MiL-FISH: Multilabeled Oligonucleotides for Fluorescence
            <i>In Situ</i>
            Hybridization Improve Visualization of Bacterial Cells

Schimak, Mario P.; Kleiner, Manuel; Wetzel, Silke; Liebeke, Manuel; Dubilier, Nicole; Fuchs, Bernhard M.

doi:10.1128/aem.02776-15

Cited by 57 publications

(48 citation statements)

References 36 publications

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“…The approach presented here can also be used to examine the spatial organization of these strains, thereby facilitating better understanding of the link between the bacterium-associated factors and the developmental stages of the light organ crypts. Recent microscopy-based techniques, such as BacSpace and multilabeled fluorescence in situ hybridization (MiL-FISH), have begun to provide insight into the spatial organization in the gut microbiome and other animal-microbe symbioses (39,40). Such imaging-based approaches will complement sequencingbased studies of microbial consortia and populations and increase our understanding of the microbial world in which animals reside.…”

Section: Discussionmentioning

confidence: 99%

Niche-Specific Impact of a Symbiotic Function on the Persistence of Microbial Symbionts within a Natural Host

Verma

Miyashiro

2016

Appl Environ Microbiol

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How the function of microbial symbionts is affected by their population/consortium structure within a host remains poorly understood. The symbiosis established between Euprymna scolopes and Vibrio fischeri is a well-characterized host-microbe association in which the function and structure of V. fischeri populations within the host are known: V. fischeri populations produce bioluminescence from distinct crypt spaces within a dedicated host structure called the light organ. Previous studies have revealed that luminescence is required for V. fischeri populations to persist within the light organ and that deletion of the lux gene locus, which is responsible for luminescence in V. fischeri, leads to a persistence defect. In this study, we investigated the impact of bioluminescence on V. fischeri population structure within the light organ. We report that the persistence defect is specific to crypt I, which is the most developmentally mature crypt space within the nascent light organ. This result provides insight into the structure/function relationship that will be useful for future mechanistic studies of squid-Vibrio symbiosis. In addition, our report highlights the potential impact of the host developmental program on the spatiotemporal dynamics of host-microbe interactions. IMPORTANCEMetazoan development and physiology depend on microbes. The relationship between the symbiotic function of microbes and their spatial structure within the host environment remains poorly understood. Here we demonstrate, using a binary symbiosis, that the host requirement for the symbiotic function of the microbial symbiont is restricted to a specific host environment. Our results also suggest a link between microbial function and host development that may be a fundamental aspect of the more complex host-microbe interactions. Microbes are a dominant form of life on Earth, and their associations with humans and other animals directly impact host development, physiology, and evolution (1-3). In many cases, the acquisition of microbes from the environment represents a key moment in the life history of the host. Studies of mammalian gut microbiota have suggested that the spatial distribution of these microbes within the host, i.e., their biogeography, is an important factor in the assemblage and maintenance of such associations (see reference 4 for a recent review). For instance, when microbial communities isolated from diverse habitats are transplanted into gnotobiotic mice, the resulting composition closely resembles that normally found in the mouse cecum (5). Body part-specific microbiota have also been observed in nonmammalian systems, such as that of the jellyfish Aurelia aurita, which shows significant differences in microbial composition between the gastric cavity and exumbrellar mucus (6). These studies suggest that hosts select certain biogeographical landscapes for their associated microbiota. However, examining how biogeography impacts the symbiotic function of microbes remains challenging for most associations, due in ...

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Section: Discussionmentioning

confidence: 99%

Niche-Specific Impact of a Symbiotic Function on the Persistence of Microbial Symbionts within a Natural Host

Verma

Miyashiro

2016

Appl Environ Microbiol

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“…This system has benefited from some of the most sophisticated 'omics and visualization tools (Woyke et al, 2006). For example, multi-labeled probing has improved visualization of the microbiome (Schimak et al, 2016) and transcriptomics and proteomics have been applied to examine host-microbiome interactions, including energy transfer between the host and microbes (Kleiner et al, 2012) and recognition of the consortia by the worm's innate immune system (Wippler et al, 2016). The major strength of this system is that it does offer the ability to study host-microbiome interactions with a low diversity microbial consortium, and it also offers a number of host and microbial genomic resources (e.g., Woyke et al, 2006;Ruehland et al, 2008).…”

Section: Overview Of Diverse and Emerging Animal-microbiome Study Sysmentioning

confidence: 99%

Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean

2017

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All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal-microbial relationships were historically explored in single host-symbiont systems. However, new explorations into the diversity of microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment. This review explores the nature of marine animal-microbiome relationships and interactions, and possible factors that may shift associations from symbiotic to dissociated states. I present a brief review of current microbiome research and opportunities, using examples of select marine animals that span diverse phyla within the Animalia, including systems that are more and less developed for symbiosis research, including two represented in my own research program. Lastly, I consider challenges and emerging solutions for moving these and other study systems into a more detailed understanding of host-microbiome interactions within a changing ocean.

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“…S1. (167,168,171,174) amino acids (71, 110-117, 120-128, 130-141, 144-166, 175-178) G1P (precursor for activated sugars) (42)(43)(44)(45)(46)(47)(48)(49)(50) activated sugars (185-209, 97, 215) glycogen (193,185,214) molecular building blocks via acetyl-CoA (36-39) IPP (87-91), pyruvate (41), DHAP (42)(43)(44)(45)(46)(47) AdoCbl (179-184) NAD(P)H (10)(11)(12)(13)(14)(15)(16), FADH 2 (3)(4)(5)(6)(7)(8)(9) PLP (1) THF derivate (17,18,(20)(21)(22)(23)(24)(25) red. ferredoxin (18,216) NTPs (51-69, 71-77, 80, 82) dNTPs (69, 70, 77, 79, 81, 82) ATP GTP (83,220) energy demanding processes synthesis of activated sugar glycogen degrataion (210), synthesis of activated sugars (186, 192-194, 196, 198, 203, 205, 207, 215), transfer of glycosyl gropus (229) lipid biosynthesis…”

Section: Huberiarchaeum Crystelensementioning

confidence: 99%

An archaeal symbiont-host association from the deep terrestrial subsurface

Schwank

Bornemann

Dombrowski

et al. 2018

Preprint

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DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense has a similar metabolism as Nanoarchaeum equitans and potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.The DPANN (Diapherotrites, Parvarchaeota, Aigarchaeota, Nanoarchaeota, Nanohaloarchaeota) [1] radiation is a proposed monophyletic group of diverse archaeal phyla whose organisms exhibit mainly reduced genomes with limited metabolic capacities [2]. While most of these archaea were suggested to live in symbiosis with other microorganisms, respective hosts were only described for Nanoarchaeota [3,4] and Micrarchaeota (ARMAN) symbionts [5][6][7]. However, no DPANN-host interaction has been described for representatives in aquifer systems, where these archaea are particularly abundant and very diverse [2].Recently, subsurface fluids discharged by a cold, CO2-driven geyser at the Colorado Plateau, Utah (Crystal Geyser) revealed the presence of multiple novel archaeal organisms,

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MiL-FISH: Multilabeled Oligonucleotides for Fluorescence In Situ Hybridization Improve Visualization of Bacterial Cells

Cited by 57 publications

References 36 publications

Niche-Specific Impact of a Symbiotic Function on the Persistence of Microbial Symbionts within a Natural Host

Niche-Specific Impact of a Symbiotic Function on the Persistence of Microbial Symbionts within a Natural Host

Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean

An archaeal symbiont-host association from the deep terrestrial subsurface

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