[PDF] Diversity Form And Function Within The Marine Mammal Microbiota eBook

Author : Natasha K. Dudek
Publisher :
Page : 203 pages
File Size : 46,92 MB
Release : 2018
Category :
ISBN : 9780438534360

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Animals can be viewed as complex, co-evolving networks of microbes and host cells. Understanding the diversity, form, and function of microbes associated with different animals is therefore essential to understanding the patterns and processes underlying evolution across all domains of life. Extant marine mammals present an interesting opportunity to study the microbiota of animals with an unusual lifestyle that has arisen independently six times since the time of their last common ancestor. The manner in which the marine mammal-associated microbiota has evolved in response to the host's marine lifestyle remains unclear. In this thesis, I describe three studies of the microbiota of marine mammals. In the first, I characterize bacterial community composition associated with sea otters, which are a keystone species that is listed as endangered by the IUCN. They are also the sole representatives of an entire lineage of marine mammal. The findings suggest that environment plays a major role in structuring sea otter-associated bacterial community composition and raises the question of whether sea otters may have a reduced bacterial biomass in their guts compared to other mammals. As seen in other marine mammal species, results show that sea otters host a diversity of 'microbial dark matter'. In chapter two of this thesis, I study such 'microbial dark matter' present in the dolphin mouth and propose two new bacterial phyla (Candidatus Delphibacteria and Candidatus Fertabacteria), the former of which our metabolic reconstruction suggests may have a direct effect on dolphin physiology and health. In the third chapter of my thesis, I operate under the assumption that novel phylogenetic diversity is correlated with novel functional diversity, and thereby discover a previously uncharacterized rectangular microbe in dolphin oral samples with several unusual morphological features, such as pili-like appendages whose architecture differs substantially from known surface structures seen in bacteria and archaea. A single-cell genomics experiment suggested that this microbe was a type of bacteria from one of the following three groups: Bacteroidetes, TM7, or Epsilonproteobacteria. Collectively, these studies provide insight into diversity, form, and function within the marine mammal microbiota, and contribute towards our understanding of the microbial diversity, both phylogenetic and functional, which has evolved on Earth.

Author : Alexandra Devon Switzer
Publisher :
Page : pages
File Size : 49,41 MB
Release : 2019
Category :
ISBN :

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This thesis describes patterns of microbial diversity in the digestive tracts of a variety of marine mammal species to better understand how host-driven and external factors affect these indigenous bacterial communities. In chapter one, the distal gut microbiota from representatives of each extant taxonomic order of marine mammals was characterized and compared to that of terrestrial mammals. The goal was to parse out the influence of intrinsic and extrinsic variables that shape the mammalian microbiome structure, specifically the relative impact of host phylogeny versus life in the sea on the marine mammal distal gut microbiota. Results revealed that marine mammals, despite their divergent evolutionary history, harbor distal gut microbiota that bears similarity across taxonomic orders, presumably due to environmental filtering from their marine environment. However, signals of phylosymbiosis are also observed among this group, the strength of which appears to be host-lineage dependent. In chapter two, we explored a scenario in which knowledge of a microbial baseline could yield clinical value for a specific marine mammal species, the harbor seal (Phoca vitulina). The assembly of the oral and distal gut microbiome of neonatal seal pups was characterized longitudinally as they aged at a rehabilitation center. Since some seals received prophylactic antibiotics, this was also an opportunity to determine the effect of antibiotic-treatment on the developing microbiome of these healthy growing seals. Results revealed a transient perturbation in the indigenous gut microbiota to which the seal pup host demonstrated resilience. This study has clinical implications for the prophylactic antibiotic protocol used in this age group. The aim of this thesis was to better characterize the marine mammal microbiome to improve the husbandry, therapeutic and preventative care of marine mammals in the future.

Author : Chase James
Publisher :
Page : 162 pages
File Size : 20,75 MB
Release : 2022
Category :
ISBN :

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In the pelagic environment, microbes act as the base of the food web (photosynthetic autotrophs), recycle nutrients (microbial loop), and perform other crucial ecosystem processes and services (such as carbon sequestration). The relative scale of these different process is driven by changes in marine microbiome community structure, diversity, and function. Over the last two decades, meta-omic sampling has provided a pathway forward with which to observe the community structure and function of the marine microbiome at a previously inaccessible resolution. However, with this increase in data complexity (large numbers of identified species and genes), it can be challenging to synthesize results across the multitude of observed taxonomic and functional groups. The goal of this thesis is to provide a general framework for understanding marine microbiome community responses (structure, diversity, and function) to environmental perturbations at previously unresolvable scales. The first study (Chapter 2) identifies the mechanisms that shape patterns in marine microbiome community structure and diversity across space and time within a coastal upwelling region. While traditional methods (such as microscopy and flow cytometry) have highlighted general patterns for broad taxonomic groups and or conspicuous taxa, this study represents a comprehensive examination of the mechanisms that shape all types of marine microbial groups, and in particular, highlights cryptic groups that could not be identified through more traditional means. The second study (Chapter 3) takes a more species-centric approach and asks, what is the rate of habitat specificity within marine microbes. Terrestrial systems often contain many species that are endemic to habitats or locales. Within the marine environment, habitats are constantly in motion, moving dynamically across space in time. The dynamic marine environment, coupled with the fast generation times of most microbes is thought by many to lead to less habitat specificity and more cosmopolitan (universally distributed) species. By identifying water mases (with internally consistent physical and chemical environments) we present a view of habitat specificity within the marine microbiome in a way that is comparable to terrestrial studies. The third study (Chapter 4) shifts to look at regional metatranscriptomic data and asks what are the mechanisms that shape the function and distribution of active marine microbes. Metatranscriptomics provides a framework to identify which taxa and their associated functions are active within a community in response to changing environmental conditions. In targeting the active community, we identify how environmental conditions can lead to in-situ functional traits within the microbial community--a crucial next step to better understanding the links between environmental conditions and the local to global magnitude of key ecological functions such as primary productivity, nutrient recycling, and carbon sequestration in the pelagic ocean.

Author :
Publisher : Academic Press
Page : 346 pages
File Size : 19,48 MB
Release : 2016-08-03
Category : Science
ISBN : 0128096179

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Host-Microbe Interactions, the latest volume in the Progress in Molecular Biology series, provides a forum for the discussion of new discoveries, approaches, and ideas in molecular biology. It contains contributions from leaders in their respective fields, along with abundant references. This volume is dedicated to the subject of host-microbe interactions. Provides the latest research on host-microbe interactions, including new discoveries, approaches, and ideas Contains contributions from leading authorities on topics relating to molecular biology Informs and updates on all the latest developments in the field

Author : Leslie Dierauf
Publisher : CRC Press
Page : 1116 pages
File Size : 37,54 MB
Release : 2001-06-27
Category : Medical
ISBN : 1420041630

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CRC Handbook of Marine Mammal Medicine, Second Edition is the only handbook specifically devoted to marine mammal medicine and health. With 66 contributors working together to craft 45 scientifically-based chapters, the text has been completely revised and updated to contain all the latest developments in this field. Building upon the solid foundation of the previous edition, the contents of this book are light-years ahead of the topics presented in the first edition. See what's new in the Second Edition: Marine mammals as sentinels of ocean health Emerging and resurging diseases Thorough revision of the Immunology chapter Diagnostic imaging chapters to illustrate new techniques Quick reference for venipuncture sites in many marine mammals Unusual mortality events and mass strandings New topics such as a chapter on careers Wider scope of coverage including species outside of the United States and Canada Filled with captivating illustrations and photographs, the Handbook guides you through the natural history of cetaceans, pinnipeds, manatees, sea otters, and polar bears. Prepared in a convenient, easy-to-use format, it is designed specifically for use in the field. Covering more than 40 topics, this one-of-a-kind reference is packed with data. The comprehensive compilation of information includes medicine, surgery, pathology, physiology, husbandry, feeding and housing, with special attention to strandings and rehabilitation. The CRC Handbook of Marine Mammal Medicine, Second Edition is still a must for anyone interested in marine mammals.

Author : Gregory Dana Bossart
Publisher : Frontiers Media SA
Page : 387 pages
File Size : 32,9 MB
Release : 2022-02-09
Category : Science
ISBN : 2889743128

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This project is posthumously dedicated to Dr. Gregory Dana Bossart. Whether you knew him as colleague, mentor, friend, family member or simply ‘knew of him’, you could not help but be awestruck by his dedication, intelligence, thoughtfulness, work ethic and passion for scientific inquiry, especially for conservation of the marine environment Many of his publications were seminal in marine mammal health, including infectious, environmental and zoonotic diseases. As we collected manuscripts for this special Frontiers edition, it was heartwarming to hear the comments from contributors. So many research scientists, field biologists and veterinarians could easily have given up and said, ‘I just can’t do this now’, especially with the added challenges posed by the current COVID-19 pandemic. Instead, contributors from around the world were determined to contribute to this collection because of their inspiration and shared commitment with Greg’s vision. The love and admiration within the marine community for Greg is phenomenal. With that said, we would be remiss if we did not say a few words about Greg as a mentor and friend. Greg had a knack for helping students realize their abilities and pursue their own independent contributions to the marine mammal community. He shared in their successes and worked tirelessly to facilitate their aspirations. Greg would involve students, early-career scientists and colleagues in projects, introduce them to collaborators and promote them and their work. Greg was a genuinely caring person. When he asked you ‘how are you doing’, he honestly wanted to know. He was always there, ready to listen and provide guidance. If you were to ask Greg what was most important to him in life, he would say God, family and marine life (and one could argue that he had a special fondness for manatees). He believed in the beauty of nature and that God had a hand in all of it. He was in pursuit of ensuring that we all share this earth responsibly and sustainably. We miss Greg dearly, but honor and celebrate him as we carry on in our pursuits.

Author : Samuel Degregori
Publisher :
Page : 0 pages
File Size : 20,2 MB
Release : 2022
Category :
ISBN :

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Gut microbes provide vital functions for animal hosts. While it is known that host ecology and evolutionary history play a role in shaping gut microbiomes, a majority of studies have focused on mammal hosts. Other vertebrates, including fish, have received little attention. Coral reef fish, in particular, exhibit a wide range of distinct feeding behaviors, evolutionary histories, and geographic distributions that likely correlate with gut microbiome composition and diversity. They also inhabit a fragile ecosystem that is highly sensitive to anthropogenic disturbance-disturbances that are known to impact coral microbiomes but may or may not affect fish gut microbiomes. My thesis leverages a large unprecedented coral reef fish gut microbiome dataset (N=550), where I sampled the gut microbiomes of 20 host species of fish with robust replication spanning three islands across the South Pacific, to better understand how host phylogeny, host diet, and host environment shape vertebrate gut microbiomes. Comparing the gut microbiomes of distantly related hosts can reveal evolutionary and ecological dynamics that govern gut microbiomes across the animal kingdom. Chapter 1 investigates the possible similarities between coral reef fish and mammal gut microbiomes to elucidate any microbial features that may have converged between the two distantly related hosts. Through multivariate and Bayesian analyses, I show that fish and mammal gut microbiomes exhibit striking similarities in composition, particularly within carnivores and herbivores. Specifically, carnivores and herbivore gut microbiomes show more similarities within their diet groups than within their host phylogenies, and share a significant number of ASVs. Herbivore fish and mammal gut microbiomes, in particular, share a significant number of amplicon sequence variants (ASVs) associated with the functional requirements of herbivory, such as Ruminococcus and Treponema. My results indicate that despite 365 million years of evolution and two drastically distinct habitats (terrestrial vs. marine), fish and mammal gut microbiomes have converged on the basis of diet. Expanding on Chapter 1, Chapter 2 moves beyond host phylogeny and diet and aims to isolate and analyze the effects of host habitat on gut microbiome composition and diversity. Previous work on environmental effects acting on animal gut microbiomes largely focused on captive hosts or wild hosts of a single species, potentially ignoring any interactions between host environment and host phylogeny in the wild. Here, I leverage my dataset of coral reef fish gut microbiomes from a diverse range of hosts from three geographically distinct habitats to better understand how host habitat shapes vertebrate gut microbiomes. I find that host habitat significantly shapes fish gut microbiome composition and diversity and these effects are highly dependent on host phylogeny. For example, within the same analyses, a fish such as R. aculeatus, had significantly different gut microbiomes between the three islands, whereas E. merra gut microbiomes were largely unaffected by island location. For the fish gut microbiomes that were significantly impacted by host habitat, many of the associated ASVs were ASVs found in Chapter 1, suggesting that host habitat may also shape gut microbiome function. While comparative approaches on wild hosts are crucial in elucidating generalizable rules that govern animal gut microbiomes, experimental approaches are also imperative to unpack the finer-scale qualities and mechanisms of these rules. Chapter 3 builds on Chapter 2 by leveraging a simulated nutrient enrichment experimental design to further investigate the effects of host environment on gut microbiome composition and diversity. Nutrient enrichment is one of the most threatening consequences of anthropogenic stress on coral reef ecosystems, and the effects of nutrient enrichment on reef fauna gut microbiomes are largely unknown. Here, I artificially enrich the territories (N=40) of a highly abundant, territorial gardening fish, Stegastes nigricans, and use multivariate and differential abundance analyses to elucidate how nutrient enrichment impacts animal gut microbiome composition and diversity. I find that nutrient enrichment effectively "enriches" the gut microbiome, with S. nigricans gut microbiomes in enriched territories exhibiting significantly higher alpha diversities than those in control territories. I also find that these changes are specific to the hindgut and do not occur in the microbiomes of the food source that S. nigricans gardens.

Author : Angela E. Douglas
Publisher : Princeton University Press
Page : 248 pages
File Size : 50,91 MB
Release : 2021-06-08
Category : Science
ISBN : 0691217718

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"This book provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. Resident microbes in healthy animals--including humans--can dictate many traits of the animal host. This animal microbiome is a second immune system conferring protection against pathogens; it can structure host metabolism in animals as diverse as reef corals and hibernating mammals; and it may influence animal behavior, from social recognition to emotional states. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet, and have contributed to animal diversification over long evolutionary timescales"--Publisher by publisher.

Author : Institute of Medicine
Publisher : National Academies Press
Page : 633 pages
File Size : 37,29 MB
Release : 2013-01-10
Category : Medical
ISBN : 0309264324

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Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.

Author : Suhelen Egan
Publisher : Frontiers Media SA
Page : 110 pages
File Size : 49,33 MB
Release : 2015-12-21
Category : Microbiology
ISBN : 288919681X

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Modern molecular -omics tools (metagenomics, metaproteomics etc.) have greatly contributed to the rapid advancement of our understanding of microbial diversity and function in the world’s oceans. These tools are now increasingly applied to host-associated environments to describe the symbiotic microbiome and obtain a holistic view of marine host-microbial interactions. Whilst all eukaryotic hosts are likely to benefit from their microbial associates, marine sessile eukaryotes, including macroalgae, seagrasses and various invertebrates (sponges, acidians, corals, hydroids etc), rely in particular on the function of their microbiome. For example, marine sessile eukaryotes are under constant grazing, colonization and fouling pressure from the millions of micro- and macroorganisms in the surrounding seawater. Host-associated microorganisms have been shown to produce secondary metabolites as defense molecules against unwanted colonization or pathogens, thus having an important function in host health and survival. Similarly microbial symbionts of sessile eukaryotes are often essential players in local nutrient cycling thus benefiting both the host and the surrounding ecosystem. Various research fields have contributed to generating knowledge of host-associated systems, including microbiology, biotechnology, molecular biology, ecology, evolution and biotechnology. Through a focus on model marine sessile host systems we believe that new insight into the interactions between host and microbial symbionts will be obtained and important areas of future research will be identified. This research topic includes original research, review and opinion articles that bring together the knowledge from different aspects of biology and highlight advances in our understanding of the diversity and function of the microbiomes on marine sessile hosts.