38 research outputs found
The effect of extrinsic mortality on genome size evolution in prokaryotes
Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called âscramblersâ. This phenotype is realised by the expansion of gene families involved in nutrient acquisition and metabolism. In contrast, a low mortality rate increases an individualâs life expectancy, which results in natural selection favouring tolerance to starvation when conditions are unfavourable. This leads to the evolution of small, streamlined genomes (âstayersâ). Our models predict that large genomes, gene family expansion and horizontal gene transfer should be observed in prokaryotes occupying ecosystems exposed to high abiotic stress, as well as those under strong predator- and/or pathogen-mediated selection. A comparison of genome size of cyanobacteria in relatively stable marine versus more turbulent freshwater environments corroborates our predictions, although other factors between these environments could also be responsible
Towards a Processual Microbial Ontology
types: ArticleStandard microbial evolutionary ontology is organized according to a
nested hierarchy of entities at various levels of biological organization. It typically
detects and defines these entities in relation to the most stable aspects of evolutionary
processes, by identifying lineages evolving by a process of vertical inheritance
from an ancestral entity. However, recent advances in microbiology indicate
that such an ontology has important limitations. The various dynamics detected
within microbiological systems reveal that a focus on the most stable entities (or
features of entities) over time inevitably underestimates the extent and nature of
microbial diversity. These dynamics are not the outcome of the process of vertical
descent alone. Other processes, often involving causal interactions between entities
from distinct levels of biological organisation, or operating at different time scales,
are responsible not only for the destabilisation of pre-existing entities, but also for
the emergence and stabilisation of novel entities in the microbial world. In this
article we consider microbial entities as more or less stabilised functional wholes,
and sketch a network-based ontology that can represent a diverse set of processes
including, for example, as well as phylogenetic relations, interactions that stabilise
or destabilise the interacting entities, spatial relations, ecological connections, and
genetic exchanges. We use this pluralistic framework for evaluating (i) the existing
ontological assumptions in evolution (e.g. whether currently recognized entities are
adequate for understanding the causes of change and stabilisation in the microbial
world), and (ii) for identifying hidden ontological kinds, essentially invisible from
within a more limited perspective. We propose to recognize additional classes of
entities that provide new insights into the structure of the microbial world, namely ââprocessually equivalentââ entities, ââprocessually versatileââ entities, and ââstabilizedââ
entities.Economic and Social Research Council, U
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Gut microbiota functions: metabolism of nutrients and other food components
The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of mammalian enzymes in the liver and gut mucosa and includes functions essential for host digestion. As such, the gut microbiota is a key factor in shaping the biochemical profile of the diet and, therefore, its impact on host health and disease. The important role that the gut microbiota appears to play in human metabolism and health has stimulated research into the identification of specific microorganisms involved in different processes, and the elucidation of metabolic pathways, particularly those associated with metabolism of dietary components and some host-generated substances. In the first part of the review, we discuss the main gut microorganisms, particularly bacteria, and microbial pathways associated with the metabolism of dietary carbohydrates (to short chain fatty acids and gases), proteins, plant polyphenols, bile acids, and vitamins. The second part of the review focuses on the methodologies, existing and novel, that can be employed to explore gut microbial pathways of metabolism. These include mathematical models, omics techniques, isolated microbes, and enzyme assays
Microbial shifts in the aging mouse gut
YesBackground: The changes that occur in the microbiome of aging individuals are unclear, especially in light of the
imperfect correlation of frailty with age. Studies in older human subjects have reported subtle effects, but these
results may be confounded by other variables that often change with age such as diet and place of residence. To
test these associations in a more controlled model system, we examined the relationship between age, frailty, and
the gut microbiome of female C57BL/6 J mice.
Results: The frailty index, which is based on the evaluation of 31 clinical signs of deterioration in mice, showed a
near-perfect correlation with age. We observed a statistically significant relationship between age and the taxonomic
composition of the corresponding microbiome. Consistent with previous human studies, the Rikenellaceae family,
which includes the Alistipes genus, was the most significantly overrepresented taxon within middle-aged and
older mice.
The functional profile of the mouse gut microbiome also varied with host age and frailty. Bacterial-encoded
functions that were underrepresented in older mice included cobalamin (B12) and biotin (B7) biosynthesis,
and bacterial SOS genes associated with DNA repair. Conversely, creatine degradation, associated with muscle wasting,
was overrepresented within the gut microbiomes of the older mice, as were bacterial-encoded ÎČ-glucuronidases, which
can influence drug-induced epithelial cell toxicity. Older mice also showed an overabundance of monosaccharide
utilization genes relative to di-, oligo-, and polysaccharide utilization genes, which may have a substantial impact on
gut homeostasis.
Conclusion: We have identified taxonomic and functional patterns that correlate with age and frailty in the mouse
microbiome. Differences in functions related to host nutrition and drug pharmacology vary in an age-dependent
manner, suggesting that the availability and timing of essential functions may differ significantly with age and frailty.
Future work with larger cohorts of mice will aim to separate the effects of age and frailty, and other factors.This work was supported by the Canadian Institutes of Health Research (CIHR) through an Emerging Team Grant to RGB, CIHR Operating Grants to Langille et al. Microbiome 2014, 2:50 Page 10 of 12 http://www.microbiomejournal.com/content/2/1/50 SEH (MOP 126018) and RAR (MOP 93718), and a CIHR Fellowship to MGIL. Infrastructure was supported by the Canada Foundation for Innovation through a grant to RGB. RGB also acknowledges the support of the Canada Research Chairs program