The skin microbiome of vertebrates

Microbiome, Год журнала: 2019, Номер 7(1)

Опубликована: Май 23, 2019

The skin constitutes the primary physical barrier between vertebrates and their external environment. Characterization of microorganisms is essential for understanding how a host evolves in association with its microbial symbionts, modeling immune system development, diagnosing illnesses, exploring origins potential zoonoses that affect humans. Although many studies have characterized human microbiome culture-independent techniques, far less known about other mammals, amphibians, birds, fish, reptiles. aim this review to summarize leveraged high-throughput sequencing better understand associate members classes within subphylum Vertebrata. Specifically, links will be explored vertebrate characteristics, including geographic location, biological sex, animal interactions, diet, captivity, maternal transfer, disease. Recent literature on parallel patterns evolutionary history communities, or phylosymbiosis, also analyzed. These factors must considered when designing future ensure conclusions drawn from basic research translate into useful applications, such as probiotics successful conservation strategies endangered threatened animals.

Язык: Английский

---

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

Microbiome, Год журнала: 2019, Номер 7(1)

Опубликована: Сен. 14, 2019

Abstract Background The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, development both players. These interdependencies inspired new view multicellular organisms “metaorganisms.” goal Collaborative Research Center “Origin Function Metaorganisms” to understand why how microbial communities form long-term associations with from diverse taxonomic groups, ranging sponges humans in addition plants. Methods In order optimize choice analysis procedures, which may differ according host organism question at hand, we systematically compared two main technical approaches for profiling communities, 16S rRNA gene amplicon metagenomic shotgun sequencing across our panel ten taxa. This includes commonly used regions amplification thus totaling five different profiles per sample. Conclusion While gene-based analyses are subject much skepticism, demonstrate that many aspects bacterial community characterization consistent methods. resulting insight facilitates selection appropriate methods wide range Overall, recommend single- over multi-step although exceptions trade-offs exist, V3 V4 V1 V2 region gene. Finally, by contrasting functional performing phylogenetic analysis, provide important novel into broad evolutionary patterns among metaorganisms, whereby transition animals an aquatic terrestrial habitat marks major event evolution host-associated composition.

Язык: Английский

---

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Янв. 23, 2021

Abstract Background Adaptive shifts in gut microbiome composition are one route by which animals adapt to seasonal changes food availability and diet. However, outside of dietary shifts, other potential environmental drivers microbial have rarely been investigated, particularly organisms living their natural environments. Results Here, we generated the largest wild nonhuman primate dataset date identify diversity function 758 samples collected from Ethiopian geladas ( Theropithecus gelada ). Because live a cold, high-altitude environment low-quality grass-based diet, they face extreme thermoregulatory energetic constraints. We tested how proxies (rainfall) stress (temperature) predicted geladas. The covaried with rainfall temperature pattern that suggests distinct responses challenges. Microbial were driven differences main components diet across seasons: rainier periods, was dominated cellulolytic/fermentative bacteria specialized digesting grass, while during dry periods break down starches found underground plant parts. Temperature had comparatively smaller, but detectable, effect on microbiome. During cold bacterial genes involved energy, amino acid, lipid metabolism increased, suggesting stimulation fermentation activity when nutritional co-occurred, potentially helping maintain energy balance challenging periods. Conclusion Together, these results shed light extent microbiota plasticity provides metabolic flexibility host, might be key factor thriving changing On longer evolutionary timescale, such provided may also allowed members adopt colonize new grassland habitats East Africa.

Язык: Английский

---

Phylogenetic scale in ecology and evolution

Global Ecology and Biogeography, Год журнала: 2018, Номер 27(2), С. 175 - 187

Опубликована: Янв. 18, 2018

Abstract Aim Many important patterns and processes vary across the phylogeny depend on phylogenetic scale. Nonetheless, scale has never been formally conceptualized, its potential remains largely unexplored. Here, we formalize concept of scale, review how considered multiple fields provide practical guidelines for use to address a range biological questions. Innovation We summarize treated in macroevolution, community ecology, biogeography macroecology, illustrating it can inform, possibly resolve, some longstanding controversies these fields. To promote empirically, define grain extent, dependence, scaling domains illustrate existing data statistical tools be used investigate effects variety well‐known processes, including diversification rates, structure, niche conservatism or species‐abundance distributions. Main conclusions Explicit consideration new more complete insight into many questions (macroevolution, macroecology). Building resources isolated efforts fields, future research centred might enrich our understanding that together, but over different scales, shape diversity life.

Язык: Английский

---

Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

Nature Microbiology, Год журнала: 2021, Номер 6(4), С. 499 - 511

Опубликована: Фев. 1, 2021

Abstract The herbivore digestive tract is home to a complex community of anaerobic microbes that work together break down lignocellulose. These microbiota are an untapped resource strains, pathways and enzymes could be applied convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces determine how substrate antibiotic selection influence membership, activity, stability chemical productivity gut communities. assembled 719 high-quality metagenome-assembled genomes (MAGs) unique at the species level. More 90% these MAGs previously unidentified microorganisms. Microbial consortia dominated by fungi outperformed bacterially in terms both methane production extent cellulose degradation, which indicates have important role release. Metabolic pathway reconstructions 737 bacteria, archaea suggest cross-domain partnerships between methanogens enabled acetate, formate methane, whereas mainly produced short-chain fatty acids, including propionate butyrate. Analyses carbohydrate-active enzyme domains present each consortium bacteria employ mostly complementary hydrolytic strategies. division labour among anaerobes degrade biomass harnessed industrial bioprocessing.

Язык: Английский

---