Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions DOI Open Access
Benoît Perez‐Lamarque, Hélène Morlon

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(3), P. 613 - 622

Published: March 13, 2024

Abstract Interspecific interactions, including host–symbiont associations, can profoundly affect the evolution of interacting species. Given phylogenies host and symbiont clades knowledge which species interact with symbiont, two questions are often asked: “Do closely related hosts symbionts?” mirror one another?.” These intertwined even collapse under specific situations, such that they confused other. However, in most a positive answer to first question, hereafter referred as “cophylogenetic signal,” does not imply close match between phylogenies. It suggests only past evolutionary history has contributed shaping present-day arise, for example, through trait matching, or from single ancient vicariance event increases probability overlap geographically. A second, “phylogenetic congruence,” is more restrictive it phylogenies, may happen, if diversification tracks diversifications were subject same succession events. Here we apply set methods (ParaFit, PACo, eMPRess), whose significance interpreted evidence phylogenetic congruence, simulations 3 biologically realistic scenarios event, tracking frequent cospeciation The latter scenario generates whereas 2 generate cophylogenetic signal absence congruence. We find tests global-fit (ParaFit PACo) significant scenarios, event-based (eMPRess) tracking. Therefore, results should be terms congruence; arise when symbionts had independent histories. Conversely, suggest strong form dependency Clarifying patterns detected by different key understanding how interspecific interactions shape shaped evolution.

Language: Английский

Western diets and chronic diseases DOI
Timon E. Adolph, Herbert Tilg

Nature Medicine, Journal Year: 2024, Volume and Issue: 30(8), P. 2133 - 2147

Published: July 31, 2024

Language: Английский

Citations

19
Longitudinal phage–bacteria dynamics in the early life gut microbiome DOI Creative Commons
Michael J. Tisza, Richard E. Lloyd, Kristi L. Hoffman

et al.

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Language: Английский

Citations

3
Crosstalk between gut microbiotas and fatty acid metabolism in colorectal cancer DOI Creative Commons
Hao Zhang, Yuan Tian, Chunjie Xu

et al.

Cell Death Discovery, Journal Year: 2025, Volume and Issue: 11(1)

Published: Feb. 26, 2025

Abstract Colorectal cancer (CRC) is the third most common malignancy globally and second leading cause of cancer-related mortality. Its development a multifactorial multistage process influenced by dynamic interplay between gut microbiota, environmental factors, fatty acid metabolism. Dysbiosis intestinal microbiota abnormalities in microbiota-associated metabolites have been implicated colorectal carcinogenesis, highlighting pivotal role microbial metabolic interactions. Fatty metabolism serves as critical nexus linking dietary patterns with activity, significantly impacting health. In CRC patients, reduced levels short-chain acids (SCFAs) SCFA-producing bacteria consistently observed. Supplementation probiotics has demonstrated tumor-suppressive effects, while therapeutic strategies aimed at modulating SCFA shown potential enhancing efficacy radiation therapy immunotherapy both preclinical clinical settings. This review explores intricate relationship metabolism, CRC, offering insights into underlying mechanisms their translational applications. Understanding this could pave way for novel diagnostic, therapeutic, preventive management CRC.

Language: Английский

Citations

2
Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota DOI Creative Commons
Sally L. Bornbusch, Lydia K. Greene,

Sylvia Rahobilalaina

et al.

Animal Microbiome, Journal Year: 2022, Volume and Issue: 4(1)

Published: April 28, 2022

Inter-population variation in host-associated microbiota reflects differences the hosts' environments, but this characterization is typically based on studies comparing few populations. The diversity of natural habitats and captivity conditions occupied by any given host species has not been captured these comparisons. Moreover, intraspecific gut microbiota, generally attributed to diet, may also stem from differential acquisition environmental microbes-an understudied mechanism which microbiomes are directly shaped microbes. To more comprehensively characterize an ecologically flexible host, ring-tailed lemur (Lemur catta; n = 209), while investigating role acquisition, we used 16S rRNA sequencing soil sampled up 13 settings, eight wilderness Madagascar five or U.S. Based matched fecal samples, microbial source tracking examine covariation between two types consortia.The microbes varied markedly within settings. Microbial was consistently greater wild than captive lemurs, indicating that metric necessarily indicator habitat condition. Variation composition inconsistent both with a single, representative community for conspecifics universal 'signal captivity' homogenizes consortia animals. Despite similar, commercial diets lemurs continents, were compositionally most suggesting non-dietary factors govern some variability. In particular, communities across geographic locations, samples different continents being distinct, there significant context-specific microbiota.As one broadest, single-species investigations primate our study highlights sensitive multiple scales differences. This finding begs reevaluation simple 'captive vs. wild' dichotomy. Beyond important implications animal care, health, conservation, mediate aspects further expands framework how interact landscapes.

Language: Английский

Citations

44
Targeted modulation of gut microbiota by traditional Chinese medicine and natural products for liver disease therapy DOI Creative Commons

Li-Ran Zhu,

Shanshan Li,

Wan-Qun Zheng

et al.

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 2, 2023

The gut microbiota not only constitutes intestinal microenvironment homeostasis and human health but also exerts indispensable roles in the occurrence progression of multiple liver diseases, including alcohol-related disease, nonalcoholic fatty autoimmune disease cancer. Given therapeutic status these their prevention early therapy are crucial, detailed mechanism urgently needs to be explored. Meanwhile, studies have shown that various traditional Chinese medicines, such as Si Miao Formula, Jiangzhi Granules, Liushen Capsules, Chaihu-Shugan Power, Cassiae Semen Gynostemma, well some natural products, Costunolide, Coprinus comatus polysaccharide, Antarctic krill oil, Oridonin Berberine, can repair injury, improve liver, regulate immunity, even inhibit cancer through targets, links, pathways. Intriguingly, aforementioned effects demonstrated by medicines products been closely related microbiota, directly driving strategy one breakthroughs treatment diseases. Based on this, this review comprehensively summarizes discusses characteristics, functions potential mechanisms targeting during treatment. Research regulatory medicine provides novel insights significant references for developing strategies. In parallel, explorations will enhance comprehension modulating treatment, thus facilitating clinical investigation application.

Language: Английский

Citations

38
Widespread extinctions of co-diversified primate gut bacterial symbionts from humans DOI
Jon G. Sanders, Daniel D. Sprockett, Yingying Li

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(6), P. 1039 - 1050

Published: May 11, 2023

Language: Английский

Citations

29
The old friends hypothesis: evolution, immunoregulation and essential microbial inputs DOI Creative Commons
G.A.W. Rook

Frontiers in Allergy, Journal Year: 2023, Volume and Issue: 4

Published: Sept. 12, 2023

In wealthy urbanised societies there have been striking increases in chronic inflammatory disorders such as allergies, autoimmunity and bowel diseases. There has also an increase the prevalence of individuals with systemically raised levels biomarkers correlating increased risk metabolic, cardiovascular psychiatric problems. These changing disease patterns indicate a broad failure mechanisms that should stop immune system from attacking harmless allergens, components self or gut contents, terminate inappropriate inflammation. The Old Friends Hypothesis postulates this immunoregulation is due to inadequate exposures microorganisms drive development system, expansion regulatory T cells (Treg) mediate immunoregulatory mechanisms. An evolutionary approach helps us identify organisms on which we are state evolved dependence for function (Old Friends). bottom line most arm come our mothers family natural environment (including animals) many these symbiotic healthy microbiota. Lifestyle changes interrupting exposure can now be identified, closely associated low socioeconomic status (SES) countries. insights will facilitate education, diets urban planning correct deficit, while simultaneously reducing other contributory factors epithelial damage.

Language: Английский

Citations

27
Ecology of the respiratory tract microbiome DOI Open Access
Ana Elena Pérez‐Cobas, Jerónimo Rodríguez-Beltrán, Fernando Baquero

et al.

Trends in Microbiology, Journal Year: 2023, Volume and Issue: 31(9), P. 972 - 984

Published: May 10, 2023

Language: Английский

Citations

25
Within-host evolution of the gut microbiome DOI Creative Commons
Tanja Đapa, Daniel P.G.H. Wong, Kimberly S. Vasquez

et al.

Current Opinion in Microbiology, Journal Year: 2023, Volume and Issue: 71, P. 102258 - 102258

Published: Jan. 5, 2023

Language: Английский

Citations

23
A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans DOI Creative Commons
Fuyong Li, Xudong Li, Christopher C. Cheng

et al.

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: March 13, 2023

Abstract Background Gut microbes play crucial roles in the development and health of their animal hosts. However, evolutionary relationships gut with vertebrate hosts, consequences that arise for ecology lifestyle are still insufficiently understood. Specifically, mechanisms by which strain-level diversity evolved, degree lineages remain stably associated how history influences ecological performance a critical gap our understanding vertebrate-microbe symbiosis. Results This study presents characterization an extended collection strains Limosilactobacillus reuteri closely related species from wide variety hosts phylogenomic comparative genomic analyses combined colonization experiments mice to gain insight into long-term relationship bacterial symbiont vertebrates. The phylogenetic analysis L. revealed early-branching primarily consist isolates rodents (four lineages) birds (one lineage), while dominated herbivores, humans, pigs, primates arose more recently were less host specific. Strains rodent lineages, despite divergence, showed tight clustering gene-content-based analyses. These but not those ones non-rodent efficiently colonize forestomach epithelium germ-free mice. findings support stable switch birds. Associations other likely dynamic transient. Interestingly, human cluster phylogenetically domesticated animals, such as chickens suggesting zoonotic transmissions. Conclusions Overall, this demonstrates can be particular over time scales allow major adaptations specialization, also emphasizes lifestyles even within single species. For , ranged autochthonous, based on vertical transmission aligned time, allochthonous possibly reliant humans. Such information contributes ability use these microbial-based therapeutics.

Language: Английский

Citations

23