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Journal articles on the topic 'Microbial inheritance'
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Marguet, Aline, Marc Lavielle, and Eugenio Cinquemani. "Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data." Bioinformatics 35, no. 14 (2019): i586—i595. http://dx.doi.org/10.1093/bioinformatics/btz378.
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Abstract Motivation Modern experimental technologies enable monitoring of gene expression dynamics in individual cells and quantification of its variability in isogenic microbial populations. Among the sources of this variability is the randomness that affects inheritance of gene expression factors at cell division. Known parental relationships among individually observed cells provide invaluable information for the characterization of this extrinsic source of gene expression noise. Despite this fact, most existing methods to infer stochastic gene expression models from single-cell data dedicate little attention to the reconstruction of mother–daughter inheritance dynamics. Results Starting from a transcription and translation model of gene expression, we propose a stochastic model for the evolution of gene expression dynamics in a population of dividing cells. Based on this model, we develop a method for the direct quantification of inheritance and variability of kinetic gene expression parameters from single-cell gene expression and lineage data. We demonstrate that our approach provides unbiased estimates of mother–daughter inheritance parameters, whereas indirect approaches using lineage information only in the post-processing of individual-cell parameters underestimate inheritance. Finally, we show on yeast osmotic shock response data that daughter cell parameters are largely determined by the mother, thus confirming the relevance of our method for the correct assessment of the onset of gene expression variability and the study of the transmission of regulatory factors. Availability and implementation Software code is available at https://github.com/almarguet/IdentificationWithARME. Lineage tree data is available upon request. Supplementary information Supplementary material is available at Bioinformatics online.
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Smith, David, Miryam Palacios-Pérez, and Sohan Jheeta. "The Enclosed Intestinal Microbiome: Semiochemical Signals from the Precambrian and Their Disruption by Heavy Metal Pollution." Life 12, no. 2 (2022): 287. http://dx.doi.org/10.3390/life12020287.
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It is increasingly likely that many non-communicable diseases of humans and associated animals are due to the degradation of their intestinal microbiomes, a situation often referred to as dysbiosis. An analysis of the resultant diseases offers an opportunity to probe the function of these microbial partners of multicellular animals. In our view, it now seems likely that vertebrate animals and their microbiomes have coevolved throughout the Ediacaran–Cambrian transition and beyond, operating by semiochemical messaging between the multicellular host and its microbial community guest. A consideration of the overall role of the mutualistic intestinal microbiome as an enclosed bioreactor throws up a variety of challenging concepts. In particular: the significance of the microbiome with respect to the immune system suggests that microeukaryotes could act as microbial sentinel cells; the ubiquity of bacteriophage viruses implies the rapid turnover of microbial composition by a viral-shunt mechanism; and high microbial diversity is needed to ensure that horizontal gene transfer allows valuable genetic functions to be expressed. We have previously postulated that microbes of sufficient diversity must be transferred from mother to infant by seemingly accidental contamination during the process of natural birth. We termed this maternal microbial inheritance and suggested that it operates alongside parental genetic inheritance to modify gene expression. In this way, the adjustment of the neonate immune system by the microbiome may represent one of the ways in which the genome of a vertebrate animal interacts with its microbial environment. The absence of such critical functions in the neonate may help to explain the observation of persistent immune-system problems in affected adults. Equally, granted that the survival of the guest microbiome depends on the viability of its host, one function of microbiome-generated semiochemicals could be to facilitate the movement of food through the digestive tract, effectively partitioning nutrition between host and guest. In the event of famine, downregulation of microbial growth and therefore of semiochemical production would allow all available food to be consumed by the host. Although it is often thought that non-communicable diseases, such as type 2 diabetes, are caused by consumption of food containing insufficient dietary fibre, our hypothesis suggests that poor-quality food is not the prime cause but that the tendency for disease follows the degradation of the intestinal microbiome, when fat build-up occurs because the relevant semiochemicals can no longer be produced. It is the purpose of this paper to highlight the possibility that the origins of the microbiome lie in the Precambrian and that the disconnection of body and microbiome gives rise to non-communicable disease through the loss of semiochemical signalling. We further surmise that this disconnect has been largely brought about by heavy metal poisoning, potentially illuminating a facet of the exposome, the sum total of environmental insults that influence the expression of the genetic inheritance of an animal.
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Feng, Ye, and Jing Zhang. "The Microorganism Investigation and Information Visualization Display in Qingliangshan Grottoes, Yan ’an." BIO Web of Conferences 59 (2023): 01007. http://dx.doi.org/10.1051/bioconf/20235901007.
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There are many grottoes of the Song and Jin Dynasties in northern Shaanxi, the Qingliangshan grottoes of Yan’an is typical representatives. Due to the influence of environmental and geographical factors, the microbial of the Qingliangshan grottoes have caused the surface weathering, pollution or discoloring of cultural relics, as well as the potential dangers, which have caused some damage to the grottoes. This paper based on the investigation of harmful microbial samples on the surface of the grottoes of Qingliangshan in northern Shaanxi Province. Using microscopy and molecular biology to analyze microbial communities, Understand the influence and harm of microorganisms on grottoes, then to display and publicize with graphical information, to make readers understand the influence of microbial disasters on the grottoes and further attract people’s attention. It is form a consensus on protecting the material and cultural heritage of grottoes and promote the inheritance of traditional Chinese culture.
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Pleška, Maroš, David Jordan, Zak Frentz, BingKan Xue, and Stanislas Leibler. "Nongenetic individuality, changeability, and inheritance in bacterial behavior." Proceedings of the National Academy of Sciences 118, no. 13 (2021): e2023322118. http://dx.doi.org/10.1073/pnas.2023322118.
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Isogenic populations often display remarkable levels of phenotypic diversity even in constant, homogeneous environments. Such diversity results from differences between individuals (“nongenetic individuality”) as well as changes during individuals’ lifetimes (“changeability”). Yet, studies that capture and quantify both sources of diversity are scarce. Here we measure the swimming behavior of hundreds of Escherichia coli bacteria continuously over two generations and use a model-independent method for quantifying behavior to show that the behavioral space of E. coli is low-dimensional, with variations occurring mainly along two independent and interpretable behavioral traits. By statistically decomposing the diversity in these two traits, we find that individuality is the main source of diversity, while changeability makes a smaller but significant contribution. Finally, we show that even though traits of closely related individuals can be remarkably different, they exhibit positive correlations across generations that imply nongenetic inheritance. The model-independent experimental and theoretical framework developed here paves the way for more general studies of microbial behavioral diversity.
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Faith, Jeremiah J., Jean-Frédéric Colombel, and Jeffrey I. Gordon. "Identifying strains that contribute to complex diseases through the study of microbial inheritance." Proceedings of the National Academy of Sciences 112, no. 3 (2015): 633–40. http://dx.doi.org/10.1073/pnas.1418781112.
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It has been 35 y since Carl Woese reported in PNAS how sequencing ribosomal RNA genes could be used to distinguish the three domains of life on Earth. During the past decade, 16S rDNA sequencing has enabled the now frequent enumeration of bacterial communities that populate the bodies of humans representing different ages, cultural traditions, and health states. A challenge going forward is to quantify the contributions of community members to wellness, disease risk, and disease pathogenesis. Here, we explore a theoretical framework for studies of the inheritance of bacterial strains and discuss the advantages and disadvantages of various study designs for assessing the contribution of strains to complex diseases.
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Noyer, Charlotte, Emilio O. Casamayor, and Mikel A. Becerro. "Environmental Heterogeneity and Microbial Inheritance Influence Sponge-Associated Bacterial Composition of Spongia lamella." Microbial Ecology 68, no. 3 (2014): 611–20. http://dx.doi.org/10.1007/s00248-014-0428-z.
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Kong, Hyun Gi, Geun Cheol Song, and Choong‐Min Ryu. "Inheritance of seed and rhizosphere microbial communities through plant–soil feedback and soil memory." Environmental Microbiology Reports 11, no. 4 (2019): 479–86. http://dx.doi.org/10.1111/1758-2229.12760.
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Kemp, Keri M., Jackson Colson, Robin G. Lorenz, Craig L. Maynard, and Jennifer S. Pollock. "Early life stress in mice alters gut microbiota independent of maternal microbiota inheritance." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 320, no. 5 (2021): R663—R674. http://dx.doi.org/10.1152/ajpregu.00072.2020.
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Exposure to early life stress (ELS) is associated with a greater risk of chronic disease development including depression and cardiovascular disease. Altered gut microbiota has been linked to both depression and cardiovascular disease in mice and humans. Rodent models of early life neglect are used to characterize the mechanistic links between early life stress (ELS) and the risk of disease later in life. However, little is understood about ELS exposure and the gut microbiota in the young mice and the influence of the maternal inheritance of the gut microbiota. We used a mouse model of ELS, maternal separation with early weaning (MSEW), and normally reared mice to determine whether the neonate microbiota is altered, and if so, are the differences attributable to changes in dam microbiota that are then transmitted to their offspring. Individual amplicon sequence variants (ASVs) displayed differential abundance in the microbiota of MSEW compared with normally reared pups at postnatal day ( PD) 28. Additionally, ELS exposure reduced the alpha diversity and altered microbial community composition at PD28. The composition, levels of alpha diversity, and abundance of individual ASVs in the microbiota of dams were similar from MSEW or normally reared cohorts. Thus, the observed shifts in the abundance of individual bacterial ASVs in the neonates and young pups are likely driven by endogenous effects of MSEW in the offspring host and are not due to inherited differences from the dam. This knowledge suggests that exposure to ELS has a direct effect on microbial factors on the risk of chronic disease development.
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Mirzaee, Malihe, Edita Holásková, Alžbeta Mičúchová, David J. Kopečný, Zhila Osmani, and Ivo Frébort. "Long-Lasting Stable Expression of Human LL-37 Antimicrobial Peptide in Transgenic Barley Plants." Antibiotics 10, no. 8 (2021): 898. http://dx.doi.org/10.3390/antibiotics10080898.
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Antimicrobial peptides play a crucial role in the innate immune system of multicellular organisms. LL-37 is the only known member of the human cathelicidin family. As well as possessing antibacterial properties, it is actively involved in various physiological responses in eukaryotic cells. Accordingly, there is considerable interest in large-scale, low-cost, and microbial endotoxin-free production of LL-37 recombinant peptides for pharmaceutical applications. As a heterologous expression biofactory, we have previously obtained homologous barley (Hordeum vulgare L.) as an attractive vehicle for producing recombinant human LL-37 in the grain storage compartment, endosperm. The long-term stability of expression and inheritance of transgenes is necessary for the successful commercialization of recombinant proteins. Here, we report the stable inheritance and expression of the LL-37 gene in barley after six generations, including two consecutive seasons of experimental field cultivation. The transgenic plants showed normal growth and remained fertile. Based on the bacteria viability test, the produced peptide LL-37 retained high antibacterial activity.
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Abdel Jaleel, Usama, Qabas Natheer Lateef, and Nassam Emad Daem. "Microbial Flora in Stable Chronic Plaque Psoriasis ( A random study of 12 patients )." AL-QADISIYAH MEDICAL JOURNAL 3, no. 4 (2017): 146–50. http://dx.doi.org/10.28922/qmj.2007.3.4.146-150.
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Psoriasis vulgaris is a common, chronic, recurrent, inflammatory disease of the skin characterized by round, erythematous, dry scaly plaques of various sizes. The lesions have predilection for he scalp, nails and extensor surfaces of limbs, elbows &knees. Psoriasis is characterized by three main pathogenic features: abnormal differentiation, keratinocyte hyperproliferation & inflammation .Accelerated epidermopoisis has been considered to the fundamental pathologic event in psoriasis (1). The cause for that is still unknown, however, psoriasis is thought be to an auto-immune disorder influenced by some inheritance interplaying with acquired environmental factors (i.e. stress, hypocalcaemia, hormonal disturbances, infections).Due to the strong association between microbial skin flora &infections influencing psoriasis, we should focus on this flora & its change.
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Smith, David, and Sohan Jheeta. "Microbiome–Gut Dissociation: Investigating the Origins of Obesity." Gastrointestinal Disorders 3, no. 4 (2021): 156–72. http://dx.doi.org/10.3390/gidisord3040017.
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The reduction of excessive weight remains a major public health challenge, with control currently limited to a calorie reduction strategy. Currently, attempts are being made at revisiting the fibre hypothesis based on the African studies of Denis Burkitt, that the lack of dietary fibre in the modern diet was responsible for the occurrence of obesity and many of the other non-communicable diseases of what he called “Western civilization”. However, the dilemma is that Burkitt himself stressed that other peoples of his day, such as the Maasai, remained healthy without consuming such high fibre diets. Equally, the present obesity epidemic is accompanied by diseases of a malfunctioning immune system and of poor mental health that do not seem to be adequately explained simply by a deficiency of dietary fibre. Though unknown in Burkitt’s day, an increasing degradation of a mutualistic intestinal microbiome would offer a better fit to the observed epidemiology, especially if the microbiome is not effectively passed on from mother to child at birth. Taking the broader view, in this article we posit a view of the microbiome as a cofactor of mammalian evolution, in which a maternal microbial inheritance complements the parental genetic inheritance of the animal, both engaging epigenetic processes. As this would require the microbiome to be fully integrated with the animal as it develops into an adult, so we have a meaningful evolutionary role for the microbiome–gut–brain axis. By a failure to correctly establish a microbiome–gut interface, the inhibition of maternal microbial inheritance sets the scene for the future development of non-communicable disease: compromised immune system function on the one hand and dysfunctional gut–brain communication on the other. The basic principle is that the fully functioning, diverse, microbiome achieves interkingdom communication by the generation of messenger chemicals, semiochemicals. It is envisaged that the in situ detection of these as yet ill-defined chemical entities by means of an ingestible sensor would indicate the severity of disease and provide a guide as to its amelioration.
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Paoletti, Madeline M., and Gregory P. Fournier. "Chimeric inheritance and crown-group acquisitions of carbon fixation genes within Chlorobiales: Origins of autotrophy in Chlorobiales and implication for geological biomarkers." PLOS ONE 17, no. 10 (2022): e0275539. http://dx.doi.org/10.1371/journal.pone.0275539.
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The geological record of microbial metabolisms and ecologies primarily consists of stable isotope fractionations and the diagenetic products of biogenic lipids. Carotenoid lipid biomarkers are particularly useful proxies for reconstructing this record, providing information on microbial phototroph primary productivity, redox couples, and oxygenation. The biomarkers okenane, chlorobactane, and isorenieratene are generally considered to be evidence of anoxygenic phototrophs, and provide a record that extends to 1.64 Ga. The utility of the carotenoid biomarker record may be enhanced by examining the carbon isotopic ratios in these products, which are diagnostic for specific pathways of biological carbon fixation found today within different microbial groups. However, this joint inference assumes that microbes have conserved these pathways across the duration of the preserved biomarker record. Testing this hypothesis, we performed phylogenetic analyses of the enzymes constituting the reductive tricarboxylic acid (rTCA) cycle in Chlorobiales, the group of anoxygenic phototrophic bacteria usually implicated in the deposition of chlorobactane and isorenieretane. We find phylogenetically incongruent patterns of inheritance across all enzymes, indicative of horizontal gene transfers to both stem and crown Chlorobiales from multiple potential donor lineages. This indicates that a complete rTCA cycle was independently acquired at least twice within Chlorobiales and was not present in the last common ancestor. When combined with recent molecular clock analyses, these results predict that the Mesoproterzoic lipid biomarker record diagnostic for Chlorobiales should not preserve isotopic fractionations indicative of a full rTCA cycle. Furthermore, we conclude that coupling isotopic and biomarker records is insufficient for reliably reconstructing microbial paleoecologies in the absence of a complementary and consistent phylogenomic narrative.
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Lin, Xingtong, Hui Han, Nan Wang, et al. "The Gut Microbial Regulation of Epigenetic Modification from a Metabolic Perspective." International Journal of Molecular Sciences 25, no. 13 (2024): 7175. http://dx.doi.org/10.3390/ijms25137175.
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Obesity is a global health challenge that has received increasing attention in contemporary research. The gut microbiota has been implicated in the development of obesity, primarily through its involvement in regulating various host metabolic processes. Recent research suggests that epigenetic modifications may serve as crucial pathways through which the gut microbiota and its metabolites contribute to the pathogenesis of obesity and other metabolic disorders. Hence, understanding the interplay between gut microbiota and epigenetic mechanisms is crucial for elucidating the impact of obesity on the host. This review primarily focuses on the understanding of the relationship between the gut microbiota and its metabolites with epigenetic mechanisms in several obesity-related pathogenic mechanisms, including energy dysregulation, metabolic inflammation, and maternal inheritance. These findings could serve as novel therapeutic targets for probiotics, prebiotics, and fecal microbiota transplantation tools in treating metabolic disruptions. It may also aid in developing therapeutic strategies that modulate the gut microbiota, thereby regulating the metabolic characteristics of obesity.
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Riding, Robert. "Abiogenic, microbial and hybrid authigenic crusts: components of Precambrian stromatolites." Geologia Croatica 61, no. 2-3 (2008): 73–103. http://dx.doi.org/10.4154/gc.2008.10.
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Authigenic seafloor carbonate crusts include fenestrate microbialite, thrombolite, and four types here designated Fine-grained Crust, Sparry Crust, Hybrid Sparry Fine-grained Crust, and Sparry Crust plus Coarse Grains. Each of the latter four types includes at least some layered examples that have generally been regarded as stromatolites. Recognition and interpretation of these various deposits assists understanding of stromatolite development. Sparry Crust is common in the Late Archaean-Mesoproterozoic. It includes botryoidal fans and other crystal pseudomorphs, microdigitate stromatolite, dendrite, isopachous laminite, and herringbone calcite. Although differing in primary mineralogy and bedform, these are all characterized by coarse sparry, commonly radial fibrous, fabric and appear light coloured in thin-section. They have commonly been referred to as seafloor cement, although they formed at the open sediment-water interface rather than as void-fills. Two of them in particular, isopachous laminite and microdigitate ‘tufa’, typically form isopachous layers with good vertical inheritance and have been regarded as stromatolites. In contrast to Sparry Crust, Fine-grained Crust has fine-grained (micritic, clotted, peloidal, filamentous) microfabric that appears dark in thin-section, and irregular uneven layering with relatively poor inheritance. Mixed crusts, composed of millimetric alternations of Sparry and Fine-grained crust, are here termed Hybrid Sparry Fine-grained Crust. Sparry Crust with coarse allochthonous grains - here termed Sparry Crust plus Coarse Grains – includes some examples that have been given formal stromatolite names, e.g., Gongylina and Omachtenia. Sparry, Hybrid, and Fine-grained crusts are common components of Precambrian stromatolites. Their relative abundances change through time. Archaean stromatolite fabrics are commonly obscured by recrystallization, but their preserved lamina arrangements suggest that many of them could be composed mainly of Sparry or Hybrid crust. During the Palaeoproterozoic-Mesoproterozoic, Sparry Crust fabrics were common in peritidal stromatolites, whereas Hybrid Crust appears to have dominated large subtidal domes and columns. Fine-grained Crust may not have become generally abundant until the Neoproterozoic, when it commonly formed both stromatolites and thrombolites. Phanerozoic normal marine stromatolites are also typically composed of Fine-grained Crust. Present-day analogues of Sparry Crust fabrics occur in some speleothem, hot spring, and splash-zone marine crusts, and of Fine-grained Crust in lithified microbial mats. Light-dark millimetric alternations of sparry and fine-grained crust that characterize Hybrid Crust have analogues in freshwater stromatolites. Taken together, these comparisons suggest that some Precambrian stromatolites are abiogenic, some microbial, and others are intimate hybrid mixtures of the two, and that - preservation permitting - these varieties can be distinguished using microfabric and lamina criteria.
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Sambuk, Elena V., Dmitry M. Muzaev, Andrey M. Rumyantsev, and Marina V. Padkina. "Saccharomyces cerevisiae killer toxins: synthesis, mechanisms of action and practical use." Ecological genetics 17, no. 3 (2019): 59–73. http://dx.doi.org/10.17816/ecogen17359-73.
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Yeast Saccharomyces cerevisiae is a unique model for studying the molecular mechanisms of exotoxin-mediated antagonistic relationships between coexisting microorganisms. The synthesis of yeast toxins can be considered as an example of allelopathy and environmental competition. The elucidation of the role of allelopathy in the formation of microbial communities is of great interest for modern ecology. Yeast toxins are widely used in medicine, the food industry and biotechnology. The review examines the nature of exotoxins, the mechanisms of inheritance and interaction of the virus and yeast cells, as well as the prospects for their practical application.
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Abdelfattah, Ahmed, Michael Wisniewski, Leonardo Schena, and Ayco J. M. Tack. "Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root." Environmental Microbiology 23, no. 4 (2021): 2199–214. http://dx.doi.org/10.1111/1462-2920.15392.
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Ma, Qiuyu, Yonghong Cui, Xu Chu, et al. "Gut Bacterial Communities of Lymantria xylina and Their Associations with Host Development and Diet." Microorganisms 9, no. 9 (2021): 1860. http://dx.doi.org/10.3390/microorganisms9091860.
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The gut microbiota of insects has a wide range of effects on host nutrition, physiology, and behavior. The structure of gut microbiota may also be shaped by their environment, causing them to adjust to their hosts; thus, the objective of this study was to examine variations in the morphological traits and gut microbiota of Lymantria xylina in response to natural and artificial diets using high-throughput sequencing. Regarding morphology, the head widths for larvae fed on a sterilized artificial diet were smaller than for larvae fed on a non-sterilized host-plant diet in the early instars. The gut microbiota diversity of L. xylina fed on different diets varied significantly, but did not change during different development periods. This seemed to indicate that vertical inheritance occurred in L. xylina mutualistic symbionts. Acinetobacter and Enterococcus were dominant in/on eggs. In the first instar larvae, Acinetobacter accounted for 33.52% of the sterilized artificial diet treatment, while Enterococcus (67.88%) was the predominant bacteria for the non-sterilized host-plant diet treatment. Gut microbe structures were adapted to both diets through vertical inheritance and self-regulation. This study clarified the impacts of microbial symbiosis on L. xylina and might provide new possibilities for improving the control of these bacteria.
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Hilliard, Margaret A., and David A. Sela. "Transmission and Persistence of Infant Gut-Associated Bifidobacteria." Microorganisms 12, no. 5 (2024): 879. http://dx.doi.org/10.3390/microorganisms12050879.
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Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from mother to infant via the fecal-oral route is likely contingent on the bifidobacterial strain and phenotype, whereas transmission via the vaginal microbiota may be restricted to Bifidobacterium breve. Additional reservoirs include breastmilk, horizontal transfer from the environment, and potentially in utero transfer. Given that diet is a strong predictor of Bifidobacterium colonization in early life and the absence of Bifidobacterium is observed regardless of breastfeeding, it is likely that additional factors are responsible for bifidobacterial colonization early in life.
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Snir, Sagi. "Lateral Transfer: A Survey and New Developments." Israel Journal of Ecology and Evolution 52, no. 3-4 (2006): 443–59. http://dx.doi.org/10.1560/ijee_52_3-4_443.
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Exponentially accumulating genetic molecular data were supposed to bring us closer to resolving one of the most fundamental issues in biology—the reconstruction of the tree of life. This tree should encompass the evolutionary history of all living creatures on earth and trace back a few billions of years to the most ancient microbial ancestor. Ironically, this abundance of data only blurs our traditional beliefs and seems to make this goal harder to achieve than initially thought. This is largelydue to lateral gene transfer, the passage of genetic material between organisms not through lineal descent. Evolution in light of lateral transfer tangles the traditional universal tree of life, turning it into a network of relationships. Lateral transfer is a significant factor in microbial evolution and is the mechanism of antibiotic resistance spread in bacteria species. In this paper we survey current methods designed to cope with lateral transfer in conjunction with vertical inheritance. We distinguish between phylogenetic-based methods and sequence-based methods and illuminate the advantages and disadvantages of each. Finally, we sketch a new statistically rigorous approach aimed at identifying lateral transfer between two genomes.
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Charon, Justine, Vanessa Rossetto Marcelino, Richard Wetherbee, Heroen Verbruggen, and Edward C. Holmes. "Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures." Viruses 12, no. 10 (2020): 1180. http://dx.doi.org/10.3390/v12101180.
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Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Ohno, Y., ES Buescher, R. Roberts, JA Metcalf, and JI Gallin. "Reevaluation of cytochrome b and flavin adenine dinucleotide in neutrophils from patients with chronic granulomatous disease and description of a family with probable autosomal recessive inheritance of cytochrome b deficiency." Blood 67, no. 4 (1986): 1132–38. http://dx.doi.org/10.1182/blood.v67.4.1132.1132.
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Abstract Chronic granulomatous disease (CGD) is a genetically heterogeneous syndrome characterized by a microbial killing defect of polymorphonuclear leukocytes (PMNs) due to lack of superoxide O2-. 2 generation. Recent studies indicate that the neutrophil O2-.-generating system consists of at least two components, flavoprotein--flavin adenine dinucleotide (FAD)--and cytochrome b. We evaluate the cytochrome b and FAD content in PMN from 30 CGD patients. The method for quantitating cytochrome b was modified by using PMN sonicates incubated with azide plus hydrogen peroxide. With this approach, several absorption peaks corresponding to myeloperoxidase and eosinophil peroxidase, which overlap with peaks of cytochrome b, were obliterated from reduced-minus-oxidized spectra, whereas the peaks of cytochrome b were not and could be readily quantitated. Cytochrome b was detected in PMNs from all 24 normal adults (47.4 +/- 2.9 pmol/7.5 X 10(6) cells), was absent in PMNs from 11 male CGD patients and one female CGD patient but was present in normal amounts in PMNs from nine male and nine female CGD patients. Stimulated nitroblue tetrazolium (NBT) tests performed on PMNs from mothers of CGD patients indicated that cytochrome b deficiency was associated with X-linked inheritance, except in one case in which probable autosomal recessive inheritance was demonstrated. The PMN NBT test of the mother of another male patient without cytochrome b deficiency suggested an X-linked form of inheritance. In related studies, the FAD content in PMN particulate fractions was reduced in 4 of 28 CGD patients studied. All four CGD patients with reduced FAD lacked cytochrome b. However, three patients with cytochrome b deficiency had normal FAD. Thus, the results indicate that PMN cytochrome b deficiency is observed in most X-linked and in some autosomal recessive CGD, that cytochrome b deficiency may be associated with FAD deficiency, and that cytochrome b and FAD are normal in most patients with non-X-linked CGD.
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Ohno, Y., ES Buescher, R. Roberts, JA Metcalf, and JI Gallin. "Reevaluation of cytochrome b and flavin adenine dinucleotide in neutrophils from patients with chronic granulomatous disease and description of a family with probable autosomal recessive inheritance of cytochrome b deficiency." Blood 67, no. 4 (1986): 1132–38. http://dx.doi.org/10.1182/blood.v67.4.1132.bloodjournal6741132.
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Chronic granulomatous disease (CGD) is a genetically heterogeneous syndrome characterized by a microbial killing defect of polymorphonuclear leukocytes (PMNs) due to lack of superoxide O2-. 2 generation. Recent studies indicate that the neutrophil O2-.-generating system consists of at least two components, flavoprotein--flavin adenine dinucleotide (FAD)--and cytochrome b. We evaluate the cytochrome b and FAD content in PMN from 30 CGD patients. The method for quantitating cytochrome b was modified by using PMN sonicates incubated with azide plus hydrogen peroxide. With this approach, several absorption peaks corresponding to myeloperoxidase and eosinophil peroxidase, which overlap with peaks of cytochrome b, were obliterated from reduced-minus-oxidized spectra, whereas the peaks of cytochrome b were not and could be readily quantitated. Cytochrome b was detected in PMNs from all 24 normal adults (47.4 +/- 2.9 pmol/7.5 X 10(6) cells), was absent in PMNs from 11 male CGD patients and one female CGD patient but was present in normal amounts in PMNs from nine male and nine female CGD patients. Stimulated nitroblue tetrazolium (NBT) tests performed on PMNs from mothers of CGD patients indicated that cytochrome b deficiency was associated with X-linked inheritance, except in one case in which probable autosomal recessive inheritance was demonstrated. The PMN NBT test of the mother of another male patient without cytochrome b deficiency suggested an X-linked form of inheritance. In related studies, the FAD content in PMN particulate fractions was reduced in 4 of 28 CGD patients studied. All four CGD patients with reduced FAD lacked cytochrome b. However, three patients with cytochrome b deficiency had normal FAD. Thus, the results indicate that PMN cytochrome b deficiency is observed in most X-linked and in some autosomal recessive CGD, that cytochrome b deficiency may be associated with FAD deficiency, and that cytochrome b and FAD are normal in most patients with non-X-linked CGD.
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Taylor, Daniel, Nia Verdon, Peter Lomax, Rosalind J. Allen, and Simon Titmuss. "Tracking the stochastic growth of bacterial populations in microfluidic droplets." Physical Biology 19, no. 2 (2022): 026003. http://dx.doi.org/10.1088/1478-3975/ac4c9b.
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Abstract Bacterial growth in microfluidic droplets is relevant in biotechnology, in microbial ecology, and in understanding stochastic population dynamics in small populations. However, it has proved challenging to automate measurement of absolute bacterial numbers within droplets, forcing the use of proxy measures for population size. Here we present a microfluidic device and imaging protocol that allows high-resolution imaging of thousands of droplets, such that individual bacteria stay in the focal plane and can be counted automatically. Using this approach, we track the stochastic growth of hundreds of replicate Escherichia coli populations within droplets. We find that, for early times, the statistics of the growth trajectories obey the predictions of the Bellman–Harris model, in which there is no inheritance of division time. Our approach should allow further testing of models for stochastic growth dynamics, as well as contributing to broader applications of droplet-based bacterial culture.
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Fasani, Elisa, Gianluigi Giannelli, Serena Varotto, et al. "Epigenetic Control of Plant Response to Heavy Metals." Plants 12, no. 18 (2023): 3195. http://dx.doi.org/10.3390/plants12183195.
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Plants are sessile organisms that must adapt to environmental conditions, such as soil characteristics, by adjusting their development during their entire life cycle. In case of low-distance seed dispersal, the new generations are challenged with the same abiotic stress encountered by the parents. Epigenetic modification is an effective option that allows plants to face an environmental constraint and to share the same adaptative strategy with their progeny through transgenerational inheritance. This is the topic of the presented review that reports the scientific progress, up to date, gained in unravelling the epigenetic response of plants to soil contamination by heavy metals and metalloids, collectively known as potentially toxic elements. The effect of the microbial community inhabiting the rhizosphere is also considered, as the evidence of a transgenerational transfer of the epigenetic status that contributes to the activation in plants of response mechanisms to soil pollution.
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Smith, David, Sohan Jheeta, Georgina I. López-Cortés, Bernadette Street, Hannya V. Fuentes, and Miryam Palacios-Pérez. "On the Inheritance of Microbiome-Deficiency: Paediatric Functional Gastrointestinal Disorders, the Immune System and the Gut–Brain Axis." Gastrointestinal Disorders 5, no. 2 (2023): 209–32. http://dx.doi.org/10.3390/gidisord5020018.
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Like the majority of non-communicable diseases that have recently gained attention, functional gastrointestinal (GI) disorders (FGID) in both children and adults are caused by a variety of medical conditions. In general, while it is often thought that common conditions such as obesity may cause other problems, for example, asthma or mental health issues, more consideration needs to be given to the possibility that they could both be brought on by a single underlying problem. Based on the variations in non-communicable disease, in recent years, our group has been revisiting the exact role of the intestinal microbiome within the Vertebrata. While the metabolic products of the microbiome have a role to play in the adult, our tentative conclusion is that the fully functioning, mutualistic microbiome has a primary role: to transfer antigen information from the mother to the neonate in order to calibrate its immune system, allowing it to survive within the microbial environment into which it will emerge. Granted that the microbiome possesses such a function, logic suggests the need for a robust, flexible, mechanism allowing for the partition of nutrition in the mature animal, thus ensuring the continued existence of both the vertebrate host and microbial guest, even under potentially unfavourable conditions. It is feasible that this partition process acts by altering the rate of peristalsis following communication through the gut–brain axis. The final step of this animal–microbiota symbiosis would then be when key microbes are transferred from the female to her progeny, either live offspring or eggs. According to this scheme, each animal inherits twice, once from its parents’ genetic material and once from the mother’s microbiome with the aid of the father’s seminal microbiome, which helps determine the expression of the parental genes. The key point is that the failure of this latter inheritance in humans leads to the distinctive manifestations of functional FGID disorders including inflammation and gut motility disturbances. Furthermore, it seems likely that the critical microbiome–gut association occurs in the first few hours of independent life, in a process that we term handshaking. Note that even if obvious disease in childhood is avoided, the underlying disorders may intrude later in youth or adulthood with immune system disruption coexisting with gut–brain axis issues such as excessive weight gain and poor mental health. In principle, investigating and perhaps supplementing the maternal microbiota provide clinicians with an unprecedented opportunity to intervene in long-term disease processes, even before the child is born.
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Wang, Runze, Binqiang Bai, Yayu Huang, et al. "Yaks Are Dependent on Gut Microbiota for Survival in the Environment of the Qinghai Tibet Plateau." Microorganisms 12, no. 6 (2024): 1122. http://dx.doi.org/10.3390/microorganisms12061122.
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The yak (Poephagus grunniens) has evolved unique adaptations to survive the harsh environment of the Qinghai–Tibetan Plateau, while their gut microorganisms play a crucial role in maintaining the health of the animal. Gut microbes spread through the animal population not only by horizontal transmission but also vertically, which enhances microbial stability and inheritance between generations of the population. Homogenization of gut microbes in different animal species occurs in the same habitat, promoting interspecies coexistence. Using the yak as a model animal, this paper discusses the adaptive strategies under extreme environments, and how the gut microbes of the yak circulate throughout the Tibetan Plateau system, which not only affects other plateau animals such as plateau pikas, but can also have a profound impact on the health of people. By examining the relationships between yaks and their gut microbiota, this review offers new insights into the adaptation of yaks and their ecological niche on the Qinghai–Tibetan plateau.
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Provorov, N. A. "Symbioses of prokaryotes and eukaryotes: from gene interactions to integration of genomes." Biomics 14, no. 3 (2022): 248–57. http://dx.doi.org/10.31301/2221-6197.bmcs.2022-21.
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Symbioses of prokaryotes and eukaryotes are considered as models to analyze the fundamental issues of genetics and evolutionary biology including trade-off between the reductionist and holistic approaches in the research of biosystems. Symbiotic models allow us to address: 1) emergence of cellular forms of life; 2) formation of multi-genomic eukaryotic cells; 3) evolution of multicellular eukaryotes as of holobionts in which microbial symbionts ensure the hosts’ nutrition, protection from antagonists and stresses as well as developmental regulation. We suggest that ecological and genetic factors responsible for natural history of super-species systems go far beyond the Darwinian paradigm of adaptive evolution based on accumulation of minor changes supported by natural (individual) selection. Specifically, partners’ cooperation involves: a) interspecies altruism, based on formation by symbionts of non-reproducible cellular forms implementing the host-beneficial functions; b) pangenesis assuming the inheritance by hosts of symbionts as of acquired genetic determinants, which are maintained in hologenomes and can donate their genes to nuclear genomes.
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Wang, Jinfeng, Jiayong Zheng, Wenyu Shi, et al. "Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus." Gut 67, no. 9 (2018): 1614–25. http://dx.doi.org/10.1136/gutjnl-2018-315988.
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ObjectiveThe initial colonisation of the human microbiota and the impact of maternal health on neonatal microbiota at birth remain largely unknown. The aim of our study is to investigate the possible dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus (GDM) and to estimate the potential risks of the microbial shift to neonates.DesignPregnant women and neonates suffering from GDM were enrolled and 581 maternal (oral, intestinal and vaginal) and 248 neonatal (oral, pharyngeal, meconium and amniotic fluid) samples were collected. To avoid vaginal bacteria contaminations, the included neonates were predominantly delivered by C-section, with their samples collected within seconds of delivery.ResultsNumerous and diverse bacterial taxa were identified from the neonatal samples, and the samples from different neonatal body sites were grouped into distinct clusters. The microbiota of pregnant women and neonates was remarkably altered in GDM, with a strong correlation between certain discriminatory bacteria and the oral glucose tolerance test. Microbes varying by the same trend across the maternal and neonatal microbiota were observed, revealing the intergenerational concordance of microbial variation associated with GDM. Furthermore, lower evenness but more depletion of KEGG orthologues and higher abundance of some viruses (eg, herpesvirus and mastadenovirus) were observed in the meconium microbiota of neonates associated with GDM.ConclusionGDM can alter the microbiota of both pregnant women and neonates at birth, which sheds light on another form of inheritance and highlights the importance of understanding the formation of early-life microbiome.
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Tai, Vera, Erick R. James, Christine A. Nalepa, Rudolf H. Scheffrahn, Steve J. Perlman, and Patrick J. Keeling. "The Role of Host Phylogeny Varies in Shaping Microbial Diversity in the Hindguts of Lower Termites." Applied and Environmental Microbiology 81, no. 3 (2014): 1059–70. http://dx.doi.org/10.1128/aem.02945-14.
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ABSTRACTThe hindguts of lower termites andCryptocercuscockroaches are home to a distinct community of archaea, bacteria, and protists (primarily parabasalids and some oxymonads). Within a host species, the composition of these hindgut communities appears relatively stable, but the evolutionary and ecological factors structuring community composition and stability are poorly understood, as are differential impacts of these factors on protists, bacteria, and archaea. We analyzed the microbial composition of parabasalids and bacteria in the hindguts ofCryptocercus punctulatusand 23 species spanning 4 families of lower termites by pyrosequencing variable regions of the small-subunit rRNA gene. Especially for the parabasalids, these data revealed undiscovered taxa and provided a phylogenetic basis for a more accurate understanding of diversity, diversification, and community composition. The composition of the parabasalid communities was found to be strongly structured by the phylogeny of their hosts, indicating the importance of historical effects, although exceptions were also identified. Particularly, spirotrichonymphids and trichonymphids likely were transferred between host lineages. In contrast, host phylogeny was not sufficient to explain the majority of bacterial community composition, but the compositions of theBacteroidetes,Elusimicrobia,Tenericutes,Spirochaetes, andSynergisteswere structured by host phylogeny perhaps due to their symbiotic associations with protists. All together, historical effects probably resulting from vertical inheritance have had a prominent role in structuring the hindgut communities, especially of the parabasalids, but dispersal and environmental acquisition have played a larger role in community composition than previously expected.
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Yan, Ruyu, Ximei Zhao, Penghui Li, Zhuanyun Si, Yang Gao, and Jifu Li. "Composition and Diversity of Soil Microbial Communities in Walnut Orchards at Different Altitudes in Southeastern Tibet." Land 12, no. 7 (2023): 1419. http://dx.doi.org/10.3390/land12071419.
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To understand the distribution of the soil microbial community in natural walnut orchards at different altitude gradients (3000–3500 m) and to reveal the mechanism of the soil microbial activity in natural walnut orchards adapting to high-altitude environments, soil samples from four groups of natural walnut orchards in Gyaca County, southeast Tibet, were studied. Illumina MiSeq sequencing technology was used to analyze the community composition and diversity of soil bacteria and fungi and their responses to the altitudes. The alpha diversity results showed that the vertical distribution pattern of the fungal community was more obvious than that of the bacterial community and the bacterial community diversity first increased (~3364 m) and then decreased with altitude. The number of amplicon sequence variants (ASVs) in the soil bacterial community was significantly higher than that in the fungal community, but soil bacterial and fungal communities in walnut orchards at different altitudes exhibited both inheritance and uniqueness. At the phylum level, the dominant bacterial phyla at different altitudes were Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi (relative abundances > 10.0% in each treatment). With the increase in altitude, the relative abundance of Actinobacteria increased gradually while that of Acidobacteria and Proteobacteria decreased gradually. The dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota (relative abundances >5.0% in each treatment). With the increase in altitude, the relative abundance of Ascomycota increased significantly. At the genus level, the number of dominant bacteria and fungi in the soil decreased gradually with increased altitude and showed anisotropic distribution characteristics. The relative abundances of Actinobacteria among the bacterial phyla—and Olpidiomycota and Zoopagomycota among the fungal phyla—were positively correlated with the altitude (p < 0.05). Most dominant bacterial and fungal phyla were highly significantly (p < 0.01) or significantly (p < 0.05) negatively correlated with the altitude. Soil nitrogen and phosphorus availabilities are the main limiting factors of microbial community diversity. Therefore, altitude caused changes in soil physicochemical properties which directly or indirectly affected the composition and diversity of soil bacterial and fungal communities, and our study provides a theoretical basis for the altitudinal pattern and succession changes in soil microbial communities in the natural walnut orchards of southeast Tibet.
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Smith, David, Miryam Palacios-Pérez, and Sohan Jheeta. "Microbiome–Gut Dissociation in the Neonate: Obesity and Coeliac Disease as Examples of Microbiome Function Deficiency Disorder." Gastrointestinal Disorders 4, no. 3 (2022): 108–28. http://dx.doi.org/10.3390/gidisord4030012.
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The purpose of this article is to provide a direction for translational research based on an analysis of the nature of complex, immune-related conditions such as obesity and coeliac disease. In essence, it seems that the prevalence of these non-communicable diseases is related to the degradation of the microbiome during the industrialisation of society, and that their nature can be used to infer the functions of the “pre-industrial” microbiome. Based on this analysis, the key point is the necessity for the fully functioning microbiome, acting alongside the parental genetic inheritance of the child, to be in place immediately after birth. In our view, this is achieved by the seemingly accidental process of maternal microbial inheritance during normal birth. Note, however, that this is not possible if the microbiome of the mother is itself degraded following previous problems. Under these conditions the health of a child may be affected from the moment of birth, although, with the exception of atopic diseases, such as eczema and food allergy, the consequences may not become apparent until late childhood or as an adult. In this way, this microbiome function deficiency hypothesis incorporates the epidemiological observations of David Strachan and David Barker in that their onset can be traced to early childhood. Coeliac disease has been chosen as an illustrative example of a multifactorial disorder due to the fact that, in addition to a series of immune system manifestations and a potential problem with food absorption, there is also a significant psychological component. Finally, it is worth noting that an ingestible sensor calibrated to the detection of interkingdom communication molecules (semiochemicals) within the intestine may offer a practical way of assessment and, perhaps, amelioration of at least some of the consequences of non-communicable disease.
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Provorov, N. A., and I. A. Tikhonovich. "Symbiogenetics and Symbiogenesis: Molecular and Ecological Bases of Integrative Evolution." Генетика 59, no. 2 (2023): 135–46. http://dx.doi.org/10.31857/s0016675823020091.
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Symbiogenetics is presented as a discipline aimed to study the combined genetic systems resulted from co-evolution of unrelated organisms. Their research complements the methodology of genetic analysis with the approaches of “genetic synthesis” aimed at characterizing the molecular and ecological factors of integration of heterologous genomes. Hologenomes and symbiogenomes that arise via integrative evolution (symbiogenesis) are dissected, like prokaryotic pangenomes, into the core and accessory parts. In hologenome, the core part, which is constant in composition, is represented by the host genome (nuclear-cytoplasmic system of heredity), and the variable accessory part composed by metagenome of the microbial community which is associated with the host and performs functions useful for it. Mechanisms of symbiogenesis go beyond the factors of evolution of free-living organisms and include: (a) interspecies altruism associated with the refusal of symbionts from autonomous existence, and upon a deep reduction, from the ability to maintain the genome; (b) inheritance by host of symbionts as of “acquired” genetic determinants (pangenesis). Under the impacts of these factors, symbionts can be transformed into cellular organelles that have lost their genetic individuality and sometimes lack genomes. Symbiogenesis is presented as a multi-stage process, including the emergence of: (i) genome-containing prokaryotic cell; (ii) multi-genomic eukaryotic cell; (iii) multicellular eukaryotes as holobionts composed of host organisms and associated microbial communities. Genome-free organelles that have retained the basic reproductive and metabolic functions can be used as models for reconstructing the early stages of cell evolution, including the emergence of cellular genome.
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Alaifan, Meshari A., Ohood Abusharifah, Rana Yagoub Bokhary, et al. "Granulomatous hepatitis in a Saudi child with IL2RA defect: a case report and literature review." Therapeutic Advances in Chronic Disease 13 (January 2022): 204062232211167. http://dx.doi.org/10.1177/20406223221116798.
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Interleukin-2 receptor alpha ( IL2RA) defect (OMIM- # 606367) is an immune disease where affected patients are vulnerable to developing recurrent microbial infections in addition to lymphadenopathy and dermatological manifestations. This condition is known to be caused by pathogenic variants in the IL2RA gene, which are inherited in an autosomal recessive fashion. In this case report, we present a patient with IL2RA defect from Saudi Arabia who presented with chronic diarrhea, poor weight gain, mild villous atrophy, malnutrition, hepatomegaly, nonspecific inflammation, and an eczematous skin rash. His genetic analysis revealed a novel, homozygous, and likely pathogenic variant, that is, c.504 C>A (Cys168Ter), located in the exon 4of the IL2RA gene, which was inherited from his parents in an autosomal recessive mode of inheritance. This variant produces a 272-amino-acid shorter IL2RA protein chain, which most likely becomes degraded in the cytosol. Thus, we assume that the c.504 C>A is a null allele that abolishes the synthesis of IL2RA, malforms the IL-2 receptor complex, and eventually causes immunodeficiency manifestations. To our knowledge, this is the first time a person with IL2RA defect has shown signs of granulomatous hepatitis on a liver biopsy.
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Dumigan, Christopher R., and Michael K. Deyholos. "Cannabis Seedlings Inherit Seed-Borne Bioactive and Anti-Fungal Endophytic Bacilli." Plants 11, no. 16 (2022): 2127. http://dx.doi.org/10.3390/plants11162127.
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Throughout the hundreds of millions of years of co-evolution, plants and microorganisms have established intricate symbiotic and pathogenic relationships. Microbial communities associated with plants are in constant flux and can ultimately determine whether a plant will successfully reproduce or be destroyed by their environment. Inheritance of beneficial microorganisms is an adaptation plants can use to protect germinating seeds against biotic and abiotic stresses as seedlings develop. The interest in Cannabis as a modern crop requires research into effective biocontrol of common fungal pathogens, an area that has seen little research. This study examines the seed-borne endophytes present across 15 accessions of Cannabis grown to seed across Western Canada. Both hemp and marijuana seedlings inherited a closely related group of bioactive endophytic Bacilli. All Cannabis accessions possessed seed-inherited Paenibacillus mobilis with the capacity to solubilize mineral phosphate. Additionally, seeds were found to carry genera of fungal isolates known to be Cannabis pathogens and post-harvest molds: Alternaria, Penicillium, Cladosporium, Chaetomium, Aspergillus, Rhizopus, and Fusarium. Thirteen seed-borne endophytes showed antibiotic activity against Alternaria, Aspergillus, Penicillium, and Fusarium. This study suggests both fungal pathogens and bacterial endophytes that antagonize them are vectored across generations in Cannabis as they compete over this shared niche.
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Amuzescu, Andreea, Mircea Tampa, Clara Matei, and Simona Roxana Georgescu. "Adult Female Acne: Recent Advances in Pathophysiology and Therapeutic Approaches." Cosmetics 11, no. 3 (2024): 74. http://dx.doi.org/10.3390/cosmetics11030074.
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Adult acne is a chronic inflammatory disease of the pilosebaceous unit characterized by the excessive production of abnormal sebum favoring an imbalance of the skin microbiota and the hyperproliferation of Cutibacterium acnes and other virulent microbial strains, leading to an inflammatory environment, innate immunity overactivation, and keratinocyte hyperproliferation in hair follicles pores. Degraded keratinocytes plug the pores, consequently forming microcomedons, which can later evolve to papules, nodules, pustules and scars. Distinct from juvenile acne, in adult female acne (AFA) the symptomatology occurs or persists in postadolescence (after age 25). Although hyperandrogenism or the excessive sensitivity of androgen receptors are the main causes, AFA can be triggered by multiple factors, either including or not including androgen disturbances. The prevalence in adult women is 15–20%. Hyperandrogenism is present in 50% of cases; 70% of hyperandrogenism cases feature polycystic ovary syndrome (PCOS), a complex endocrine and metabolic condition. Genetic susceptibility occurs in 80% of acne cases, often with familial inheritance. Beyond classical stepwise therapeutic protocols (topical agents, isotretinoin, antibiotics, hormonal therapy with estrogens, progestins, spironolactone), novel approaches include the highly effective topical antiandrogen clascoterone, the management of insulin resistance by diet, exercise, stress avoidance, and adjuvant therapies such as berberine. Vaccines against the pathogenic proinflammatory C. acnes hyaluronidase A are in development.
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Long, Hongan, Parul Johri, Jean-Francois Gout, et al. "Paramecium Genetics, Genomics, and Evolution." Annual Review of Genetics 57, no. 1 (2023): 391–410. http://dx.doi.org/10.1146/annurev-genet-071819-104035.
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The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently been made in the area of comparative and population genomics. Paramecium species combine some of the lowest known mutation rates with some of the largest known effective populations, along with likely very high recombination rates, thereby harboring a population-genetic environment that promotes an exceptionally efficient capacity for selection. As a consequence, the genomes are extraordinarily streamlined, with very small intergenic regions combined with small numbers of tiny introns. The subject of the bulk of Paramecium research, the ancient Paramecium aurelia species complex, is descended from two whole-genome duplication events that retain high degrees of synteny, thereby providing an exceptional platform for studying the fates of duplicate genes. Despite having a common ancestor dating to several hundred million years ago, the known descendant species are morphologically indistinguishable, raising significant questions about the common view that gene duplications lead to the origins of evolutionary novelties.
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Smith, David, Sohan Jheeta, Hannya V. Fuentes, Bernadette Street, and Miryam Palacios-Pérez. "Microbiome–Gut Dissociation in the Neonate: Autism-Related Developmental Brain Disease and the Origin of the Placebo Effect." Gastrointestinal Disorders 4, no. 4 (2022): 291–311. http://dx.doi.org/10.3390/gidisord4040028.
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While the importance of the intestinal microbiome has been realised for a number of years, the significance of the phrase microbiota–gut–brain axis is only just beginning to be fully appreciated. Our recent work has focused on the microbiome as if it were a single entity, modifying the expression of the genetic inheritance of the individual by the generation of interkingdom signalling molecules, semiochemicals, such as dopamine. In our view, the purpose of the microbiome is to convey information about the microbial environment of the mother so as to calibrate the immune system of the new-born, giving it the ability to distinguish harmful pathogens from the harmless antigens of pollen, for example, or to help distinguish self from non-self. In turn, this requires the partition of nutrition between the adult and its microbiome to ensure that both entities remain viable until the process of reproduction. Accordingly, the failure of a degraded microbiome to interact with the developing gut of the neonate leads to failure of this partition in the adult: to low faecal energy excretion, excessive fat storage, and concomitant problems with the immune system. Similarly, a weakened gut–brain axis distorts interoceptive input to the brain, increasing the risk of psychiatric diseases such as autism. These effects account for David Barker’s 1990 suggestion of “the fetal and infant origins of adult disease”, including schizophrenia, and David Strachan’s 1989 observation of childhood immune system diseases, such as hay fever and asthma. The industrialisation of modern life is increasing the intensity and scale of these physical and psychiatric diseases and it seems likely that subclinical heavy metal poisoning of the microbiome contributes to these problems. Finally, the recent observation of Harald Brüssow, that reported intestinal bacterial composition does not adequately reflect the patterns of disease, would be accounted for if microbial eukaryotes were the key determinant of microbiome effectiveness. In this view, the relative success of “probiotic” bacteria is due to their temporary immune system activation of the gut–brain axis, in turn suggesting a potential mechanism for the placebo effect.
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Yuan, Meng, Zhengzhong Li, Qunlan Zhou, et al. "Enhancement of Digestive Enzyme Activity in Enterococcus faecalis Using ARTP Mutagenesis." Microorganisms 12, no. 12 (2024): 2425. http://dx.doi.org/10.3390/microorganisms12122425.
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Enterococcus faecalis is used as a probiotic in animal and human food supplements. Atmospheric and room temperature plasma (ARTP) systems have frequently been used to screen for effective mutant probiotics. In this study, E. faecalis was treated with ARTP, and high-yielding digestive enzyme mutant strains were obtained by measuring the activities of α-amylase, lipase, and neutral protease. A total of 833 mutant strains were obtained after 40–60 s of ARTP treatment, and after screening for digestive enzyme activity, EF-448, EF-798, and EF-804 were obtained. The three strains demonstrated an 180% increase in α-amylase activity, a 30% increase in lipase activity, and a more than 40% increase in neutral protease activity. Furthermore, the enzyme activities remained stable after nine generations. In addition, the strains exhibited high auto-aggregation capacity (over 91%) and high cell hydrophobicity (over 93%). After exposure to simulated intestinal fluid for 6 h, the survival rates of EF-448 and EF-798 were 85.71% and 82.32%, respectively. Moreover, the three mutant strains retained antioxidant capacity and DPPH free radical scavenging ability, and there was no hemolysis. A safety experiment has shown that there is no mortality of Macrobrachium rosenbergii within 14 days after receiving injections of mutant strains at different concentrations. In conclusion, this study obtained three mutant strains with high production of digestive enzymes and stable inheritance through ARTP mutagenesis of E. faecalis, providing an efficient microbial resource.
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Ibrahim, Nur Aifiah Binti. "Biosynthesis of DNA for disease detection." Jurnal Mangifera Edu 9, no. 2 (2025): 1–12. https://doi.org/10.31943/mangiferaedu.v9i2.206.
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An aquatic plant breathes through pores in the atmosphere, creating a bacterial loop cycle. Harmful toxins and pathogens invade the foreign substrate and recessive genes. The purpose of this study is gene editing and gene expression containing information to produce proteins and fight back pathogens. The Methodology of this study is the biosphere of RNA involved in the transcription and translation of DNA to detect several diseases. It is a narrative review of DNA biosynthesis in identifying the mutations for genes, chromosomes, or proteins. Genetic alterations in cancer development have urged many researchers to continue their expedition to find prevention strategies and treatments that are curable for the disease. Thus, gene therapies include gene augmentation, gene slicing, gene suicide, and gene editing by treating certain diseases. The momentum of replacing a damaged gene with a healthy gene using gene therapy in treating a wide range of diseases is quite impressive. An inborn child will have a healthy gene by inheriting it from the parent to the infant for further development. Circular RNAs are meant for protein synthesis. The nutrients are the building blocks of amino acids. The regrowth of new tissues is used to rejuvenate organ transplants. It is highly apprehensive for microbial cells to produce on their own. Not all bacteria are good, but the ones that fight off pathogens in the circular loops of plasmids. The DNA of bacterial cells is composed of chromosomal traits of inheritance in providing nutritious meals and becoming an antibody.
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Guo, Yu-Wei, Yang Liu, Peng-Cheng Huang, et al. "Adaptive Changes and Genetic Mechanisms in Organisms Under Controlled Conditions: A Review." International Journal of Molecular Sciences 26, no. 5 (2025): 2130. https://doi.org/10.3390/ijms26052130.
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Adaptive changes encompass physiological, morphological, or behavioral modifications occurring in organisms in response to specific environmental conditions. These modifications may become established within a population through natural selection. While adaptive changes can influence individuals or populations over short timeframes, evolution involves the inheritance and accumulation of these changes over extended periods under environmental pressures through natural selection. At present, addressing climate change, emerging infectious diseases, and food security are the main challenges faced by scientists. A comprehensive and profound understanding of the mechanisms of adaptive evolution is of great significance for solving these problems. The genetic basis of these adaptations can be examined through classical genetics, which includes stochastic gene mutations and chromosomal instability, as well as epigenetics, which involves DNA methylation and histone modifications. These mechanisms not only govern the rate and magnitude of adaptive changes but also affect the transmission of adaptive traits to subsequent generations. In the study of adaptive changes under controlled conditions, short-term controlled experiments are commonly utilized in microbial and animal research to investigate long-term evolutionary trends. However, the application of this approach in plant research remains limited. This review systematically compiles the findings on adaptive changes and their genetic foundations in organisms within controlled environments. It aims to provide valuable insights into fundamental evolutionary processes, offering novel theoretical frameworks and research methodologies for future experimental designs, particularly in the field of plant studies.
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Adam, Panagiotis S., Guillaume Borrel, and Simonetta Gribaldo. "Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes." Proceedings of the National Academy of Sciences 115, no. 6 (2018): E1166—E1173. http://dx.doi.org/10.1073/pnas.1716667115.
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Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood–Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of uncultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal–bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.
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Yang, Xiuqing, Jingwen Mao, Zongsheng Jiang, et al. "The Carboniferous Shikebutai Iron Deposit in Western Tianshan, Northwestern China: Petrology, Fe-O-C-Si Isotopes, and Implications for Iron Pathways." Economic Geology 114, no. 6 (2019): 1207–22. http://dx.doi.org/10.5382/econgeo.4681.
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Abstract Submarine volcanic-hosted iron deposits are important sources of iron ore in northwestern China. Here we present the petrological characteristics and coupled Fe-O, C, and Si isotope data of iron ores from the Shikebutai submarine volcanic-hosted hematite deposit in the Western Tianshan region. Several stratiform and lenticular hematite-dominated orebodies occur in Carboniferous submarine volcano-sedimentary sequences in this region. The ores are mainly composed of hematite, quartz, and minor siderite with distinct alternating iron-rich and silica-rich bands. The hematite shows δ56Fe and δ18O values in the range of –0.31 to 0.80‰ and 2.2 to 7.0‰, respectively, and the jasper yields δ30Si values of –1.90 to –1.20‰. Iron and Si were both derived from hydrothermal fluids related to submarine magmatism/volcanism. The Fe-bearing minerals in the Shikebutai deposit define distinct formation pathways. Hematite is the primary dehydrated Fe(III) oxyhydroxide, and the Fe isotope data indicate fractionation resulting from the partial oxidation of Fe(II). The O isotope data reflect inheritance from the submarine hydrothermal fluids source. Jasper was produced during coprecipitation of silica adsorbed onto the Fe(III) oxyhydroxides. The siderite-rich iron ore/volcaniclastic rock samples with a high and variable total organic carbon content (0.14–5.57%) show negative δ13C values (–3.0 to –1.1‰) and light δ56Fe values (–1.11 to –0.84‰). Our isotope data, together with the common occurrence of hematite inclusions in siderite, suggest that siderite was mainly produced by microbial dissimilatory iron reduction during diagenesis. The geologic, petrological, and isotopic data suggest that the Carboniferous Shikebutai deposit was precipitated through chemical and biogenic processes.
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Liu, Yuying, Baokun He, Thomas K. Hoang, Dat Q. Tran, and J. Marc Rhoads. "Deletion of adenosine A2A receptor blocks the beneficial effects of Lactobacillus reuteri on Treg-deficiency-induced autoimmunity." Journal of Immunology 200, no. 1_Supplement (2018): 176.21. http://dx.doi.org/10.4049/jimmunol.200.supp.176.21.
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Abstract The lack of Foxp3+ regulatory T cells (Tregs) causes a lethal, CD4+T cell-driven autoimmune disease in scurfy (SF) mice and humans characterized by immunodysregulation, polyendocrinopathy, enteropathy, with X-linked inheritance (or IPEX syndrome). We observed that adenosine 2A receptor (A2A) activation limits inflammation and tissue damage, and that Lactobacillus reuteri DSM 17938 (LR) modulates the abnormal fecal microbial community associated with the disease, stimulating the production of bioactive metabolites, especially inosine by activating A2A expressed on T cells. To conclusively provide evidence of a central role of A2A in the actions of LR, we generated A2A null SF mice (SF·A2A−/−). Male mice were given daily by gavage culture media (MRS) or LR in MRS (107CFU/day), starting at d8 to d22 for plasma and tissue analysis or long-term survival We found that A2A receptor deletion in SF mice did not affect early life events, the development of a lymphoproliferative disorder, or hyper-production of proinflammatory cytokines. LR treatment prolonged survival and reduced multi-organ inflammation in SF mice. In marked contrast, A2A receptor deletion reversed the effect of LR in prolonging lifespan in SF mice and negated the effects of LR on inflammation in the liver and lungs of SF mice. A2A deletion also inhibited LR-mediated reduction of TH1/TH2 cells and reversed the effect of LR on plasma pro-inflammatory cytokines. In conclusion, (a) the absence of the A2A receptor does not affect the development of disease in SF mice, and (b) the A2A receptor plays a critical role in immunomodulation produced by LR treatment. Lactobacillus reuteri and A2A receptor activation may have a role in other Treg dysfunction-mediated autoimmune diseases.
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Cote-L’Heureux, Auden, Xyrus X. Maurer-Alcalá, and Laura A. Katz. "Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events." PLOS Genetics 18, no. 6 (2022): e1010239. http://dx.doi.org/10.1371/journal.pgen.1010239.
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Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as the rapid spread of antibiotic resistance among bacteria and the origin of photosynthesis in eukaryotes. While lateral gene transfer (LGT) is recognized as an evolutionary force in prokaryotes, the role of LGT in eukaryotic evolution is less clear. With the exception of the transfer of genes from organelles to the nucleus, a process termed endosymbiotic gene transfer (EGT), the extent of interdomain transfer from prokaryotes to eukaryotes is highly debated. A common critique of studies of interdomain LGT is the reliance on the topology of single-gene trees that attempt to estimate more than one billion years of evolution. We take a more conservative approach by identifying cases in which a single clade of eukaryotes is found in an otherwise prokaryotic gene tree (i.e. exclusive presence). Starting with a taxon-rich dataset of over 13,600 gene families and passing data through several rounds of curation, we identify and categorize the function of 306 interdomain LGT events into diverse eukaryotes, including 189 putative EGTs, 52 LGTs into Opisthokonta (i.e. animals, fungi and their microbial relatives), and 42 LGTs nearly exclusive to anaerobic eukaryotes. To assess differential gene loss as an explanation for exclusive presence, we compare branch lengths within each LGT tree to a set of vertically-inherited genes subsampled to mimic gene loss (i.e. with the same taxonomic sampling) and consistently find shorter relative distance between eukaryotes and prokaryotes in LGT trees, a pattern inconsistent with gene loss. Our methods provide a framework for future studies of interdomain LGT and move the field closer to an understanding of how best to model the evolutionary history of eukaryotes.
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Курышева, Ольга Александровна, Андрей Васильевич Налетов та Дмитрий Иванович Масюта. "СИНДРОМ ВИСКОТТА–ОЛДРИЧА (СЛУЧАЙ ИЗ ПРАКТИКИ): АЛЛОГЕННАЯ ТРАНСПЛАНТАЦИЯ КОСТНОГО МОЗГА". Children's medicine of the North-West 12, № 4 (2024): 224–31. https://doi.org/10.56871/cmn-w.2024.26.82.019.
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В статье представлены результаты собственного клинического наблюдения случая синдрома Вискотта–Олдрича — комбинированного первичного иммунодефицита, который характеризуется Х-сцепленным рецессивным типом наследования, и у трети больных проявляется триадой: рецидивирующими микробно-воспалительными заболеваниями, экземой (атопическим дерматитом) и кровотечениями, обусловленными тромбоцитопенией и дисфункцией тромбоцитов. Заболевание встречается только у лиц мужского пола и составляет приблизительно 3% всех первичных иммунодефицитов. В приведенном клиническом примере диагноз пациенту установлен на основании типичной клинической картины (экзема, тромбоцитопения, иммунодефицит) и подтвержден методом молекулярно-генетической диагностики. В представленном клиническом примере актуальным является описание этапности проведения терапии пациенту, которая, несмотря на высокий риск развития жизнеугрожающих осложнений, завершилась проведением неродственной аллогенной трансплантации гемопоэтических стволовых клеток от полностью совместимого неродственного донора. В ходе последующего наблюдения за ребенком было установлено, что, несмотря на все возможные риски развития осложнений, было достигнуто удовлетворительное функционирование трансплантата с восстановлением кроветворения по тромбоцитарному ростку. Описаны посттрансплантационный период, осложнения, проведенная терапия и рекомендации. Изучение представленного клинического примера поможет повысить эффективность ранней диагностики синдрома Вискотта–Олдрича и своевременно выстроить правильный план лечения пациента. The article presents the results of our own clinical observation of a case of Wiskott-Aldrich syndrome, a combined primary immunodeficiency characterized by an X-linked recessive type of inheritance and manifested in a third of patients by a triad: recurrent microbial-inflammatory diseases, eczema (atopic dermatitis) and bleeding due to thrombocytopenia and platelet dysfunction. The disease occurs only in males and accounts for approximately 3% of all primary immunodeficiencies. In the given clinical example, the patient's diagnosis is based on a typical clinical picture (eczema, thrombocytopenia, immunodeficiency) and confirmed by the method of molecular genetic diagnostics. In the presented clinical example, it is relevant to describe the stages of therapy for a patient who, despite the high risk of life-threatening complications, ended with an unrelated allogeneic hematopoietic stem cell transplant from a fully compatible unrelated donor. During the follow-up of the child, it was found that, despite all the possible risks of complications, satisfactory functioning of the transplant was achieved with the restoration of platelet hematopoiesis. The post-transplant period, complications, therapy, and recommendations are described. The study of the presented clinical example will help to increase the effectiveness of early diagnosis of Wiskott-Aldrich syndrome and timely develop the correct treatment plan for the patient.
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Abdelfattah, Ahmed, Michael Wisniewski, Leonardo Schena, and Ayco J. M. Tack. "Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root." January 11, 2021. https://doi.org/10.1111/1462-2920.15392.
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While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe‐free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non‐randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities.
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Zapién-Campos, Román, Florence Bansept, Michael Sieber, and Arne Traulsen. "On the effect of inheritance of microbes in commensal microbiomes." BMC Ecology and Evolution 22, no. 1 (2022). http://dx.doi.org/10.1186/s12862-022-02029-2.
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Abstract Background Our current view of nature depicts a world where macroorganisms dwell in a landscape full of microbes. Some of these microbes not only transit but establish themselves in or on hosts. Although hosts might be occupied by microbes for most of their lives, a microbe-free stage during their prenatal development seems to be the rule for many hosts. The questions of who the first colonizers of a newborn host are and to what extent these are obtained from the parents follow naturally. Results We have developed a mathematical model to study the effect of the transfer of microbes from parents to offspring. Even without selection, we observe that microbial inheritance is particularly effective in modifying the microbiome of hosts with a short lifespan or limited colonization from the environment, for example by favouring the acquisition of rare microbes. Conclusion By modelling the inheritance of commensal microbes to newborns, our results suggest that, in an eco-evolutionary context, the impact of microbial inheritance is of particular importance for some specific life histories.
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Lu, Yuyang, Jia Gao, Ruo-Chen Xie, Hua Su, Yaoyao Zhang, and Wei Wang. "Inheritance of extraordinary metabolic activity from parental bacteria individuals." Proceedings of the National Academy of Sciences 122, no. 19 (2025). https://doi.org/10.1073/pnas.2502818122.
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Many phenotypic traits, such as fermentation activity, have been shown to be instable due to stochastic gene expression and environmental influence. While previous studies only have obtained understanding at the level of the microbial community, the fate of extraordinary traits of an individual through generations of reproduction has yet to be adequately investigated. This work uses the lactic acid bacteri Lactiplantibacillus plantarum as a research model to study the activity inheritance between parental generations and filial generations. An integrated single-cell manipulation strategy is established, including fluorescent screening using an extracellular pH probe and a microwell array, micropicking using a micropipette, and amplifying an individual bacterium via single-cell culture. Consequently, it is found that daughter bacteria can well inherit the strong acid-producing activity from their parental bacterial individuals, although as the reproduction proceeds over 30 generations, the offspring gradually regresses to the mediocre, thus setting a caveat for the limiting generations for desired inheritance. This is likely due to the deterioration of the cell living environment. This work illustrates the inheritable features of bacterial metabolic traits at the level of individual bacteria and is therefore fundamentally insightful for biotechnological applications like bioenergy production that require consistent or at least predictable metabolic performance.
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Khan, Dibyendu, Rajdeep Shaw, Ashutosh Kabiraj, Arpita Paul, and Rajib Bandopadhyay. "Microbial inheritance through seed: a clouded area needs to be enlightened." Archives of Microbiology 207, no. 1 (2025). https://doi.org/10.1007/s00203-024-04225-8.
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Chase, Alexander B., Douglas Sweeney, Mitchell N. Muskat, Dulce G. Guillén-Matus, and Paul R. Jensen. "Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites." mBio 12, no. 6 (2021). http://dx.doi.org/10.1128/mbio.02700-21.
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Microbial natural products are traditionally exploited for their pharmaceutical potential, yet our understanding of the evolutionary processes driving BGC evolution and compound diversification remains poorly developed. While HGT is recognized as an integral driver of BGC distributions, we find that the effects of vertical inheritance on BGC diversification had direct implications for species-level specialized metabolite production.