Microbiome & Microbiology Review

Here’s a concise overview of the key findings from the latest research articles on microbiome topics in August 2023:

1. Pest Fruit Flies and Microbiome Dynamics:

• Study focused on gut bacteria in pest fruit flies during adulthood.
• Bacterial populations declined after emergence but recovered within 24 hours.
• Shifts in bacterial composition occurred post-emergence.
• Implication of flexibility in the fly gut microbiome.

2. Antibiotics, Gut Microbiome, and Resistance:

• Antibiotics disrupted gut commensals, increasing nutrients and reducing inhibitory metabolites.
• Carbapenem-resistant Enterobacteriaceae (CRE) benefited from enriched nutrients.
• Antibiotics altered the microbiome’s resistance to CRE colonization.

3. Gut Microbiome in Spondyloarthritis:

• Explored gut microbiome differences in spondyloarthritis patients with Blastocystis.
• Specific microbial changes associated with Blastocystis colonization.
• Suggests interactions between Blastocystis and gut microbiome in disease context.

4. Cnidarian Microbiome Insights:

• Reviewed cnidarian microbiomes across different studies.
• Host, depth, and habitat influenced cnidarian-associated microbial communities.
• Identified specific microbial associations and baseline insights for coral health.

5. Selenium and Rumen Eukaryotic Diversity:

• Investigated effects of Selenium supplementation on goat rumen diversity.
• Different Se levels led to changes in eukaryotic genera.
• Used 18S rRNA sequencing to explore Se’s influence on rumen microbes.

6. Pig Respiratory Tract Antibiotic Resistome:

• Explored antibiotic resistance genes in pig respiratory tract.
• Certain ARGs linked to specific genetic elements.
• Gammaproteobacteria, including Escherichia coli, carriers of ARGs.
• Associations between ARGs and lung health identified.

7. Mangrove Sediment Microbial Communities:

• Utilized long-read metagenomics to explore microbial communities in mangrove sediments.
• Improved assembly quality with PacBio sequencing, leading to more high-quality genomes.
• Identified microbial contributions to carbon cycling, including organic carbon degradation and carbon fixation.
• Proposed a new candidate bacterial phylum “Candidatus Cosmopoliota” with versatile metabolic potential.

8. Seasonal Patterns in Southern Ocean Microbes:

• Studied prokaryotic membrane transporters in the Southern Ocean during different seasons.
• Used metatranscriptomics and metaproteomics to analyze organic substrate and iron transporters.
• Found distinct seasonal variations in membrane transporter abundances, indicating changing microbial needs for carbon and iron.

9. Interactive Metagenome Exploration Platform:

• Introduced BinaRena, an interactive platform for exploring and binning metagenomes.
• Provided a user-friendly graphic interface for visualizing, editing, and comparing contigs.
• Enabled researchers to fine-tune binning plans, calculate completeness, and analyze metagenomic data.

10. Personalized Health Monitoring through Gut Microbiota:

• Developed a statistical framework to predict and analyze personalized health status using gut microbiota.
• Created a health index, identified healthy patterns, and assessed bacterial contributions to health.
• Correlated health index with physiological indicators, diversity, and functional redundancy.

The followings is a review of these studies in more detail:

1) Gut bacterial population and community dynamics following adult emergence in pest tephritid fruit flies:

This study investigated the dynamics of gut bacterial communities in two pest tephritid fruit fly species, the melon fly (Zeugodacus cucurbitae) and the Mediterranean fruit fly (medfly, Ceratitis capitata), during the transition from pupal to adult life stages. The researchers used a combination of techniques including culturing, quantitative PCR (qPCR), and 16S V4 sequencing to analyze changes in bacterial populations and community composition.

The study revealed that bacterial populations in the gut of both fruit fly species declined significantly by 10 to 100-fold upon adult emergence, followed by a recovery within 24 hours after eclosion. Bacterial titers then increased, reaching around 10^7 colony-forming units (CFUs) or 10^8 16S rRNA copies within a week after emergence. Additionally, the researchers observed changes in the composition of amplicon sequence variants (ASVs), indicating shifts in the microbial community over time. The medfly showed different microbiome compositions at different time points, suggesting higher levels of variation before stabilization.

These findings highlight the dynamic nature of gut microbiomes in tephritid fruit flies during the transition from pupal to adult stages. The study suggests that this period of flux provides opportunities for the introduction and establishment of new microbial strains in the gut, indicating plasticity in the community structure. Understanding these dynamics could contribute to insights into the assembly of gut microbiota and the interactions between insects and their associated microbes.

2) Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites:

This study explores the impact of antibiotics on the growth and colonization of carbapenem-resistant Enterobacteriaceae (CRE) in the intestinal microbiota. CRE are bacteria resistant to carbapenem antibiotics, which are often used as last-resort treatments for infections. The researchers investigate how broad-spectrum antibiotics disrupt the natural balance of the gut microbiota, allowing CRE to expand and thrive in the intestines.

The study reveals that antibiotics lead to a reduction in gut microbial populations, including beneficial commensal bacteria like Bifidobacteriaceae and Bacteroidales. This reduction results in an enrichment of nutrients and a depletion of inhibitory microbial metabolites in the gut environment. As a consequence, CRE are able to utilize these enriched nutrients as sources of carbon and nitrogen, promoting their growth and colonization in the intestine.

The researchers show that antibiotic treatment reduces the abundance of inhibitory microbial metabolites while simultaneously providing CRE with the resources they need to thrive. This creates a favorable environment for CRE to expand in the gut and potentially cause infections. The findings highlight the complex interactions between antibiotics, gut microbiota, and antibiotic-resistant pathogens, shedding light on the mechanisms that contribute to the spread of drug-resistant bacteria in the intestinal ecosystem.

3) Differential gut microbiome in spondyloarthritis patients associated with Blastocystis colonization:

This study investigates the gut microbiome differences between patients with spondyloarthritis (SpA) and control individuals, specifically focusing on the potential impact of Blastocystis colonization. Spondyloarthritis is an autoimmune disease that affects the spine and joints. Blastocystis is a common single-celled microorganism found in the human intestine, and its role in intestinal health is still debated.

The researchers analyzed the gut microbiomes of 36 SpA patients and 13 control individuals. They found that the gut microbiomes of these two groups exhibited differences in terms of richness, diversity, and taxonomic composition. Additionally, they observed that Blastocystis colonization had differing effects on the gut microbiome based on the individuals’ health status:

1. In control individuals, Blastocystis colonization increased the richness and diversity of the gut microbiome. This suggests that Blastocystis might play a role in shaping the microbial diversity in healthy individuals.
2. In SpA patients, Blastocystis colonization did not seem to have a significant impact on the gut microbiome. This could be due to disease-related factors that override the potential influence of Blastocystis.

The researchers also identified specific changes in the gut microbiome associated with Blastocystis colonization in SpA patients. For instance, Blastocystis-positive SpA patients showed increased levels of certain bacterial groups, such as Pseudomonadota and Succinivibrio, which are associated with the class Gammaproteobacteria and the family Succinivibrionaceae, respectively. On the other hand, Blastocystis-negative SpA patients showed increased levels of other bacterial groups like Lactobacillus and Clostridium.

Furthermore, the study used predictive analysis (PICRUSt) to explore the potential functional implications of these microbiome changes. Blastocystis-positive SpA patients exhibited pathways related to antioxidant capacities and reducing intestinal inflammation. In contrast, Blastocystis-negative SpA patients showed changes in pathways associated with cell division/proliferation, which could potentially lead to larger shifts in the gut microbiome.

Overall, the findings suggest that the gut microbiome of SpA patients undergoes changes that may trigger protective mechanisms in response to inflammation, aiming to restore balance in the intestinal environment. The role of Blastocystis in this context appears to be influenced by both the individual’s health status and disease-related factors.

4) Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations:

Cnidarians, which include coral species and other related organisms, form complex associations with microorganisms that play essential roles in their health and resilience. This study aims to understand the factors that influence the microbiomes of cnidarians by conducting a comprehensive analysis of existing microbiome studies across different cnidarian species, depths, and habitats.

The researchers conducted a systematic review that unified and reanalyzed 16S rRNA gene sequences from a vast number of cnidarian microbiome samples. The dataset included samples from 12,010 cnidarian microbiomes, 3,388 poriferan (sponge) samples, 370 seawater samples, and 245 cultured Symbiodiniaceae (symbiotic algae). By analyzing this extensive dataset, the researchers aimed to identify patterns in microbial associations and factors influencing cnidarian microbiomes.

Key findings from the study:

1. Diverse Microbial Communities: The study revealed an incredible diversity of 86 archaeal and bacterial phyla associated with cnidarians. This diversity highlights the complexity of microbial interactions within cnidarian hosts.
2. Shared Microbial Communities: Different groups of cnidarians showed varying levels of microbial community sharing. Shallow-water Alcyonacea and Actinaria species exhibited highly shared and relatively abundant microbial communities. In contrast, Scleractinia species and most deeper cnidarians showed less shared communities.
3. Influential Factors: The composition, richness, diversity, and structure of cnidarian microbiomes were found to be primarily influenced by factors such as host phylogeny, sampling depth, ocean body, microhabitat, and sampling date.
4. Endozoicomonas Clades: The study identified both generalist and specific clades of the Endozoicomonas genus within cnidarians and poriferans, suggesting associations with specific hosts and habitats.
5. Baseline for Stress Assessment: The systematic review provides a comprehensive framework for understanding the factors that shape cnidarian microbiomes. This baseline knowledge can be used to assess changes and dysbiosis in cnidarian microbiomes under stress conditions, such as coral bleaching events.

By analyzing a large and diverse dataset, this study provides valuable insights into the complex microbial associations within cnidarians and contributes to our understanding of the ecological roles of these microorganisms in maintaining the health and resilience of cnidarian hosts.

5) The effects of Selenohomolanthionine supplementation on the rumen eukaryotic diversity of Shaanbei white cashmere wether goats:

Selenium (Se) is a crucial microelement for animal health, yet its impact on the diversity of rumen eukaryotic communities remains relatively unexplored. This study investigates the influence of Se supplementation on the rumen eukaryotic diversity in Shaanbei white cashmere wether goats.

The study involved goats fed a basal diet with different levels of organic Se supplementation in the form of Selenohomolanthionine (SeHLan). The Se supplementation levels included low Se, medium Se, and high Se groups. The researchers used 18S rRNA amplicon sequencing to analyze the rumen eukaryotic diversity and composition.

Key findings from the study:

1. Dominant Eukaryotic Kingdoms: The dominant eukaryotic kingdoms in all samples were Eukaryota (77.95%) and Fungi (14.10%).
2. Prominent Phyla: The primary rumen eukaryotic phylum was Ciliophora (92.14%), while fungal phyla were dominated by Ascomycota (40.77%), Basidiomycota (23.77%), Mucoromycota (18.32%), and unidentified_Fungi (13.89%).
3. Dominant Genera: The dominant eukaryotic genera were Entodinium (55.44%), Ophryoscolex (10.51%), and Polyplastron (10.19%). Among fungi, the dominant genera were Mucor (15.39%), Pichia (9.88%), Aspergillus (8.24%), Malassezia (7.73%), and unidentified_Neocallimastigaceae (7.72%).
4. Effect of Se Supplementation: The relative abundance of eukaryotic genera Ophryoscolex, Enoploplastron, and fungal genus Mucor differed significantly among the treatment groups. This suggests that Se supplementation impacted the composition of rumen eukaryotic communities.
5. Correlation Analysis: The study revealed a negative correlation between ciliate protozoa and fungi in the rumen, indicating potential interactions between these groups.

By employing high-throughput sequencing technology, this study provides insights into the effects of Se supplementation on rumen eukaryotic diversity patterns in Shaanbei white cashmere wether goats. The findings contribute to our understanding of how Se supplementation may influence the microbial communities within the rumen of these animals.

6) Characterization of the pig lower respiratory tract antibiotic resistome:

This study aims to understand the composition and distribution of antibiotic resistance genes (ARGs) in the microbiome of the lower respiratory tract of pigs. Antibiotic resistance is a growing concern in both the pig industry and human health due to its impact on disease treatment. However, the specific makeup of antibiotic resistance genes in the pig lower respiratory tract microbiome is not well-known, nor is their relationship with mobile genetic elements (MGEs) and lung health.

Key findings from the study:

1. Antibiotic Resistance Genes (ARGs): The researchers identified a total of 372 different ARGs, encompassing 1228 open reading frames, within the pig lower respiratory tract microbiome. These genes confer resistance to various antibiotics.
2. Tetracycline Resistance: Twelve ARGs responsible for tetracycline resistance were linked to a mobile genetic element called Tn916 family. This suggests that these resistance genes might be spread through this specific element.
3. Transposase Gene: Multiple types of ARGs were associated with a gene called tnpA, which is a transposase gene. Transposases are involved in the movement of genetic material, including ARGs, within genomes.
4. Conservation of MGEs: Similar patterns of linkage between ARGs and MGEs were observed not only in pig lower respiratory tract microbiomes but also in pig gut microbiomes and human lung microbiomes. This suggests the potential for these MGEs to facilitate the transfer of antibiotic resistance genes between pigs and humans.
5. Major Carriers of ARGs: Gammaproteobacteria were found to be the primary carriers of antibiotic resistance genes. Within this group, Escherichia coli stood out, harboring more than 50 ARGs and over 10 MGEs.
6. Association with Lung Health: The study also identified 73 ARGs whose relative abundances were linked to the severity of lung lesions. This indicates a potential connection between the presence of specific antibiotic resistance genes and the health of the pig’s lower respiratory tract.

Overall, this study provides an initial understanding of the antibiotic resistance gene profiles present in the lower respiratory tract microbiome of pigs. The findings shed light on the potential for antibiotic resistance genes to spread between pigs and humans, and they also highlight the association between specific ARGs and lung health in pigs.

7) Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments:
This study utilized metagenomic analysis based on PacBio single-molecule real-time (SMRT) and Illumina sequencing techniques to investigate the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments. The incorporation of PacBio long reads improved assembly quality, resulting in more high-quality metagenome-assembled genomes (MAGs). The study revealed that prokaryotes and fungi in mangrove sediment contribute significantly to carbon cycling, including the degradation of organic carbons, fermentation, autotrophy, and carbon fixation. A new candidate bacterial phylum named “Candidatus Cosmopoliota” was proposed, which showed a versatile metabolic potential for utilizing various organic substrates, anaerobic fermentation, and carbon fixation.

8) Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean:
This research investigated the expression of prokaryotic membrane transporters for organic substrates and iron in the Southern Ocean during different seasons. Metatranscriptomics and metaproteomics were used to analyze the differences in membrane transporter profiles between spring and late summer. The study found that there were distinct patterns in the abundance of membrane transporters for organic compounds and iron between the two seasons. This suggests that there are seasonal changes in microbial requirements for carbon and iron under different environmental conditions.

9) BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes:
The study introduced BinaRena, an interactive platform designed to aid human operators in exploring metagenome assemblies and performing binning. BinaRena provides a user-friendly graphic interface that allows users to visualize contigs based on various data types and perform contig-level operations. The platform enables researchers to edit, inspect, and compare binning plans, as well as calculate completeness and contamination of user-selected contigs. BinaRena effectively supports human researchers in interpreting and fine-tuning metagenomic data.

10) Statistical modeling of gut microbiota for personalized health status monitoring:
This study developed a statistical monitoring framework for predicting and analyzing personalized health status based on gut microbiota composition. The framework involved creating a health index, identifying healthy patterns, and analyzing the contribution of each bacterium to the health index of the diseased population. The researchers used real-data analysis to demonstrate the effectiveness of their approach in tracking personalized health status. The results showed that the health index correlated with physiological indicators, diversity, and functional redundancy, providing new insights into the potential role of microbial taxa in the cycling of carbon and iron.

Conclusions

These studies provide insights into microbiome dynamics, antibiotic resistance, host-microbe interactions, and potential health implications in various contexts. They also offer insights into microbial communities’ roles in different ecosystems, the development of interactive tools for metagenomic analysis, and potential applications in personalized health monitoring.