Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae

Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host-interactions remain thus far unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 21.2% of bacterial diversity. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Sorochlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Sponge-associated chlamydiae genomes mostly resembled environmental chlamydial endosymbionts, but not pathogens, and encoded genes for degrading diverse compounds associated with sponges, such as taurine. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an explored reservoir of novel natural products. This finding suggests that chlamydiae may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of this phylum on marine ecosystems.

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Marine sediments illuminate Chlamydiae diversity and evolution

10.1101/577767 ◽

2019 ◽

Author(s):

Jennah E. Dharamshi ◽

Daniel Tamarit ◽

Laura Eme ◽

Courtney Stairs ◽

Joran Martijn ◽

...

Keyword(s):

Marine Sediments ◽

Genomic Diversity ◽

The Arctic ◽

Community Members ◽

Environmental Distribution ◽

Microbial Eukaryotes ◽

Sister Clade ◽

Animal Pathogens ◽

Abundance And Diversity ◽

Ocean Ridge

The bacterial phylum Chlamydiae, which is so far comprised of obligate symbionts of eukaryotic hosts, are well-known as human and animal pathogens1-3. However, the Chlamydiae also include so-called environmental lineages4-6that primarily infect microbial eukaryotes7. Studying environmental chlamydiae, whose genomes display extended metabolic capabilities compared to their pathogenic relatives8-10has provided first insights into the evolution of the pathogenic and obligate intracellular lifestyle that is characteristic for this phylum. Here, we report an unprecedented relative abundance and diversity of novel lineages of the Chlamydiae phylum, representing previously undetected, yet potentially important, community members in deep marine sediments. We discovered that chlamydial lineages dominate the microbial communities in the Arctic Mid-Ocean Ridge11, which revealed the dominance of chlamydial lineages at anoxic depths, reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic unit. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, thereby dramatically expanding known interspecies genomic diversity in this phylum. Phylogenomic and comparative analyses revealed several deep-branching Chlamydiae clades, including a sister clade of the pathogenic Chlamydiaceae. Altogether, our study provides new insights into the diversity, evolution and environmental distribution of the Chlamydiae.

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Extensive genomic diversity of closely related Wolbachia strains

Microbiology ◽

10.1099/mic.0.027581-0 ◽

2009 ◽

Vol 155 (7) ◽

pp. 2211-2222 ◽

Cited By ~ 59

Author(s):

Nadeeza Ishmael ◽

Julie C. Dunning Hotopp ◽

Panagiotis Ioannidis ◽

Sarah Biber ◽

Joyce Sakamoto ◽

...

Keyword(s):

Gene Transfer ◽

Lateral Gene Transfer ◽

Ixodes Scapularis ◽

Protein A ◽

Hypothetical Protein ◽

Genomic Diversity ◽

Comparative Genome Hybridization ◽

Obligate Intracellular ◽

Dna Mismatch ◽

Obligate Intracellular Bacteria

Using microarray-based comparative genome hybridization (mCGH), the genomic content of Wolbachia pipientis wMel from Drosophila melanogaster was compared to the closely related Wolbachia from D. innubila (wInn), D. santomea (wSan), and three strains from D. simulans (wAu, wRi, wSim). A large number of auxiliary genes are identified in these five strains, with most absent/divergent genes being unique to a given strain. Each strain caused an average of ∼60 genes to be removed from the core genome. As such, these organisms do not appear to have the streamlined genomes expected of obligate intracellular bacteria. Prophage, hypothetical and ankyrin repeat genes are over-represented in the absent/divergent genes, with 21–87 % of absent/divergent genes coming from prophage regions. The only wMel region absent/divergent in all five query strains is that containing WD_0509 to WD_0511, including a DNA mismatch repair protein MutL-2, a degenerate RNase, and a conserved hypothetical protein. A region flanked by the two portions of the WO-B prophage in wMel is found in four of the five Wolbachia strains as well as on a plasmid of a rickettsial endosymbiont of Ixodes scapularis, suggesting lateral gene transfer between these two obligate intracellular species. Overall, these insect-associated Wolbachia have highly mosaic genomes, with lateral gene transfer playing an important role in their diversity and evolution.

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Resurrection of a Global, Metagenomically Defined Microvirus

10.1101/743518 ◽

2019 ◽

Author(s):

Paul C. Kirchberger ◽

Howard Ochman

Keyword(s):

Enteric Bacteria ◽

Survival Strategies ◽

Intracellular Bacteria ◽

Sequence Motifs ◽

E Coli ◽

Obligate Intracellular ◽

Resolution System ◽

Viral Progeny ◽

Obligate Intracellular Bacteria

AbstractThe Gokushovirinae (family Microviridae) are a group of single-stranded, circular DNA bacteriophages that have been detected in metagenomic datasets from every ecosystem on the planet. Despite their abundance, little is known about their biology or their bacterial hosts: isolates are exceedingly rare, known only from a very small number of obligate intracellular bacteria. By synthesizing circularized phage genomes from prophages embedded in diverse enteric bacteria, we produced viable gokushovirus phage particles that could reliably infect E. coli, thereby allowing experimental analysis of its life cycle and growth characteristics. Revived phages integrate into host genomes by hijacking a phylogenetically conserved chromosome-dimer resolution system, in a manner reminiscent of cholera phage CTX. Sequence motifs required for lysogeny are detectable in other metagenomically defined gokushoviruses, but we show that even partial motifs enable phages to persist in a state of pseudolysogeny by continuously producing viral progeny inside hosts without leading to collapse of their host culture. This ability to employ multiple, disparate survival strategies is likely key to the long-term persistence and global distribution of Gokushovirinae. The capacity to harness gokushoviruses as an experimentally tractable model system thus substantially changes our knowledge of the nature and biology of these ubiquitous phages.

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Pathogenic Potential of Novel Chlamydiae and Diagnostic Approaches to Infections Due to These Obligate Intracellular Bacteria

Clinical Microbiology Reviews ◽

10.1128/cmr.19.2.283-297.2006 ◽

2006 ◽

Vol 19 (2) ◽

pp. 283-297 ◽

Cited By ~ 120

Author(s):

Daniele Corsaro ◽

Gilbert Greub

Keyword(s):

Mammalian Cell Culture ◽

Host Cells ◽

The Novel ◽

Human Pathogens ◽

Pathogenic Potential ◽

Obligate Intracellular ◽

Animal Pathogens ◽

Diagnostic Approaches ◽

Obligate Intracellular Bacteria ◽

Simkania Negevensis

SUMMARY Novel chlamydiae are newly recognized members of the phylum Chlamydiales that are only distantly related to the classic Chlamydiaceae, i.e., Chlamydia and Chlamydophila species. They also exibit an obligate biphasic intracellular life cycle within eukaryote host cells. Some of these new chlamydiae are currently considered potential emerging human and/or animal pathogens. Parachlamydia acanthamoebae and Simkania negevensis are both emerging respiratory human pathogens, Waddlia chondrophila could be a novel abortigenic bovine agent, and Piscichlamydia salmonis has recently been identified as an agent of the gill epitheliocystis in the Atlantic salmon. Fritschea spp. and Rhabdochlamydia spp. seem to be confined to arthropods, but some evidence for human exposure exists. In this review, we first summarize the data supporting a pathogenic potential of the novel chlamydiae for humans and other vertebrates and the interactions that most of these chlamydiae have with free-living amoebae. We then review the diagnostic approaches to infections potentially due to the novel chlamydiae, especially focusing on the currently available PCR-based protocols, mammalian cell culture, the amoebal coculture system, and serology.

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ITN—VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics

Viruses ◽

10.3390/v13050766 ◽

2021 ◽

Vol 13 (5) ◽

pp. 766

Author(s):

Winfried Goettsch ◽

Niko Beerenwinkel ◽

Li Deng ◽

Lars Dölken ◽

Bas E. Dutilh ◽

...

Keyword(s):

Control Strategies ◽

Fundamental Importance ◽

Viral Growth ◽

International Training ◽

Host Interactions ◽

Animal Pathogens ◽

Interdisciplinary Nature ◽

Common Goals

Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.

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The growing repertoire of genetic tools for dissecting chlamydial pathogenesis

Pathogens and Disease ◽

10.1093/femspd/ftab025 ◽

2021 ◽

Author(s):

Arkaprabha Banerjee ◽

David E Nelson

Keyword(s):

Genetic Engineering ◽

Intracellular Bacteria ◽

Human Pathogens ◽

Pathogenic Potential ◽

Host Preferences ◽

Genetic Tools ◽

Obligate Intracellular ◽

Obligate Intracellular Bacteria ◽

Multiple Species

Abstract Multiple species of obligate intracellular bacteria in the genus Chlamydia are important veterinary and/or human pathogens. These pathogens all share similar biphasic developmental cycles and transition between intracellular vegetative reticulate bodies and infectious elementary forms, but vary substantially in their host preferences and pathogenic potential. A lack of tools for genetic engineering of these organisms has long been an impediment to the study of their biology and pathogenesis. However, the refinement of approaches developed in C. trachomatis over the last ten years, and adaptation of some of these approaches to other Chlamydia spp. in just the last few years, has opened exciting new possibilities for studying this ubiquitous group of important pathogens.

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Natural Products in Polyclad Flatworms

Marine Drugs ◽

10.3390/md19020047 ◽

2021 ◽

Vol 19 (2) ◽

pp. 47

Author(s):

Justin M. McNab ◽

Jorge Rodríguez ◽

Peter Karuso ◽

Jane E. Williamson

Keyword(s):

Natural Products ◽

Secondary Metabolites ◽

Marine Invertebrates ◽

Symbiotic Bacteria ◽

Chemical Defences ◽

Number Of Species ◽

Bioactive Secondary Metabolites ◽

Potential Sources ◽

Polyclad Flatworms

Marine invertebrates are promising sources of novel bioactive secondary metabolites, and organisms like sponges, ascidians and nudibranchs are characterised by possessing potent defensive chemicals. Animals that possess chemical defences often advertise this fact with aposematic colouration that potential predators learn to avoid. One seemingly defenceless group that can present bright colouration patterns are flatworms of the order Polycladida. Although members of this group have typically been overlooked due to their solitary and benthic nature, recent studies have isolated the neurotoxin tetrodotoxin from these mesopredators. This review considers the potential of polyclads as potential sources of natural products and reviews what is known of the activity of the molecules found in these animals. Considering the ecology and diversity of polyclads, only a small number of species from both suborders of Polycladida, Acotylea and Cotylea have been investigated for natural products. As such, confirming assumptions as to which species are in any sense toxic or if the compounds they use are biosynthesised, accumulated from food or the product of symbiotic bacteria is difficult. However, further research into the group is suggested as these animals often display aposematic colouration and are known to prey on invertebrates rich in bioactive secondary metabolites.

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Fossil Record of Parasitism on Marine Invertebrates with Special Emphasis on the Platyceratid-Crinoid Interaction

The Paleontological Society Papers ◽

10.1017/s1089332600001091 ◽

2002 ◽

Vol 8 ◽

pp. 195-210 ◽

Cited By ~ 33

Author(s):

Tomasz K. Baumiller ◽

Forest J. Gahn

Keyword(s):

Fossil Record ◽

Marine Invertebrates ◽

Marine Diversity ◽

Parasitic Interactions ◽

Explicit Criteria ◽

Lower Frequencies

The paleontological literature on marine invertebrates is rich in supposed examples of parasitism and our tabulation shows a nearly even distribution of reported cases through the post-Cambrian Phanerozoic. Slightly lower frequencies characterize the Triassic and Jurassic and higher frequencies the Cretaceous and Tertiary, and the pattern roughly mirrors Sepkoski's (1984) marine diversity curve. The total number of parasitic associations for any geologic period rarely exceeds a dozen, yet few of the reported examples provide explicit criteria distinguishing parasitism from predation, commensalism, or mutualism. We evaluated the published examples using the following criteria: (1) evidence of a long-term relationship between two organisms, (2) benefit of interaction to supposed parasite, and (3) detriment of interaction to the host We found that only in exceptional cases were these criteria fulfilled. One example that provides much information on parasitic interactions involves platyceratids and crinoids and we summarize the evidence for the parasitic interaction between these two groups of organisms.

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Plasmodium knowlesi: a relevant, versatile experimental malaria model

Parasitology ◽

10.1017/s0031182016002286 ◽

2016 ◽

Vol 145 (1) ◽

pp. 56-70 ◽

Cited By ~ 8

Author(s):

ERICA M. PASINI ◽

ANNE-MARIE ZEEMAN ◽

ANNEMARIE VOORBERG-VAN DER WEL ◽

CLEMENS H. M. KOCKEN

Keyword(s):

Parasite Species ◽

Vaccine Development ◽

Plasmodium Knowlesi ◽

Host Interactions ◽

Model Studies ◽

Human Red Blood Cells ◽

Malaria Model ◽

Human Primate

SUMMARYThe primate malariaPlasmodium knowlesihas a long-standing history as an experimental malaria model. Studies using this model parasite in combination with its various natural and experimental non-human primate hosts have led to important advances in vaccine development and in our understanding of malaria invasion, immunology and parasite–host interactions. The adaptation to long-termin vitrocontinuous blood stage culture in rhesus monkey,Macaca fascicularisand human red blood cells, as well as the development of various transfection methodologies has resulted in a highly versatile experimental malaria model, further increasing the potential of what was already a very powerful model. The growing evidence thatP. knowlesiis an important human zoonosis in South-East Asia has added relevance to former and future studies of this parasite species.

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Biological Control and Mitigation of Aflatoxin Contamination in Commodities

Toxins ◽

10.3390/toxins13020104 ◽

2021 ◽

Vol 13 (2) ◽

pp. 104

Author(s):

Ferenc Peles ◽

Péter Sipos ◽

Szilvia Kovács ◽

Zoltán Győri ◽

István Pócsi ◽

...

Keyword(s):

Biological Control ◽

Secondary Metabolites ◽

Competitive Exclusion ◽

Aflatoxin Contamination ◽

Post Harvest ◽

Physical Chemical ◽

Synthetic Chemicals ◽

Ruminal Degradation

Aflatoxins (AFs) are toxic secondary metabolites produced mostly by Aspergillus species. AF contamination entering the feed and food chain has been a crucial long-term issue for veterinarians, medicals, agroindustry experts, and researchers working in this field. Although different (physical, chemical, and biological) technologies have been developed, tested, and employed to mitigate the detrimental effects of mycotoxins, including AFs, universal methods are still not available to reduce AF levels in feed and food in the last decades. Possible biological control by bacteria, yeasts, and fungi, their excretes, the role of the ruminal degradation, pre-harvest biocontrol by competitive exclusion or biofungicides, and post-harvest technologies and practices based on biological agents currently used to alleviate the toxic effects of AFs are collected in this review. Pre-harvest biocontrol technologies can give us the greatest opportunity to reduce AF production on the spot. Together with post-harvest applications of bacteria or fungal cultures, these technologies can help us strictly reduce AF contamination without synthetic chemicals.

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