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Microbial Ecology Feb 2023Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and... (Review)
Review
Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.
Topics: Ecosystem; Soil; Soil Microbiology; Biodiversity; Microbiota; Climate Change
PubMed: 35112151
DOI: 10.1007/s00248-022-01962-5 -
Frontiers in Oral Health 2021In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for...
In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of species in dental caries in studies using NGS data. Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality. Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54-3.90); = 0.01]. . is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.
PubMed: 35048071
DOI: 10.3389/froh.2021.770917 -
Nutrients Dec 2021Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using... (Meta-Analysis)
Meta-Analysis
Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using high-throughput sequencing technologies. We conducted a systematic review in PubMed and Embase including 32 cross-sectional studies assessing the gut microbiome composition by high-throughput sequencing in obese and non-obese adults. A significantly lower alpha diversity (Shannon index) in obese versus non-obese adults was observed in nine out of 22 studies, and meta-analysis of seven studies revealed a non-significant mean difference (-0.06, 95% CI -0.24, 0.12, = 81%). At the phylum level, significantly more Firmicutes and fewer Bacteroidetes in obese versus non-obese adults were observed in six out of seventeen, and in four out of eighteen studies, respectively. Meta-analyses of six studies revealed significantly higher Firmicutes (5.50, 95% 0.27, 10.73, = 81%) and non-significantly lower Bacteroidetes (-4.79, 95% CI -10.77, 1.20, = 86%). At the genus level, lower relative proportions of and and higher , , , , , , , , , , , , and were found in obese versus non-obese adults. Although a proportion of studies found lower diversity and differences in gut microbiome composition in obese versus non-obese adults, the observed heterogeneity across studies precludes clear answers.
Topics: Bacteria; Feces; Gastrointestinal Microbiome; High-Throughput Nucleotide Sequencing; Humans; Obesity
PubMed: 35010887
DOI: 10.3390/nu14010012 -
Plants (Basel, Switzerland) Dec 2021Resurrection plants have an extraordinary ability to survive extreme water loss but still revive full metabolic activity when rehydrated. These plants are useful models... (Review)
Review
Resurrection plants have an extraordinary ability to survive extreme water loss but still revive full metabolic activity when rehydrated. These plants are useful models to understand the complex biology of vegetative desiccation tolerance. Despite extensive studies of resurrection plants, many details underlying the mechanisms of desiccation tolerance remain unexplored. To summarize the progress in resurrection plant research and identify unexplored questions, we conducted a systematic review of 15 model angiosperm resurrection plants. This systematic review provides an overview of publication trends on resurrection plants, the geographical distribution of species and studies, and the methodology used. Using the Preferred Reporting Items for Systematic reviews and Meta-Analyses protocol we surveyed all publications on resurrection plants from 2000 and 2020. This yielded 185 empirical articles that matched our selection criteria. The most investigated plants were (17.5%), (13.7%), (reclassified as ) (11.9%), (8.5%), and (8.1%), with all other species accounting for less than 8% of publications. The majority of studies have been conducted in South Africa, Bulgaria, Germany, and China, but there are contributions from across the globe. Most studies were led by researchers working within the native range of the focal species, but some international and collaborative studies were also identified. The number of annual publications fluctuated, with a large but temporary increase in 2008. Many studies have employed physiological and transcriptomic methodologies to investigate the leaves of resurrection plants, but there was a paucity of studies on roots and only one metagenomic study was recovered. Based on these findings we suggest that future research focuses on resurrection plant roots and microbiome interactions to explore microbial communities associated with these plants, and their role in vegetative desiccation tolerance.
PubMed: 34961255
DOI: 10.3390/plants10122784 -
Microbiome Dec 2021The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are... (Review)
Review
BACKGROUND
The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies.
METHODOLOGY
We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction.
RESULTS
We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168).
CONCLUSIONS
There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
Topics: Humans; Mass Screening; Microbiota; Public Health; South Africa; Uganda
PubMed: 34911583
DOI: 10.1186/s40168-021-01195-7 -
Nutrients Oct 2021Postprandial hyperglycaemia is associated with increased risk of cardiovascular disease. Recent studies highlight the role of the gut microbiome in influencing...
Postprandial hyperglycaemia is associated with increased risk of cardiovascular disease. Recent studies highlight the role of the gut microbiome in influencing postprandial glycaemic (PPG) and lipidaemic (PPL) responses. The authors of this review sought to address the question: "To what extent does individual gut microbiome diversity and composition contribute to PPG and PPL responses?". CINAHL Plus, PubMed, Web of Science, and the Cochrane Central Register of Controlled Trials (CENTRAL) databases were searched from January 2010 to June 2020. Following screening, 22 studies were eligible to be included in the current review. All trials reported analysis of gut microbiome diversity and composition and PPG and/or PPL. Results were reported according to the 'Preferred Reporting Items for Systematic Reviews and Meta-Analysis' (PRISMA) statement. Individual microbiota structure was found to play a key role in determining postprandial metabolic responses in adults and is attributed to a complex interplay of diet, microbiota composition, and metagenomic activity, which may be predicted by metagenomic analysis. Alterations of gut microbiota, namely relative abundance of bacterial phylum Actinobacteria and Proteobacteria, along with Enterobacteriaceae, were associated with individual variation in postprandial glycaemic response in adults. The findings of the current review present new evidence to support a personalised approach to nutritional recommendations and guidance for optimal health, management, and treatment of common metabolic disorders. In conclusion, personalised nutrition approaches based on individual microbial composition may improve postprandial regulation of glucose and lipids, providing a potential strategy to ameliorate cardiometabolic health outcomes.
Topics: Gastrointestinal Microbiome; Humans; Hyperglycemia; Hyperlipidemias; Nutritional Physiological Phenomena; Postprandial Period
PubMed: 34836140
DOI: 10.3390/nu13113887 -
BMC Microbiology Nov 2021Although recent studies have indicated that imbalance in the respiratory microbiome composition is linked to several chronic respiratory diseases, the association... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Although recent studies have indicated that imbalance in the respiratory microbiome composition is linked to several chronic respiratory diseases, the association between the lung microbiome and lung cancer has not been extensively studied. Conflicting reports of individual studies on respiratory microbiome alterations in lung cancer complicate the matter for specifying how the lung microbiome is linked to lung cancer. Consequently, as the first meta-analysis on this topic, we integrate publicly available 16S rRNA gene sequence data on lung tissue samples of lung cancer patients to identify bacterial taxa which differ consistently between case and control groups.
RESULTS
The findings of the current study suggest that the relative abundance of several bacterial taxa including Actinobacteria phylum, Corynebacteriaceae and Halomonadaceae families, and Corynebacterium, Lachnoanaerobaculum, and Halomonas genera is significantly decreased (p < 0.05) in lung tumor tissues of lung cancer patients in comparison with tumor-adjacent normal tissues.
CONCLUSIONS
Despite the underlying need for scrutinizing the findings further, the present study lays the groundwork for future research and adds to our limited understanding of the key role of the lung microbiome and its complex interaction with lung cancer. More data on demographic factors and tumor tissue types would help establish a greater degree of accuracy in characterizing the lung microbial community which accords with subtypes and stages of the disease and fully capturing the changes of the lung microbiome in lung cancer.
Topics: Adult; Aged; Aged, 80 and over; Bacteria; DNA, Bacterial; Female; Humans; Lung; Lung Neoplasms; Male; Microbiota; RNA, Ribosomal, 16S
PubMed: 34763672
DOI: 10.1186/s12866-021-02375-z -
Biology Oct 2021General gut microbial dysbiosis in diabetes mellitus, including gestational diabetes mellitus (GDM), has been reported in a large body of literature. However, evidence... (Review)
Review
General gut microbial dysbiosis in diabetes mellitus, including gestational diabetes mellitus (GDM), has been reported in a large body of literature. However, evidence investigating the association between specific taxonomic classes and GDM is lacking. Thus, we performed a systematic review of peer-reviewed observational studies and trials conducted among women with GDM within the last ten years using standard methodology. The National Institutes of Health (NIH) quality assessment tools were used to assess the quality of the included studies. Fourteen studies investigating microbial interactions with GDM were found to be relevant and included in this review. The synthesis of literature findings demonstrates that Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria phyla, such as , Ruminococcaceae, Enterobacteriaceae, , and were positively associated with GDM. In contrast, and , which produce butyrate, are negatively associated with GDM. These bacteria were associated with inflammation, adiposity, and glucose intolerance in women with GDM. Lack of good diet management demonstrated the alteration of gut microbiota and its impact on GDM glucose homeostasis. The majority of the studies were of good quality. Therefore, there is great potential to incorporate personalized medicine targeting microbiome modulation through dietary intervention in the management of GDM.
PubMed: 34681126
DOI: 10.3390/biology10101027 -
Frontiers in Physiology 2021Our understanding of human gut microbiota has expanded in recent years with the introduction of high-throughput sequencing methods. These technologies allow for the...
Our understanding of human gut microbiota has expanded in recent years with the introduction of high-throughput sequencing methods. These technologies allow for the study of metagenomic, metatranscriptomic, and metabolomic bacterial alterations as they relate to human disease. Work in this area has described the human gut microbiome in both healthy individuals and those with chronic gastrointestinal diseases, such as eosinophilic esophagitis (EoE). A systematic review of the current available literature on metagenomic, metatranscriptomic, and metabolomic changes in EoE was performed. This review was performed following the PRISMA guidelines for reporting systematic reviews and meta-analyses. All relevant publications up to March 2021 were retrieved using the search engines PubMed, Google Scholar, and Web of Science. They were then extracted, assessed, and reviewed. Only original studies published in English were included. A total of 46 potential manuscripts were identified for review. Twelve met criteria for further review based on relevance screening and 9 met criteria for inclusion, including 6 studies describing the microbiome in EoE and 3 detailing metabolomic/tissue biochemistry alterations in EoE. No published studies examined metatranscriptomic changes. Samples for microbiome analysis were obtained via esophageal biopsy ( = 3), esophageal string test ( = 1), salivary sampling ( = 1), or stool specimen ( = 1). Samples analyzing tissue biochemistry were obtained via esophageal biopsy ( = 2) and blood plasma ( = 1). There were notable differences in how samples were collected and analyzed. Metabolomic and tissue biochemical alterations were described using Raman spectroscopy, which demonstrated distinct differences in the spectral intensities of glycogen, lipid, and protein content compared to controls. Finally, research in proteomics identified an increase in the pro-fibrotic protein thrombospondin-1 in patients with EoE compared with controls. While there are notable changes in the microbiome, these differ with the collection technique and method of analysis utilized. Techniques characterizing metabolomics and tissue biochemistry are now being utilized to further study patients with EoE. The lack of published data related to the human microbiome, metagenome, metatranscriptome, and metabolome in patients with EoE highlights the need for further research in these areas.
PubMed: 34566693
DOI: 10.3389/fphys.2021.731034 -
Frontiers in Immunology 2021It has been hypothesized that gut and oral dysbiosis may contribute to the development of primary Sjögren's syndrome (pSS). The aim of this systematic review was to...
INTRODUCTION
It has been hypothesized that gut and oral dysbiosis may contribute to the development of primary Sjögren's syndrome (pSS). The aim of this systematic review was to assemble available data regarding the oral and gut microbiota in pSS and to compare them to data from healthy individuals and patients with dry symptoms without a diagnosis of Sjögren's syndrome or lupus disease to identify dysbiosis and discuss the results.
METHODOLOGY
Using the PRISMA guidelines, we systematically reviewed studies that compared the oral and gut microbiota of Sjögren's patients and controls. The PubMed database and Google Scholar were searched.
RESULTS
Two-hundred and eighty-nine studies were found, and 18 studies were included: 13 referred to the oral microbiota, 4 referred to the gut microbiota, and 1 referred to both anatomical sites. The most frequent controls were healthy volunteers and patients with sicca symptoms. The most common analysis method used was 16S-targeted metagenomics. The results were mostly heterogeneous, and the results regarding diversity were not always in accordance. Dysbiosis in pSS was not confirmed, and reduced salivary secretion seems to explain more microbial changes than the underlying disease.
CONCLUSION
These heterogeneous results might be explained by the lack of a standardized methodology at each step of the process and highlight the need for guidelines. Our review provides evidence that sicca patients seem to be more relevant than healthy subjects as a control group.
Topics: Control Groups; Dysbiosis; Humans; Microbiota; Sjogren's Syndrome
PubMed: 34394092
DOI: 10.3389/fimmu.2021.699011