strain, APC 3343T, was isolated from the intestine of a deep-sea loosejaw dragon fish, Malacosteus niger, caught at a depth of 1000 m in the Northwest Atlantic Ocean. Cells were aerobic, rod-shaped, yellow/orange-pigmented, non-motile and Gram-negative. Growth of strain APC 3343T was observed at 4-30 °C (optimum, 21-25 °C), pH 5.5-10 (optimum, pH 7-8) and 0.5-8 % (w/v) NaCl (optimum, 2-4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain APC 3343T was most closely related to members of the genus Winogradskyella, with the most closely related type strains being Winogradskyella algae Kr9-9T (98.46 % identity), Winogradskyella damuponensis F081-2T (98.07 %), Winogradskyella eximia CECT 7946T (97.93 %), Winogradskyella litoriviva KMM 6491T (97.79 %) and Winogradskyella endarachnes HL2-2T (97.79 %). Major fatty acids (>10 % of total) were iso-C16 : 0 3-OH, iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-6 (MK-6). Polar lipids were phosphatidylethanolamine, three unknown aminolipids and eight unknown lipids. The draft genome sequence was 3.8 Mb in length with a G+C content of 33.43 mol%. Based on the phenotypic characteristics and phylogenetic analysis, strain APC 3343T is deemed to be a novel species of the genus Winogradskyella, and for which the name Winogradskyella bathintestinalis sp. nov. is proposed. The type strain of this species is APC 3343T (=DSM 115832T=NCIMB 15464T).

Bioactivity Screening and Genomic Analysis Reveals Deep-Sea Fish Microbiome Isolates as Sources of Novel Antimicrobials

With the increase in antimicrobial resistance and the subsequent demand for novel therapeutics, the deep-sea fish microbiome can be a relatively untapped source of antimicrobials, including bacteriocins. Previously, bacterial isolates were recovered from the gut of deep-sea fish sampled from the Atlantic Ocean.In this study, we used in vitro methods to screen a subset of these isolates for antimicrobial activity, and subsequently mined genomic DNA from isolates of interest for bacteriocin and other antimicrobial metabolite genes. We observed antimicrobial activity against foodborne pathogens, including Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis and Micrococcus luteus. In total, 147 candidate biosynthetic gene clusters were identified in the genomic sequences, including 35 bacteriocin/RiPP-like clusters. Other bioactive metabolite genes detected included non-ribosomal peptide synthases (NRPS), polyketide synthases (PKS; Types 1 and 3), beta-lactones and terpenes. Moreover, four unique bacteriocin gene clusters were annotated and shown to encode novel peptides: a class IIc bacteriocin, two class IId bacteriocins and a class I lanthipeptide (LanM subgroup). Our dual in vitro and in silico approach allowed for a more comprehensive understanding of the bacteriocinogenic potential of these deep-sea isolates and an insight into the antimicrobial molecules that they may produce.

Metagenomics reveals the habitat specificity of biosynthetic potential of secondary metabolites in global food fermentations

BACKGROUND

Fermented foods are considered to be beneficial for human health. Secondary metabolites determined by biosynthetic gene clusters (BGCs) are precious bioactive compounds with various biological activities. However, the diversity and distribution of the biosynthetic potential of secondary metabolites in global food fermentations remain largely unknown. In this study, we performed a large-scale and comprehensive investigation for the BGCs in global food fermentations by metagenomics analysis.

RESULTS

We recovered 653 bacterial metagenome-assembled genomes (MAGs) from 367 metagenomic sequencing datasets covering 15 general food fermentation types worldwide. In total, 2334 secondary metabolite BGCs, including 1003 novel BGCs, were identified in these MAGs. Bacillaceae, Streptococcaceae, Streptomycetaceae, Brevibacteriaceae and Lactobacillaceae contained high abundances of novel BGCs (≥ 60 novel BGCs). Among 2334 BGCs, 1655 were habitat-specific, originating from habitat-specific species (80.54%) and habitat-specific genotypes within multi-habitat species (19.46%) in different food fermentation types. Biological activity analysis suggested that 183 BGC-producing secondary metabolites exhibited high probabilities of antibacterial activity (> 80%). These 183 BGCs were distributed across all 15 food fermentation types, and cheese fermentation contained the most BGC number.

CONCLUSIONS

This study demonstrates that food fermentation systems are an untapped reservoir of BGCs and bioactive secondary metabolites, and it provides novel insights into the potential human health benefits of fermented foods. Video Abstract.

Gut microbial communities of hybridising pygmy angelfishes reflect species boundaries

Hybridisation and introgression of eukaryotic genomes can generate new species or subsume existing ones, with direct and indirect consequences for biodiversity. An understudied component of these evolutionary forces is their potentially rapid effect on host gut microbiomes, and whether these pliable microcosms may serve as early biological indicators of speciation. We address this hypothesis in a field study of angelfishes (genus Centropyge), which have one of the highest prevalence of hybridisation within coral reef fish. In our study region of the Eastern Indian Ocean, the parent fish species and their hybrids cohabit and display no differences in their diet, behaviour, and reproduction, often interbreeding in mixed harems. Despite this ecological overlap, we show that microbiomes of the parent species are significantly different from each other in form and function based on total community composition, supporting the division of parents into distinct species, despite the confounding effects of introgression acting to homogenize parent species identity at other molecular markers. The microbiome of hybrid individuals, on the other hand, are not significantly different to each of the parents, instead harbouring an intermediate community composition. These findings suggest that shifts in gut microbiomes may be an early indicator of speciation in hybridising species.

Trophic level and proteobacteria abundance drive antibiotic resistance levels in fish from coastal New England

BACKGROUND

The natural marine environment represents a vast reservoir of antimicrobial resistant bacteria. The wildlife that inhabits this environment plays an important role as the host to these bacteria and in the dissemination of resistance. The relationship between host diet, phylogeny, and trophic level and the microbiome/resistome in marine fish is not fully understood. To further explore this relationship, we utilize shotgun metagenomic sequencing to define the gastrointestinal tract microbiomes of seven different marine vertebrates collected in coastal New England waters.

RESULTS

We identify inter and intraspecies differences in the gut microbiota of these wild marine fish populations. Furthermore, we find an association between antibiotic resistance genes and host dietary guild, which suggests that higher trophic level organisms have a greater abundance of resistance genes. Additionally, we demonstrate that antibiotic resistance gene burden is positively correlated with Proteobacteria abundance in the microbiome. Lastly, we identify dietary signatures within the gut of these fish and find evidence of possible dietary selection for bacteria with specific carbohydrate utilization potential.

CONCLUSIONS

This work establishes a link between host lifestyle/dietary guild, and microbiome composition and the abundance of antibiotic resistance genes within the gastrointestinal tract of marine organisms. We expand the current understanding of marine organism-associated microbial communities and their role as reservoirs of antimicrobial resistance genes.

Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén

Soil contamination by heavy metals, particularly mercury (Hg), is a problem that can seriously affect the environment, animals, and human health. Hg has the capacity to biomagnify in the food chain. That fact can lead to pathologies, of those which affect the central nervous system being the most severe. It is convenient to know the biological environmental indicators that alert of the effects of Hg contamination as well as the biological mechanisms that can help in its remediation. To contribute to this knowledge, this study conducted comparative analysis by the use of Shotgun metagenomics of the microbial communities in rhizospheric soils and bulk soil of the mining region of Almadén (Ciudad Real, Spain), one of the most affected areas by Hg in the world The sequences obtained was analyzed with MetaPhlAn2 tool and SUPER-FOCUS. The most abundant taxa in the taxonomic analysis in bulk soil were those of Actinobateria and Alphaproteobacteria. On the contrary, in the rhizospheric soil microorganisms belonging to the phylum Proteobacteria were abundant, evidencing that roots have a selective effect on the rhizospheric communities. In order to analyze possible indicators of biological contamination, a functional potential analysis was performed. The results point to a co-selection of the mechanisms of resistance to Hg and the mechanisms of resistance to antibiotics or other toxic compounds in environments contaminated by Hg. Likewise, the finding of antibiotic resistance mechanisms typical of the human clinic, such as resistance to beta-lactams and glycopeptics (vancomycin), suggests that these environments can behave as reservoirs. The sequences involved in Hg resistance (operon mer and efflux pumps) have a similar abundance in both soil types. However, the response to abiotic stress (salinity, desiccation, and contaminants) is more prevalent in rhizospheric soil. Finally, sequences involved in nitrogen fixation and metabolism and plant growth promotion (PGP genes) were identified, with higher relative abundances in rhizospheric soils. These findings can be the starting point for the targeted search for microorganisms suitable for further use in bioremediation processes in Hg-contaminated environments.

Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis

The skin mucosa of fish serves as a primary barrier against pathogens. In lesion sites in diseased fish, the mucosal barrier is expected to be compromised, with a substantial presence of potential pathogens. An understanding of the skin microbiome and its functional repertoire would provide important insights into host-microbe interactions, which has important implications for prophylactic measures in aquaculture. This study revealed the skin microbiomes and their functional annotations from healthy and diseased stinging catfish (Heteropneustes fossilis) based on 16S rRNA metagenomics. The OTUs consisted of four major phyla, Proteobacteria, Bacteroidota, Actinobacteriota and Firmicutes. Among members of the predominant phyla, Proteobacteria were rich in healthy fishes, but Bacteroidota and Firmicutes were significantly differentiated in healthy and diseased fish. The diversified microbiome was high in the skin of healthy fishes and did not significantly differ from that of the diseased groups. At the genus level, Pseudomonas showed the highest abundance in healthy fish but was nearly absent in diseased fish, whereas Flavobacterium showed the highest abundance in diseased fish. Linear discriminant analysis identified two phyla (Bacteroidota, Firmicutes) and two genera (Flavobacterium, Allorhizobium) that were consistently identified in diseased fishes. Functional prediction analysis specified that the genes related to physiological functions such as metabolism, immune and digestive systems and environmental adaptations could be highly expressed in diseased fishes. The present study indicates that the compositions, richness and functions of the bacterial community could influence the health status of cultured stinging catfish. Aquaculture-associated pathogenic bacteria may be identified, and preventive measures can be taken for the surveillance of fish health.

Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach

Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.

Microbiomes and Obligate Symbiosis of Deep-Sea Animals

Microbial communities associated with deep-sea animals are critical to the establishment of novel biological communities in unusual environments. Over the past few decades, rapid exploration of the deep sea has enabled the discovery of novel microbial communities, some of which form symbiotic relationships with animal hosts. Symbiosis in the deep sea changes host physiology, behavior, ecology, and evolution over time and space. Symbiont diversity within a host is often aligned with diverse metabolic pathways that broaden the environmental niche for the animal host. In this review, we focus on microbiomes and obligate symbionts found in different deep-sea habitats and how they facilitate survival of the organisms that live in these environments. In addition, we discuss factors that govern microbiome diversity, host specificity, and biogeography in the deep sea. Finally, we highlight the current limitations of microbiome research and draw a road map for future directions to advance our knowledge of microbiomes in the deep sea. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.