@article {pmid35768947, year = {2022}, author = {Jing, H and Xiao, X and Zhang, Y and Li, Z and Jian, H and Luo, Y and Han, Z}, title = {Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0198821}, doi = {10.1128/spectrum.01988-21}, pmid = {35768947}, issn = {2165-0497}, support = {2018YFC0309800//National key R&D program of China/ ; 2016YFC0304905//National key R&D program of China/ ; 91751116//Training program of the major research plan of the national natural foundation of China/ ; 41776147//National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Archaea/genetics ; *Bacteria/genetics/metabolism ; *Microbiota/genetics ; Nitrogen/metabolism ; Oceans and Seas ; }, abstract = {The unique geological features of hadal trenches are known to influence both the structure and ecological function of microbial communities. It is also well known that heterotrophs and chemoautotrophs dominate the hadal and abyssal pelagic zones, respectively. Here, a metagenomic investigation was conducted on sediment samples obtained from the abyssal-hadal transition zone in the Mariana Trench to gain a better understanding of the general diversity and potential function of the core microbiome in this zone. A high level of cosmopolitanism existed in the core microbiome referred from a high community similarity among different stations. Niche differentiation along the fine-scale of different sediment layers was observed, especially for major archaeal groups, largely due to sediment depth and the source of organic matter. A prevalence of nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation in the abyssal-hadal biosphere was also demonstrated. The predominance of heterotrophic over chemolithoautotrophic pathways in this transition zone was found, and a high abundance of genes related to respiration and carbon fixation (i.e., the intact Calvin and rTCA cycles) were detected as well, which might reflect the intensive microbial activities known to occur in this deep biosphere. The presence of those metabolic processes and associated microbes were reflected by functional and genetic markers generated from the metagenomic data in the current study. However, their roles and contributions to the nitrogen/carbon biogeochemical cycles and flux in the abyssal-hadal transition zone still need further analysis. IMPORTANCE The Mariana Trench is the deepest oceanic region on earth, its microbial ecological exploration has become feasible with the rapid progress of submersible and metagenomic sequencing. We investigated the community compositions and metabolic functions of the core microbiome along the abyssal-hadal transition zone of the Mariana Trench, although most studies by far were focused on the pelagic zone. We found a predominance of heterotrophic groups and related metabolic pathways, which were closely associated with nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation.}, }
@article {pmid35608350, year = {2022}, author = {Tong, X and Yu, X and Du, Y and Su, F and Liu, Y and Li, H and Liu, Y and Mu, K and Liu, Q and Li, H and Zhu, J and Xu, H and Xiao, F and Li, Y}, title = {Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0041422}, doi = {10.1128/spectrum.00414-22}, pmid = {35608350}, issn = {2165-0497}, support = {2018YFC2000505//National Key Research and Development Program of China/ ; 2020YFC2009003//National Key Research and Development Program of China/ ; 2021-I2M-1-050//CAMS Innovation Fund for Medical Sciences/ ; 81870013//National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Cell-Free Nucleic Acids/genetics ; *Epstein-Barr Virus Infections ; Female ; Herpesvirus 4, Human ; Humans ; *Microbiota/genetics ; *Noninvasive Prenatal Testing ; Pregnancy ; Retrospective Studies ; }, abstract = {While circulating cell-free DNA (cfDNA) is becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a microbial cfDNA baseline in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Because noninvasive prenatal testing (NIPT) shares many similarities with the sequencing protocol of metagenomics, we utilized the standard low-pass whole-genome-sequencing-based NIPT to establish a microbial cfDNA baseline in healthy people. Sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening were retrospectively collected and reanalyzed for microbiome DNA screening. It was found that more than 95% of exogenous cfDNA was from bacteria, 3% from eukaryotes, and 0.4% from viruses, indicating the gut/environment origins of many microorganisms. Overall and regional abundance patterns were well illustrated, with huge regional diversity and complexity, and unique interspecies and symbiotic relationships were observed for TORCH organisms (Toxoplasma gondii, others [Treponema pallidum {causing syphilis}, hepatitis B virus {HBV}, and human parvovirus B19 {HPV-B19}], rubella virus, cytomegalovirus [CMV], and herpes simplex virus [HSV]) and another common virus, Epstein-Barr virus (EBV). To sum up, our study revealed the complexity of the baseline circulating microbial cfDNA and showed that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner. IMPORTANCE While circulating cell-free DNA (cfDNA) has been becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a baseline for microbial cfDNA in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Standard low-pass whole-genome-sequencing-based NIPT shares many similarities with the sequencing protocol for metagenomics and could provide a microbial cfDNA baseline in healthy people; thus, a reference cfDNA data set of the human microbiome was established with sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening. Our study revealed the complexity of circulating microbial cfDNA and indicated that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner, especially with regard to geographic patterns and coexistence networks.}, }
@article {pmid35604174, year = {2022}, author = {Zhang, Z and Nie, S and Sang, Y and Mo, S and Li, J and Kashif, M and Su, G and Yan, B and Jiang, C}, title = {Effects of Spartina alterniflora Invasion on Nitrogen Fixation and Phosphorus Solubilization in a Subtropical Marine Mangrove Ecosystem.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0068221}, doi = {10.1128/spectrum.00682-21}, pmid = {35604174}, issn = {2165-0497}, support = {No. 2019GXNSFFA245011//Natural Science Fund for Distinguished Young Scholars of Guangxi Zhuang Autonomous Region of China/ ; AD20297142//China-ASEAN International Innovative Center for Health Industry of Traditional Chinese Medicine/ ; No. GUIKEZY21195021//Funding Project of Chinese Central Government Guiding to the Guangxi Local Science and Technology Development/ ; No. YCSW2021064//Innovation Project of Guangxi Graduate Education/ ; }, mesh = {*Ecosystem ; Introduced Species ; Nitrogen Fixation ; *Phosphorus ; Poaceae/physiology ; Wetlands ; }, abstract = {Nitrogen fixation (NF) and phosphorus solubilization (PS) play a key role in maintaining the stability of mangrove ecosystems. In China, the invasion of Spartina alterniflora has brought a serious threat to the mangrove ecosystem. However, systematic research on NF and PS in mangrove sediments has not been conducted, and limited studies have focused on the response of NF and PS to S. alterniflora invasion, particularly at different sediment depths. In the present study, shotgun metagenomics and quantitative PCR were used to study the 0- to 100-cm sediment profile of the mangrove ecosystem in the Beibu Gulf of China. Results showed that the PS potential of mangrove sediments was primarily caused by enzymes encoded by phoA, phoD, ppx, ppa, and gcd genes. S. alterniflora changed environmental factors, such as total nitrogen, total phosphorus, and total organic carbon, and enhanced the potential of NF and PS in sediments. Moreover, most microorganisms involved in NF or PS (NFOPSMs) responded positively to the invasion of S. alterniflora. Cd, available iron, and salinity were the key environmental factors that affected the distribution of NF and PS genes (NFPSGs) and NFOPSMs. A strong coupling effect was observed between NF and PS in the mangrove ecosystem. S. alterniflora invasion enhanced the coupling of NF and PS and the interaction of microorganisms involved in NF and PS (NFAPSM), thereby promoting the turnover of NP and improving sediment quality. Finally, 108 metagenome-assembled genomes involved in NF or PS were reconstructed to further evaluate NFOPSMs. IMPORTANCE This study revealed the efficient nutrient cycling mechanism of mangroves. Positive coupling effects were observed in sediment quality, NF and PS processes, and NFOPSMs with the invasion of S. alterniflora. This research contributed to the understanding of the effects of S. alterniflora invasion on the subtropical mangrove ecosystem and provided theoretical guidance for mangrove protection, restoration, and soil management. Additionally, novel NFOPSMs provided a reference for the development of marine biological fertilizers.}, }
@article {pmid35579429, year = {2022}, author = {Devi, P and Maurya, R and Mehta, P and Shamim, U and Yadav, A and Chattopadhyay, P and Kanakan, A and Khare, K and Vasudevan, JS and Sahni, S and Mishra, P and Tyagi, A and Jha, S and Budhiraja, S and Tarai, B and Pandey, R}, title = {Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0231121}, doi = {10.1128/spectrum.02311-21}, pmid = {35579429}, issn = {2165-0497}, support = {INV-033578//Bill and Melinda Gates Foundation (BMGF)/ ; }, mesh = {*Achromobacter denitrificans/genetics ; Bacillus cereus ; *COVID-19 ; *Coinfection ; Humans ; *Microbiota/genetics ; Phylogeny ; Prospective Studies ; SARS-CoV-2/genetics ; Severity of Illness Index ; }, abstract = {The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.}, }
@article {pmid35536037, year = {2022}, author = {Hu, C and Beyda, ND and Garey, KW}, title = {A Vancomycin HPLC Assay for Use in Gut Microbiome Research.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0168821}, doi = {10.1128/spectrum.01688-21}, pmid = {35536037}, issn = {2165-0497}, support = {U01AI124290//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {Anti-Bacterial Agents ; Chromatography, High Pressure Liquid/methods ; *Gastrointestinal Microbiome ; Humans ; Reproducibility of Results ; *Vancomycin/pharmacokinetics ; }, abstract = {The human microbiome project has revolutionized our understanding of the interaction between commensal microbes and human health. By far, the biggest perturbation of the microbiome involves use of broad-spectrum antibiotics excreted in the gut. Thus, pharmacodynamics of microbiome changes in relation to drug exposure pharmacokinetics is an emerging field. However, reproducibility studies are necessary to develop the field. A simple and fast high-performance liquid chromatography-photodiode array detector (HPLC) method was validated for quantitative fecal vancomycin analysis. Reproducibility of results were tested based on sample storage time, homogeneity of antibiotic within stool, and concentration consistency after lyophilization. The HPLC method enabled the complete elution of vancomycin within ~4.2 min on the reversed-phase C18 column under the isocratic elution mode, with excellent recovery (85% to 110%) over a 4-log, quantitative range (0.4-100 μg/mL). Relative standard derivations (RSD) of intra-day and inter-day results ranged from 0.4% to 5.4%. Using sample stool aliquots of various weights consistently demonstrated similar vancomycin concentrations (mean RSD: 6%; range: 2-16%). After correcting for water concentrations, vancomycin concentrations obtained after lyophilization were similar to the concentrations obtained from the original samples (RSD less than 10%). These methodologies establish sample condition standards for a quantitative HPLC to enable vancomycin pharmacokinetic studies with the human microbiome. IMPORTANCE Research on antibiotic effect on the gut microbiome is an emerging field with standardization of research methods needed. In this study, a simple and fast high-performance liquid chromatography method was validated for quantitative fecal vancomycin analysis. Reproducibility of results were tested to standardize storage time, homogeneity of antibiotic within stool, and concentration consistency after lyophilization. These methodologies establish sample condition standards for a quantitative HPLC to enable vancomycin pharmacokinetic studies with the human microbiome.}, }
@article {pmid35475684, year = {2022}, author = {Rubin, IMC and Mollerup, S and Broholm, C and Knudsen, SB and Baker, A and Helms, M and Holm, MKA and Kallemose, T and Westh, H and Dahl Knudsen, J and Pinholt, M and Petersen, AM}, title = {No Effect of Lactobacillus rhamnosus GG on Eradication of Colonization by Vancomycin-Resistant Enterococcus faecium or Microbiome Diversity in Hospitalized Adult Patients.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0234821}, doi = {10.1128/spectrum.02348-21}, pmid = {35475684}, issn = {2165-0497}, support = {Research Grant//Hvidovre University Hospital/ ; Indirect research grant//Chr.Hansen/ ; }, mesh = {Adult ; Aged ; Child ; *Enterococcus faecium ; *Gram-Positive Bacterial Infections/drug therapy ; Humans ; *Lactobacillus rhamnosus ; *Microbiota ; *Probiotics/therapeutic use ; Vancomycin/pharmacology/therapeutic use ; *Vancomycin-Resistant Enterococci ; }, abstract = {The purpose of this trial was to evaluate the efficacy of a 4-week supplementation of Lactobacillus rhamnosus GG (LGG) in eliminating the gastrointestinal carrier state of vancomycin-resistant Enterococcus faecium (VREfm) in hospitalized adults. The primary outcome of the study was the number of patients with cleared VREfm colonization after the 4-week intervention. Secondary outcomes were clearance of VREfm colonization at weeks 8, 16, and 24, number of VREfm infections (isolated from nonintestinal foci), and changes in fecal microbiome diversity after the intervention. The trial was a multicenter, randomized, double-blind, placebo-controlled trial in hospitalized adult VREfm carriers. Patients were enrolled and randomized to receive 60 billion CFU of LGG daily or placebo for 4 weeks. For a subgroup of patients, rectal swabs for VREfm were collected also at 8, 16, and 24 weeks and analyzed using shotgun metagenomics. Patients ingesting a minimum of 50% of the probiotic during the 4-week intervention were included in subsequent outcome analyses (48 of 81 patients). Twelve of 21 patients in the LGG group (57%) compared to 15 of 27 patients in the placebo group (56%) cleared their VREfm carriage. Eighteen patients completed the entire 24-week intervention with the same minimum compliancy. Of these, almost 90% in both groups cleared their VREfm carriage. We found a statistically significant difference between VREfm clearers and nonclearers regarding metronidazole and vancomycin usage as well as length of hospitalization after inclusion. The microbiome analyses revealed no significant difference in alpha diversity between the LGG and the placebo group. Beta diversity differed between the groups and the different time points. This study did not show an effect of LGG in eradication of VREfm after a 4-week intervention. IMPORTANCE Whereas other studies exploring the effect of L. rhamnosus in clearing VREfm from the intestine included children and adults, with a wider age range, our study consisted of a geriatric patient cohort. The natural clearance of VREfm in this study was almost 60% after 4 weeks, thus much higher than described previously. Also, this study characterizes the microbiome of VREfm patients in detail. This article showed no effect of the probiotic L. rhamnosus in clearing VREfm from the intestine of patients.}, }
@article {pmid35435739, year = {2022}, author = {Verbanic, S and Deacon, JM and Chen, IA}, title = {The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0277721}, doi = {10.1128/spectrum.02777-21}, pmid = {35435739}, issn = {2165-0497}, support = {DP2GM123457//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Camille Dreyfus Teacher-Scholar//Camille and Henry Dreyfus Foundation (Dreyfus Foundation)/ ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Humans ; Metagenomics ; *Microbiota ; Virome ; *Viruses/genetics ; Wound Healing ; }, abstract = {Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds (diabetic, venous, arterial, or pressure) before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations with covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes. IMPORTANCE Chronic wounds are an increasing medical burden. These wounds are known to be rich in microbial content, including both bacteria and bacterial viruses (phages). The viruses may play an important role in shaping bacterial community structure and function. We analyzed the virome and bacterial composition of 20 patients with chronic wounds. The viruses found in wounds are highly diverse compared to normal skin, unlike the bacterial composition, where diversity is decreased. These data represent an initial look at this relatively understudied component of the chronic wound microbiome and may help inform future phage-based interventions.}, }
@article {pmid35765106, year = {2022}, author = {Urbaniak, C and Morrison, MD and Thissen, JB and Karouia, F and Smith, DJ and Mehta, S and Jaing, C and Venkateswaran, K}, title = {Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {100}, pmid = {35765106}, issn = {2049-2618}, support = {NNH14ZTT002N/NASA/NASA/United States ; NASA Postdoctorsal Program Fellowship/NASA/NASA/United States ; 80NSSC18K0113/NASA/NASA/United States ; 80NSSC18K0113/NASA/NASA/United States ; }, mesh = {Bacteria/genetics ; Humans ; *Malassezia ; Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months.<br><br>METHODS: Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results.<br><br>RESULTS: Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 105 cfu/m2 CONCLUSIONS: Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity. Video Abstract.}, }
@article {pmid35763072, year = {2022}, author = {Wang, Z and Zhang, Z and Lu, C and Zhou, J and Wang, Z and Han, J and Su, X}, title = {Effects of Sporisorium reiliana polysaccharides and Phoenix dactylifera monosaccharides on the gut microbiota and serum metabolism in mice with fructose-induced hyperuricemia.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {436}, pmid = {35763072}, issn = {1432-072X}, support = {ZS20190105//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ ; Y202146257//General Project of Zhejiang Provincial Department of Education/ ; }, mesh = {Animals ; Fructose/adverse effects ; *Gastrointestinal Microbiome ; *Hyperuricemia/chemically induced/drug therapy ; Mice ; Monosaccharides ; *Phoeniceae ; Polysaccharides ; Uric Acid ; }, abstract = {In recent decades, the prevalence of hyperuricemia has increased, and dietary fructose is an important risk factor for the development of this disease. This study investigated and compared the effects of Sphacelotheca reiliana polysaccharides and Phoenix dactylifera monosaccharides on a series of physiological and biochemical indicators and on the metagenomes and serum metabolites in mice with hyperuricemia caused by a high-fructose diet. S. reiliana polysaccharides inhibited uric acid biosynthesis and promoted uric acid excretion, thereby alleviating the hyperuricemia phenotype. In addition, hyperuricemia was closely related to the gut microbiota. After treatment with S. reiliana polysaccharides, the abundances of Bacteroidetes and Proteobacteria in the mouse intestines were decreased, the expression of genes involved in glycolysis/gluconeogenesis metabolic pathways and purine metabolism was downregulated, and the dysfunction of the gut microbiota was alleviated. With regard to serum metabolism, the abundance of hippuric acid, uridine, kynurenic acid, propionic acid and arachidonoyl decreased, and the abundances of serum metabolites in inflammatory pathways involved in kidney injury and gout, such as bile acid metabolism, purine metabolism and tryptophan metabolism pathways, decreased. P. dactylifera monosaccharides aggravated hyperuricemia. This research provides a valuable reference for the development of sugar applications.}, }
@article {pmid35536001, year = {2022}, author = {Higginson, EE and Sayeed, MA and Pereira Dias, J and Shetty, V and Ballal, M and Srivastava, SK and Willis, I and Qadri, F and Dougan, G and Mutreja, A}, title = {Microbiome Profiling of Enterotoxigenic Escherichia coli (ETEC) Carriers Highlights Signature Differences between Symptomatic and Asymptomatic Individuals.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0015722}, doi = {10.1128/mbio.00157-22}, pmid = {35536001}, issn = {2150-7511}, support = {NIHR 200640//National Institute for Health Research (NIHR)/ ; //International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B)/ ; 106158/Z/14/Z//Wellcome Trust (WT)/ ; 617 OPP1141321//Bill and Melinda Gates Foundation (GF)/ ; }, mesh = {Adult ; Bacteria/genetics ; Child ; Diarrhea/microbiology ; *Enterotoxigenic Escherichia coli/genetics ; *Escherichia coli Infections/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in children in low- and middle-income countries (LMICs). However, large-scale pathogen burden studies in children have identified ETEC in the guts of both symptomatic patients and controls. The factors that influence this balance are poorly understood, but it is postulated that the gut microbiome may play a role in either resistance or progression to disease. In this study, we profiled the microbiomes of children and adults from Bangladesh who were asymptomatically or symptomatically infected with ETEC. Symptomatic patients had significantly higher numbers of sequenced reads mapping to both E. coli and two ETEC toxins, suggesting higher bacterial burden. They were also significantly more likely to be coinfected with enteroaggregative E. coli (EAEC) and had higher proportions of other Gammaproteobacteria, including Klebsiella, Salmonella, and Haemophilus. Colonization with ETEC was also associated with increased prevalence of antimicrobial resistance (AMR) genes, most notably those of the β-lactamase class. Taxonomic profiles were distinctly different between all groups in both species richness and composition, although the direction of these changes was different in adults and children. As seen previously, children with high E. coli burdens also had higher proportions of Streptococcus spp., while healthy children were more heavily colonized by Bifidobacterium spp. Our study provides insight into the microbiome changes that occur upon infection with ETEC in an endemic setting and provides rationale for future studies investigating how the microbiome may protect or predispose individuals to symptomatic infections with gastrointestinal pathogens. IMPORTANCE Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in children in low- and middle-income countries. However, these bacteria are often identified in both patients and healthy controls. We do not yet understand why only some people get sick, but it has been suggested that the gut microbiome might play a role. In this study, we used metagenomic sequencing to profile the gut microbiomes of individuals in Bangladesh, with or without a symptomatic ETEC infection. In general, individuals with high levels of ETEC also harbored other pathogenic E. coli strains, higher proportions of Gammaproteobacteria such as Salmonella and Klebsiella, and a higher burden of antimicrobial resistance genes in their guts. Healthy children, in contrast, had higher levels of bifidobacteria. These data confirm that the composition of the gut microbiome is different between symptomatic and asymptomatic people and provides important preliminary information on the impact of the gut microbiome in intestinal infections.}, }
@article {pmid35502903, year = {2022}, author = {Brealey, JC and Lecaudey, LA and Kodama, M and Rasmussen, JA and Sveier, H and Dheilly, NM and Martin, MD and Limborg, MT}, title = {Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0067922}, doi = {10.1128/mbio.00679-22}, pmid = {35502903}, issn = {2150-7511}, support = {901436//Fiskeri - og havbruksnæringens forskningsfond (FHF)/ ; DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; 817729//European Union Horizon 2020/ ; }, mesh = {Animals ; Bacteria/genetics ; *Cestoda/genetics ; Dysbiosis ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Parasites ; }, abstract = {The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.}, }
@article {pmid34897962, year = {2022}, author = {Sahu, RP and Kazy, SK and Bose, H and Mandal, S and Dutta, A and Saha, A and Roy, S and Dutta Gupta, S and Mukherjee, A and Sar, P}, title = {Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India.}, journal = {Environmental microbiology}, volume = {24}, number = {6}, pages = {2837-2853}, doi = {10.1111/1462-2920.15867}, pmid = {34897962}, issn = {1462-2920}, support = {MoES/PO(SEISMO)/1(288)/2016//Ministry of Earth Sciences/ ; }, mesh = {Bacteria ; Carbon Cycle ; *Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37 × 106) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co-occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient- and energy-limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy.}, }
@article {pmid35761577, year = {2022}, author = {Kothe, CI and Mohellibi, N and Renault, P}, title = {Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111265}, doi = {10.1016/j.foodres.2022.111265}, pmid = {35761577}, issn = {1873-7145}, mesh = {Animals ; Biodiversity ; Brazil ; *Cheese/analysis ; Food Microbiology ; *Lactobacillales/genetics ; *Lactococcus lactis/genetics ; Metagenomics ; Streptococcus thermophilus/genetics ; Yeasts ; }, abstract = {Brazilian artisanal cheeses date from the first Portuguese settlers and evolved via local factors, resulting in unique products that are now part of the patrimony and identity of different Brazilian regions. In this study, we combined several culture-independent approaches, including 16S/ITS metagenetics, assembly- and deep profiling-metagenomics to characterize the originality of the microbiota of five varieties of Brazilian artisanal cheeses from the South and Southeast regions of Brazil. Their core microbiota contained mainly lactic acid bacteria (LAB), of which Lactococcus lactis subsp. lactis was the most frequent, followed by Streptococcus thermophilus in the South region. Moreover, several samples from the Southeast region contained, as dominant LAB, two other food Streptococci belonging to a new species of the salivarius group and S. infantarius. Rinds of samples from the Southeast region were dominated by the halotolerant bacterium Corynebacterium variabile, and the yeasts Diutina catenulata, followed by Debaryomyces hansenii and Kodamaea ohmeri. Rinds from the South region contained mainly LAB due to their short ripening time, and the predominant yeast was D. hansenii. Phylogenomic analysis based on L. lactis metagenome-assembled genomes (MAGs) showed that most Brazilian strains are closely related and form a different clade from those whose genomes are available at this time, indicating that they belong to a specific group. Lastly, functional analysis showed that S. infantarius acquired a ∼ 26 kb DNA fragment from S. thermophilus starter strains that carry the LacSZ system, allowing fast lactose assimilation, an adaptation advantage for growth in milk. Finally, our study identified several areas of concern, such as the presence of somatic cell DNA and high levels of antibiotic resistance genes in several cheese microbiota, suggesting that milk from diseased animals may still be used occasionally. Overall, the data from this study highlight the potential value of the traditional and artisanal cheese production network in Brazil, and provide a metagenomic-based scheme to help manage this resource safely.}, }
@article {pmid35761554, year = {2022}, author = {Sequino, G and Valentino, V and Villani, F and De Filippis, F}, title = {Omics-based monitoring of microbial dynamics across the food chain for the improvement of food safety and quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111242}, doi = {10.1016/j.foodres.2022.111242}, pmid = {35761554}, issn = {1873-7145}, mesh = {*Food Chain ; Food Safety ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {The diffusion of high-throughput sequencing has dramatically changed the study of food microbial ecology. Amplicon-based description of the microbial community may be routinary implemented in the food industry to understand how the processing parameters and the raw material quality may affect the microbial community of the final product, as well as how the community changes during the shelf-life. In addition, application of shotgun metagenomics may represent an invaluable resource to understand the functional potential of the microbial community, identifying the presence of spoilage-associated activities or genes related to pathogenesis. Finally, retrieving Metagenome-Assembled Genomes (MAGs) of relevant species may be useful for strain-tracking along the food chain and in case of food poisoning outbreaks. This review gives an overview of the possible applications of sequencing-based approaches in the study of food microbial ecology, highlighting limitations that still prevent the spreading of these techniques to the food industry.}, }
@article {pmid35762794, year = {2022}, author = {Roguet, A and Newton, RJ and Eren, AM and McLellan, SL}, title = {Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0011822}, doi = {10.1128/msystems.00118-22}, pmid = {35762794}, issn = {2379-5077}, abstract = {Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.}, }
@article {pmid35752638, year = {2022}, author = {Lemos, LN and de Carvalho, FM and Santos, FF and Valiatti, TB and Corsi, DC and de Oliveira Silveira, AC and Gerber, A and Guimarães, APC and de Oliveira Souza, C and Brasiliense, DM and Maia Castelo-Branco, DSC and Anzai, EK and Bessa-Neto, FO and de Melo, GM and de Souza, GH and Ferraz, LFC and de Nazaré Miranda Bahia, M and Mattos, MS and da Silva, RGB and Veiga, R and Simionatto, S and Monteiro, WAP and de Oliveira Lima, WA and Kiffer, CRV and Cayô, R and Gales, AC and de Vasconcelos, ATR}, title = {Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {366}, pmid = {35752638}, issn = {2052-4463}, mesh = {Animals ; Archaea/genetics ; Cattle ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Metagenomics ; Pilot Projects ; Swine ; }, abstract = {The One Health concept is a global strategy to study the relationship between human and animal health and the transfer of pathogenic and non-pathogenic species between these systems. However, to the best of our knowledge, no data based on One Health genome-centric metagenomics are available in public repositories. Here, we present a dataset based on a pilot-study of 2,915 metagenome-assembled genomes (MAGs) of 107 samples from the human (N = 34), cattle (N = 28), swine (N = 15) and poultry (N = 30) gut microbiomes. Samples were collected from the five Brazilian geographical regions. Of the draft genomes, 1,273 were high-quality drafts (≥90% of completeness and ≤5% of contamination), and 1,642 were medium-quality drafts (≥50% of completeness and ≤10% of contamination). Taxonomic predictions were based on the alignment and concatenation of single-marker genes, and the most representative phyla were Bacteroidota, Firmicutes, and Proteobacteria. Many of these species represent potential pathogens that have already been described or potential new families, genera, and species with potential biotechnological applications. Analyses of this dataset will highlight discoveries about the ecology and functional role of pathogens and uncultivated Archaea and Bacteria from food-producing animals and humans. Furthermore, it also represents an opportunity to describe new species from underrepresented taxonomic groups.}, }
@article {pmid35751094, year = {2022}, author = {Fritsch, DA and Jackson, MI and Wernimont, SM and Feld, GK and MacLeay, JM and Brejda, JJ and Cochrane, CY and Gross, KL}, title = {Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {245}, pmid = {35751094}, issn = {1746-6148}, mesh = {Animals ; Diarrhea/veterinary ; Diet/veterinary ; Dietary Fiber/therapeutic use ; *Dog Diseases/drug therapy ; Dogs ; Feces ; Indoles ; Inflammation/veterinary ; *Microbiota ; Prospective Studies ; }, abstract = {BACKGROUND: Chronic large bowel diarrhea is a common occurrence in pet dogs. While nutritional intervention is considered the primary therapy, the metabolic and gut microfloral effects of fiber and polyphenol-enriched therapeutic foods are poorly understood.<br><br>METHODS: This prospective clinical study enrolled 31 adult dogs from private veterinary practices with chronic, active large bowel diarrhea. Enrolled dogs received a complete and balanced dry therapeutic food containing a proprietary fiber bundle for 56 days. Metagenomic and metabolomic profiling were performed on fecal samples at Days 1, 2, 3, 14, 28, and 56; metabolomic analysis was conducted on serum samples taken at Days 1, 2, 3, 28, and 56.<br><br>RESULTS: The dietary intervention improved clinical signs and had a clear effect on the gut microfloral metabolic output of canines with chronic diarrhea, shifting gut metabolism from a predominantly proteolytic to saccharolytic fermentative state. Microbial metabolism of tryptophan to beneficial indole postbiotics and the conversion of plant-derived phenolics into bioavailable postbiotics were observed. The intervention altered the endocannabinoid, polyunsaturated fatty acid, and sphingolipid profiles, suggesting a modulation in gastrointestinal inflammation. Changes in membrane phospholipid and collagen signatures were indicative of improved gut function and possible alleviation of the pathophysiology related to chronic diarrhea.<br><br>CONCLUSIONS: In dogs with chronic diarrhea, feeding specific dietary fibers increased gut saccharolysis and bioavailable phenolic and indole-related compounds, while suppressing putrefaction. These changes were associated with improved markers of gut inflammation and stool quality.}, }
@article {pmid35751044, year = {2022}, author = {Maeda, Y and Motooka, D and Kawasaki, T and Oki, H and Noda, Y and Adachi, Y and Niitsu, T and Okamoto, S and Tanaka, K and Fukushima, K and Amiya, S and Hara, R and Oguro-Igashira, E and Matsuki, T and Hirata, H and Takeda, Y and Kida, H and Kumanogoh, A and Nakamura, S and Takeda, K}, title = {Longitudinal alterations of the gut mycobiota and microbiota on COVID-19 severity.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {572}, pmid = {35751044}, issn = {1471-2334}, support = {20fk0108265//Japan Agency for Medical Research and Development/ ; 18gm1010005//AMED-CREST grants/ ; }, mesh = {*COVID-19 ; Enterococcus ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; SARS-CoV-2 ; }, abstract = {BACKGROUND: The impact of SARS-CoV-2 infection on the gut fungal (mycobiota) and bacterial (microbiota) communities has been elucidated individually. This study analyzed both gut mycobiota and microbiota and their correlation in the COVID-19 patients with severe and mild conditions and follow-up to monitor their alterations after recovery.<br><br>METHODS: We analyzed the gut mycobiota and microbiota by bacterial 16S and fungal ITS1 metagenomic sequencing of 40 severe patients, 38 mild patients, and 30 healthy individuals and reanalyzed those of 10 patients with severe COVID-19 approximately 6 months after discharge.<br><br>RESULTS: The mycobiota of the severe and mild groups showed lower diversity than the healthy group, and in some, characteristic patterns dominated by a single fungal species, Candida albicans, were detected. Lower microbial diversity in the severe group was observed, but no differences in its diversity or community structure were detected between the mild and healthy groups. The microbiota of the severe group was characterized by an increase in Enterococcus and Lactobacillus, and a decrease in Faecalibacterium and Bacteroides. The abundance of Candida was positively correlated with that of Enterococcus in patients with COVID-19. After the recovery of severe patients, alteration of the microbiota remained, but the mycobiota recovered its diversity comparable to that of mild and healthy groups.<br><br>CONCLUSION: In mild cases, the microbiota is stable during SARS-CoV-2 infection, but in severe cases, alterations persist for 6 months after recovery.}, }
@article {pmid35751037, year = {2022}, author = {Li, J and Zhao, Q and Huang, JP and Jia, JY and Zhu, TF and Hong, T and Su, J}, title = {The functional microbiota of on- and off-year moso bamboo (Phyllostachys edulis) influences the development of the bamboo pest Pantana phyllostachysae.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {307}, pmid = {35751037}, issn = {1471-2229}, mesh = {Animals ; Gene Expression Regulation, Plant ; Larva ; *Microbiota ; *Moths ; Plant Leaves ; Poaceae ; }, abstract = {BACKGROUND: Development of Pantana phyllostachysae, a moso bamboo pest, is affected by its diet. Understanding the mechanism underlying the different insect-resistant capacities of on- and off-year moso bamboo fed by P. phyllostachysae is crucial for managing pest outbreaks. As microbes were proven to influence plant immunity, we compared gut microbial communities of P. phyllostachysae with different diets by metabarcoding sequencing. By using sterilization assay, microbes were removed from leaf surfaces, and thus we confirmed that microbes inhabiting moso bamboo leaves impact the weight of P. phyllostachysae larva. Furthermore, the gut microbial communities of P. phyllostachysae fed on on- and off-year bamboo leaves were compared, to identify the functional microbial communities that impact the interaction between bamboo leaves and P. phyllostachysae.<br><br>RESULTS: We found that species from orders Lactobacillales and Rickettsiales are most effective within functional microbiota. Functional prediction revealed that gut microbes of larva fed on on-year leaves were related to naphthalene degradation, while those fed on off-year leaves were related to biosynthesis of ansamycins, polyketide sugar unit biosynthesis, metabolism of xenobiotics, and tetracycline biosynthesis. Most functional microbes are beneficial to the development of larva that feed on on-year bamboo leaves, but damage the balance of intestinal microenvironment and immune systems of those larva that feed on off-year leaves.<br><br>CONCLUSIONS: This work developed an efficient strategy for microbiome research of Lepidopteran insects and provided insights into microbiota related to the interaction between host plants and P. phyllostachysae. We provided microbial candidates for the ecological control of P. phyllostachysae according to the function of effective microbiota.}, }
@article {pmid35691354, year = {2022}, author = {Silveira, DD and Farooq, AJ and Wallace, SJ and Lapolli, FR and Nivala, J and Weber, KP}, title = {Structural and functional spatial dynamics of microbial communities in aerated and non-aerated horizontal flow treatment wetlands.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 4}, pages = {156600}, doi = {10.1016/j.scitotenv.2022.156600}, pmid = {35691354}, issn = {1879-1026}, mesh = {*Environmental Pollutants ; *Microbiota ; RNA, Ribosomal, 16S ; Waste Disposal, Fluid/methods ; *Water Purification/methods ; Wetlands ; }, abstract = {A multiphasic study using structural and functional analyses was employed to investigate the spatial dynamics of the microbial community within five horizontal subsurface flow treatment wetlands (TWs) of differing designs in Germany. The TWs differed in terms of the depth of media saturation, presence of plants (Phragmites australis), and aeration. In addition to influent and effluent water samples, internal samples were taken at different locations (12.5 %, 25 %, 50 %, and 75 % of the fractional distance along the flow path) within each system. 16S rRNA sequencing was used for the investigation of microbial community structure and was compared to microbial community function and enumeration data. The microbial community structure in the unaerated systems was similar, but different from the aerated TW profiles. Spatial positioning along the flow path explained the majority of microbial community dynamics/differences within this study. This was mainly attributed to the availability of nutrients closer to the inlet which also regulated the fixed biofilm/biomass densities. As the amount of fixed biofilm decreased from the inlet to the TW outlets, structural diversity increased, suggesting different microbial communities were present to handle the more easily utilized/degraded pollutants near the inlet vs. the more difficult to degrade and recalcitrant pollutants closer to the outlets. This study also confirmed that effluent water samples do not accurately describe the microbial communities responsible for water treatment inside a TW, highlighting the importance of using internal samples for investigating microbial communities in TWs. The results of this study reinforce an existing knowledge gap regarding the potential for TW design modifications which incorporate microbial community spatial dynamics (heterogeneity). It is suggested that utilizing step-feeding could allow for improved water treatment within the same areal footprint, and modifications enhancing co-metabolic processes could assist in improving the treatment of more difficult to degrade or recalcitrant compounds such as micropollutants.}, }
@article {pmid35597403, year = {2022}, author = {Kim, DW and Jeong, HS and Kim, E and Lee, H and Choi, CH and Lee, SJ}, title = {Oral delivery of stem-cell-loaded hydrogel microcapsules restores gut inflammation and microbiota.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {347}, number = {}, pages = {508-520}, doi = {10.1016/j.jconrel.2022.05.028}, pmid = {35597403}, issn = {1873-4995}, mesh = {Animals ; Capsules ; Hydrogels/pharmacology ; Inflammation ; *Inflammatory Bowel Diseases/drug therapy ; *Mesenchymal Stem Cells ; Mice ; *Microbiota ; }, abstract = {Mesenchymal stem cells (MSCs) are an attractive candidate for the treatment of inflammatory bowel disease (IBD), but their poor delivery rate to an inflamed colon is a major factor hampering the clinical potential of stem cell therapies. Moreover, there remains a formidable hurdle to overcome with regard to survival and homing in to injured sites. Here, we develop a strategy utilizing monodisperse hydrogel microcapsules with a thin intermediate oil layer prepared by a triple-emulsion drop-based microfluidic approach as an in-situ oral delivering carrier. The oral delivery of stem-cell-loaded hydrogel microcapsules (SC-HM) enhances MSC survival and retention in the hostile stomach environment due to the intermediate oil layer and low value of the overall stiffness, facilitating programmable cell release during gastrointestinal peristalsis. SC-HM is shown to induce tissue repair, reduce the colonic macrophage infiltration responsible for the secretion of the pro-inflammatory factors, and significantly mitigate the severity of IBD in a mouse model, where MSCs released by SC-HM successfully accumulate at the colonic crypt. Moreover, a metagenomics analysis reveals that SC-HM ameliorates the dysbiosis of specific bacterial genera, including Bacteroides acidifaciens, Lactobacillus (L.) gasseri, Lactobacillus reuteri, and L. intestinalis, implying optimization of the microorganism's composition and abundance. These findings demonstrate that SC-HM is a potential IBD treatment candidate.}, }
@article {pmid35545448, year = {2022}, author = {Chen, DW and Garud, NR}, title = {Rapid evolution and strain turnover in the infant gut microbiome.}, journal = {Genome research}, volume = {32}, number = {6}, pages = {1124-1136}, doi = {10.1101/gr.276306.121}, pmid = {35545448}, issn = {1549-5469}, mesh = {Adult ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Metagenomics ; *Microbiota/genetics ; Mothers ; }, abstract = {Although the ecological dynamics of the infant gut microbiome have been intensely studied, relatively little is known about evolutionary dynamics in the infant gut microbiome. Here we analyze longitudinal fecal metagenomic data from more than 700 infants and their mothers over the first year of life and find that the evolutionary dynamics in infant gut microbiomes are distinct from those of adults. We find evidence for more than a 10-fold increase in the rate of evolution and strain turnover in the infant gut compared with healthy adults, with the mother-infant transition at delivery being a particularly dynamic period in which gene loss dominates. Within a few months after birth, these dynamics stabilize, and gene gains become increasingly frequent as the microbiome matures. We furthermore find that evolutionary changes in infants show signatures of being seeded by a mixture of de novo mutations and transmissions of pre-evolved lineages from the broader family. Several of these evolutionary changes occur in parallel across infants, highlighting candidate genes that may play important roles in the development of the infant gut microbiome. Our results point to a picture of a volatile infant gut microbiome characterized by rapid evolutionary and ecological change in the early days of life.}, }
@article {pmid35500534, year = {2022}, author = {Mirza, AI and Zhu, F and Knox, N and Forbes, JD and Bonner, C and Van Domselaar, G and Bernstein, CN and Graham, M and Marrie, RA and Hart, J and Yeh, EA and Arnold, DL and Bar-Or, A and O'Mahony, J and Zhao, Y and Hsiao, W and Banwell, B and Waubant, E and Tremlett, H}, title = {The metabolic potential of the paediatric-onset multiple sclerosis gut microbiome.}, journal = {Multiple sclerosis and related disorders}, volume = {63}, number = {}, pages = {103829}, doi = {10.1016/j.msard.2022.103829}, pmid = {35500534}, issn = {2211-0356}, mesh = {Adolescent ; Canada ; Child ; Female ; *Gastrointestinal Microbiome ; Glatiramer Acetate ; Humans ; Male ; *Multiple Sclerosis ; Starch ; }, abstract = {BACKGROUND: The aim of this study was to examine the gut microbiome's metabolic potential in paediatric-onset MS patients (symptom onset <18 years).<br><br>METHODS: We included 17 MS participants and 20 controls similar for sex, age, race, and stool consistency from the Canadian Paediatric Demyelinating Disease Network study. Stool-derived gut metagenome gene abundances were used to estimate relative abundances and turnover scores of individual microbial metabolites and the composition and diversity of carbohydrate-active enzymes (CAZymes). MS participants and controls were compared using the Wilcoxon rank-sum test, as were the disease-modifying drug (DMD) exposed and naïve MS participants.<br><br>RESULTS: The median age(s) at MS symptom onset=16.1 years (interquartile range [IQR]=1.7), and at stool sample procurement=16.9/15.8 years (IQR=2.0/1.4), for the MS participants/controls. Most MS and control participants were girls (80-82%). Five (29%) of the MS participants had never been exposed to a DMD pre-stool sample and 12 (71%) had (7 to beta-interferon and 5 glatiramer acetate). While the relative abundance of metabolites did not differ between MS participants and controls, turnover scores did. MS participants had a greater potential to metabolize lipopolysaccharides than controls (score difference=1.6E-04, p = 0.034) but lower potential to metabolize peptidoglycan molecules and starch (score differences<2.2E-02, p<0.040). Further, although CAZymes diversity did not differ (p>0.050), starch-degrading subfamilies were underrepresented in MS participants versus controls (relative abundance differences >-0.34, p<0.040) and in the DMD exposed verses DMD naïve MS participants (relative abundance differences>-0.20, p<0.049).<br><br>CONCLUSION: Paediatric-onset MS participants had an altered gut microbiome-related metabolic potential compared to controls, including higher breakdown of lipopolysaccharide molecules, but lower resistant starch metabolism.}, }
@article {pmid35739659, year = {2022}, author = {Li, YJ and Chuang, CH and Cheng, WC and Chen, SH and Chen, WL and Lin, YJ and Lin, CY and Shih, YH}, title = {A metagenomics study of hexabromocyclododecane degradation with a soil microbial community.}, journal = {Journal of hazardous materials}, volume = {430}, number = {}, pages = {128465}, doi = {10.1016/j.jhazmat.2022.128465}, pmid = {35739659}, issn = {1873-3336}, mesh = {Humans ; *Hydrocarbons, Brominated/analysis ; Metagenomics ; *Microbiota ; Soil ; *Soil Pollutants ; }, abstract = {Hexabromocyclododecanes (HBCDs) are globally prevalent and persistent organic pollutants (POPs) listed by the Stockholm Convention in 2013. They have been detected in many environmental media from waterbodies to Plantae and even in the human body. Due to their highly bioaccumulative characterization, they pose an urgent public health issue. Here, we demonstrate that the indigenous microbial community in the agricultural soil in Taiwan could decompose HBCDs with no additional carbon source incentive. The degradation kinetics reached 0.173 day-1 after the first treatment and 0.104 day-1 after second exposure. With additional C-sources, the rate constants decreased to 0.054-0.097 day-1. The hydroxylic debromination metabolites and ring cleavage long-chain alkane metabolites were identified to support the potential metabolic pathways utilized by the soil microbial communities. The metagenome established by Nanopore sequencing showed significant compositional alteration in the soil microbial community after the HBCD treatment. After ranking, comparing relative abundances, and performing network analyses, several novel bacterial taxa were identified to contribute to HBCD biotransformation, including Herbaspirillum, Sphingomonas, Brevundimonas, Azospirillum, Caulobacter, and Microvirga, through halogenated / aromatic compound degradation, glutathione-S-transferase, and hydrolase activity. We present a compelling and applicable approach combining metagenomics research, degradation kinetics, and metabolomics strategies, which allowed us to decipher the natural attenuation and remediation mechanisms of HBCDs.}, }
@article {pmid35743947, year = {2022}, author = {Doytchinov, VV and Dimov, SG}, title = {Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/life12060916}, pmid = {35743947}, issn = {2075-1729}, support = {70-25-72 from 03.08.2021//NATIONAL CENTER FOR POLAR STUDIES - SOFIA UNIVERSITY "ST. KLIMENT OHRIDSKI"/ ; }, abstract = {Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.}, }
@article {pmid35660621, year = {2022}, author = {He, J and Zhang, N and Shen, X and Muhammad, A and Shao, Y}, title = {Deciphering environmental resistome and mobilome risks on the stone monument: A reservoir of antimicrobial resistance genes.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 3}, pages = {156443}, doi = {10.1016/j.scitotenv.2022.156443}, pmid = {35660621}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Antimicrobial resistance (AMR) in the environment has attracted increasing attention as an emerging global threat to public health. Stone is an essential ecosystem in nature and also an important material for human society, having architectural and aesthetic values. However, little is known about the AMR in stone ecosystems, particularly in the stone monument, where antimicrobials are often applied against biodeterioration. Here, we provide the first detailed metagenomic study of AMR genes across different types of biodeteriorated stone monuments, which revealed abundant and diverse AMR genes conferring resistance to drugs (antibiotics), biocides, and metals. Totally, 132 AMR subtypes belonging to 27 AMR types were detected including copper-, rifampin-, and aminocoumarins-resistance genes, of which diversity was mainly explained by the spatial turnover (replacement of genes between samples) rather than nestedness (loss of nested genes between samples). Source track analysis confirms that stone resistomes are likely driven by anthropogenic activities across stone heritage areas. We also detected various mobile genetic elements (namely mobilome, e.g., prophages, plasmids, and insertion sequences) that could accelerate replication and horizontal transfer of AMR genes. Host-tracking analysis further identified multiple biodeterioration-related bacterial genera such as Pseudonocardia, Sphingmonas, and Streptomyces as the major hosts of resistome. Taken together, these findings highlight that stone microbiota is one of the natural reservoirs of antimicrobial-resistant hazards, and the diverse resistome and mobilome carried by active biodeteriogens may improve their adaptation on stone and even deactivate the antimicrobials applied against biodeterioration. This enhanced knowledge may also provide novel and specific avenues for environmental management and stone heritage protection.}, }
@article {pmid35654195, year = {2022}, author = {Beale, DJ and Bissett, A and Nilsson, S and Bose, U and Nelis, JLD and Nahar, A and Smith, M and Gonzalez-Astudillo, V and Braun, C and Baddiley, B and Vardy, S}, title = {Perturbation of the gut microbiome in wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 3}, pages = {156324}, doi = {10.1016/j.scitotenv.2022.156324}, pmid = {35654195}, issn = {1879-1026}, mesh = {Animals ; *Environmental Pollutants ; *Fluorocarbons ; Fresh Water ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Turtles/metabolism ; }, abstract = {Per- and polyfluoroalkyl substances (PFAS) are environmentally persistent and pervasive. Understanding the toxicity of PFAS to wildlife is difficult, both due to the complexity of biotic and abiotic perturbations in the taxa under study and the practical and ethical problems associated with studying the impacts of environmental pollutants on free living wildlife. One avenue of inquiry into the effects of environmental pollutants, such as PFAS, is assessing the impact on the host gut microbiome. Here we show the microbial composition and biochemical functional outputs from the gut microbiome of sampled faeces from euthanised and necropsied wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels. The microbial community composition was profiled by 16S rRNA gene sequencing using a Nanopore MinION and the biochemical functional outputs of the gut microbiome were profiled using a combination of targeted central carbon metabolism metabolomics using liquid chromatography coupled to a triple quadrupole mass spectrometer (LC-QqQ-MS) and untargeted metabolomics using liquid chromatography coupled to a quadrupole time of flight mass spectrometer (LC-QToF-MS). Total PFAS was measured in the turtle serum using standard methods. These preliminary data demonstrated a 60-fold PFAS increase in impacted turtles compared to the sampled aquatic environment. The microbiome community was also impacted in the PFAS exposed turtles, with the ratio of Firmicutes-to-Bacteroidetes rising from 1.4 at the reference site to 5.5 at the PFAS impacted site. This ratio increase is indicative of host stress and dysfunction of the gut microbiome that was correlated with the biochemical metabolic function data, metabolites observed that are indications of stress and inflammation in the gut microbiome. Utilising the gut microbiome of sampled faeces collected from freshwater turtles provides a non-destructive avenue for investigating the impacts of PFAS in native wildlife, and provides an avenue to explore other contaminants in higher-order taxa within the environment.}, }
@article {pmid35614211, year = {2022}, author = {Zhang, Y and Bhosle, A and Bae, S and McIver, LJ and Pishchany, G and Accorsi, EK and Thompson, KN and Arze, C and Wang, Y and Subramanian, A and Kearney, SM and Pawluk, A and Plichta, DR and Rahnavard, A and Shafquat, A and Xavier, RJ and Vlamakis, H and Garrett, WS and Krueger, A and Huttenhower, C and Franzosa, EA}, title = {Discovery of bioactive microbial gene products in inflammatory bowel disease.}, journal = {Nature}, volume = {606}, number = {7915}, pages = {754-760}, pmid = {35614211}, issn = {1476-4687}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; R01 DK127171/DK/NIDDK NIH HHS/United States ; }, mesh = {Chronic Disease ; *Gastrointestinal Microbiome ; Genes, Microbial ; Humans ; *Inflammatory Bowel Diseases ; Metagenomics ; }, abstract = {Microbial communities and their associated bioactive compounds1-3 are often disrupted in conditions such as the inflammatory bowel diseases (IBD)4. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive5-7. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.}, }
@article {pmid35729161, year = {2022}, author = {Zhang, L and Jonscher, KR and Zhang, Z and Xiong, Y and Mueller, RS and Friedman, JE and Pan, C}, title = {Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3551}, pmid = {35729161}, issn = {2041-1723}, support = {R01AT011618//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT011618//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {Autoantibodies ; Child ; *Diabetes Mellitus, Type 1/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota ; Seroconversion ; }, abstract = {The immune system of some genetically susceptible children can be triggered by certain environmental factors to produce islet autoantibodies (IA) against pancreatic β cells, which greatly increases their risk for Type-1 diabetes. An environmental factor under active investigation is the gut microbiome due to its important role in immune system education. Here, we study gut metagenomes that are de-novo-assembled in 887 at-risk children in the Environmental Determinants of Diabetes in the Young (TEDDY) project. Our results reveal a small set of core protein families, present in >50% of the subjects, which account for 64% of the sequencing reads. Time-series binning generates 21,536 high-quality metagenome-assembled genomes (MAGs) from 883 species, including 176 species that hitherto have no MAG representation in previous comprehensive human microbiome surveys. IA seroconversion is positively associated with 2373 MAGs and negatively with 1549 MAGs. Comparative genomics analysis identifies lipopolysaccharides biosynthesis in Bacteroides MAGs and sulfate reduction in Anaerostipes MAGs as functional signatures of MAGs with positive IA-association. The functional signatures in the MAGs with negative IA-association include carbohydrate degradation in lactic acid bacteria MAGs and nitrate reduction in Escherichia MAGs. Overall, our results show a distinct set of gut microorganisms associated with IA seroconversion and uncovered the functional genomics signatures of these IA-associated microorganisms.}, }
@article {pmid35727547, year = {2022}, author = {Cowart, DA and Murphy, KR and Cheng, CC}, title = {Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2498}, number = {}, pages = {225-251}, pmid = {35727547}, issn = {1940-6029}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Ecosystem ; Environmental Monitoring/methods ; Metagenomics/methods ; }, abstract = {Environmental DNA (eDNA) analysis has emerged in recent years as a powerful tool for the detection, monitoring, and characterization of aquatic metazoan communities, including vulnerable species. The rapid rate of adopting the eDNA approach across diverse habitats and taxonomic groups attests to its value for a wide array of investigative goals, from understanding natural or changing biodiversity to informing on conservation efforts at local and global scales. Regardless of research objectives, eDNA workflows commonly include the following essential steps: environmental sample acquisition, processing and preservation of samples, and eDNA extraction, followed by eDNA sequencing library preparation, high-capacity sequencing and sequence data analysis, or other methods of genetic detection. In this chapter, we supply instructional details for the early steps in the workflow to facilitate researchers considering adopting eDNA analysis to address questions in marine environments. Specifically, we detail sampling, preservation, extraction, and quantification protocols for eDNA originating from marine water, shallow substrates, and deeper sediments. eDNA is prone to degradation and loss, and to contamination through improper handling; these factors crucially influence the outcome and validity of an eDNA study. Thus, we also provide guidance on avoiding these pitfalls. Following extraction, purified eDNA is often sequenced on massively parallel sequencing platforms for comprehensive faunal diversity assessment using a metabarcoding or metagenomic approach, or for the detection and quantification of specific taxa by qPCR methods. These components of the workflow are project-specific and thus not included in this chapter. Instead, we briefly touch on the preparation of eDNA libraries and discuss comparisons between sequencing approaches to aid considerations in project design.}, }
@article {pmid35725732, year = {2022}, author = {Odrzywolek, K and Karwowska, Z and Majta, J and Byrski, A and Milanowska-Zabel, K and Kosciolek, T}, title = {Deep embeddings to comprehend and visualize microbiome protein space.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10332}, pmid = {35725732}, issn = {2045-2322}, support = {POIR.01.01.01-00-0347/17//European Regional Development Fund/ ; 2019/35/D/NZ2/04353//Narodowe Centrum Nauki/ ; 2019/35/D/NZ2/04353//Narodowe Centrum Nauki/ ; PPN/PPO/2018/1/00014//Narodowa Agencja Wymiany Akademickiej/ ; }, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Proteins/genetics ; }, abstract = {Understanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the possibility of predicting their function through conventional homology-based approaches is limited, which indicates the need for further research on alignment-free methods. Here, we leverage a deep-learning-based representation of proteins to assess its utility in alignment-free analysis of microbial proteins. We trained a language model on the Unified Human Gastrointestinal Protein catalogue and validated the resulting protein representation on the bacterial part of the SwissProt database. Finally, we present a use case on proteins involved in SCFA metabolism. Results indicate that the deep learning model manages to accurately represent features related to protein structure and function, allowing for alignment-free protein analyses. Technologies that contextualize metagenomic data are a promising direction to deeply understand the microbiome.}, }
@article {pmid35352015, year = {2022}, author = {Speth, DR and Yu, FB and Connon, SA and Lim, S and Magyar, JS and Peña-Salinas, ME and Quake, SR and Orphan, VJ}, title = {Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily.}, journal = {The ISME journal}, volume = {16}, number = {7}, pages = {1750-1764}, pmid = {35352015}, issn = {1751-7370}, support = {019.153LW.039//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 51250//John Templeton Foundation (JTF)/ ; DE-SC0016469//DOE | Office of Science (SC)/ ; }, mesh = {Geologic Sediments/microbiology ; *Hydrothermal Vents/microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.}, }
@article {pmid35715496, year = {2022}, author = {Shell, WA and Rehan, SM}, title = {Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {603}, pmid = {35715496}, issn = {2399-3642}, support = {9659-15//National Geographic Society/ ; }, mesh = {Agriculture ; Animals ; Bees ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Plants ; }, abstract = {The holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism's microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.}, }
@article {pmid35720380, year = {2022}, author = {Patterson, GT and Osorio, EY and Peniche, A and Dann, SM and Cordova, E and Preidis, GA and Suh, JH and Ito, I and Saldarriaga, OA and Loeffelholz, M and Ajami, NJ and Travi, BL and Melby, PC}, title = {Pathologic Inflammation in Malnutrition Is Driven by Proinflammatory Intestinal Microbiota, Large Intestine Barrier Dysfunction, and Translocation of Bacterial Lipopolysaccharide.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {846155}, doi = {10.3389/fimmu.2022.846155}, pmid = {35720380}, issn = {1664-3224}, mesh = {Animals ; Bacteria ; Cecum/microbiology ; *Gastrointestinal Diseases ; *Gastrointestinal Microbiome ; Inflammation ; *Intestinal Diseases ; Lipopolysaccharides ; *Malnutrition ; Mice ; Weight Loss ; }, abstract = {Acute malnutrition, or wasting, is implicated in over half of all deaths in children under five and increases risk of infectious disease. Studies in humans and preclinical models have demonstrated that malnutrition is linked to an immature intestinal microbiota characterized by increased prevalence of Enterobacteriaceae. Observational studies in children with moderate acute malnutrition (MAM) have also observed heightened systemic inflammation and increased circulating bacterial lipopolysaccharides (LPS; endotoxin). However, the mechanisms that underpin the systemic inflammatory state and endotoxemia, and their pathophysiological consequences, remain uncertain. Understanding these pathophysiological mechanisms is necessary to design targeted treatments that will improve the unacceptable rate of failure or relapse that plague current approaches. Here we use a mouse model of MAM to investigate the mechanisms that promote inflammation in the malnourished host. We found that mice with MAM exhibited increased systemic inflammation at baseline, increased translocation of bacteria and bacterial LPS, and an exaggerated response to inflammatory stimuli. An exaggerated response to bacterial LPS was associated with increased acute weight loss. Remarkably, intestinal inflammation and barrier dysfunction was found in the cecum and colon. The cecum showed a dysbiotic microbiota with expansion of Gammaproteobacteria and some Firmicutes, and contraction of Bacteroidetes. These changes were paralleled by an increase in fecal LPS bioactivity. The inflammatory phenotype and weight loss was modulated by oral administration of non-absorbable antibiotics that altered the proportion of cecal Gammaproteobacteria. We propose that the heightened inflammation of acute malnutrition is the result of changes in the intestinal microbiota, intestinal barrier dysfunction in the cecum and colon, and increased systemic exposure to LPS.}, }
@article {pmid35718910, year = {2022}, author = {Wang, S and Li, B and Mao, H and Zhu, M and Zhang, X and Xiang, X and Wang, Z}, title = {[Effects of rice wheat intervention on intestinal microflora of rats based on metagenomics].}, journal = {Wei sheng yan jiu = Journal of hygiene research}, volume = {51}, number = {3}, pages = {449-455}, doi = {10.19813/j.cnki.weishengyanjiu.2022.03.018}, pmid = {35718910}, issn = {1000-8020}, mesh = {Animals ; Carbohydrates ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Glycoside Hydrolases ; Lipids ; Male ; Metagenomics ; *Oryza ; Rats ; Rats, Sprague-Dawley ; Triticum ; }, abstract = {OBJECTIVE: To investigate the effects of rice on intestinal microflora in rats.<br><br>METHODS: Thirty 4-week-old male SD rats were randomly divided into control group, rice group and wheat group according to body weight. The control group was fed with AIN-93 diet, the rice group and the wheat group was fed with the AIN-93 diet which the carbohydrate was replaced with rice and wheat, respectively, for 4 weeks. At the end of the experiment, lipid related biochemical indexes were determined, and the contents of the distal colon(feces) of rats were collected for macro factor detection.<br><br>RESULTS: From the beginning to the end of feeding, there was no difference in weight gain among the groups. After the end of the experiment, there was no difference among lipid-related indicators and blood glucose. α diversity showed that there was no difference in the diversity of intestinal microbiota between the rice and wheat groups, and the gene abundance analysis of intestinal microbiota in the wheat group showed that the gene abundance of intestinal microbiota was lower. The difference analysis of intestinal microbiota result showed that compared with the rice group, the wheat group was composed of higher proportion of verrucomicrophyla and lower proportion of Bacteroidetes. Lefse analysis showed that the surface group was enriched with Akkermansia Muciniphila, Bifidobacterium animalis, and a variety of beneficial bacteria such as Faecalibaculum rodentium and Intestinimonas butyriciproducens, while Prevotella copri was rich in the rice group. Glycoside hydrolases 8, glycoside hydrolases 16, glycoside hydrolases 99 and glycosyl transferase family 56.<br><br>CONCLUSION: Rice or wheat as different carbohydrate sources have different effects on the composition of intestinal microflora and carbohydrate-related active enzymes in rats.}, }
@article {pmid35711426, year = {2022}, author = {Hua, H and Meydan, C and Afshin, EE and Lili, LN and D'Adamo, CR and Rickard, N and Dudley, JT and Price, ND and Zhang, B and Mason, CE}, title = {A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {889702}, doi = {10.3389/fimmu.2022.889702}, pmid = {35711426}, issn = {1664-3224}, mesh = {DNA, Bacterial/genetics ; Feces/microbiology ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/methods ; }, abstract = {While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.}, }
@article {pmid35710760, year = {2022}, author = {Escudero-Martinez, C and Coulter, M and Alegria Terrazas, R and Foito, A and Kapadia, R and Pietrangelo, L and Maver, M and Sharma, R and Aprile, A and Morris, J and Hedley, PE and Maurer, A and Pillen, K and Naclerio, G and Mimmo, T and Barton, GJ and Waugh, R and Abbott, J and Bulgarelli, D}, title = {Identifying plant genes shaping microbiota composition in the barley rhizosphere.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3443}, pmid = {35710760}, issn = {2041-1723}, support = {BB/S002871/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S002871/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S002871/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Personal Fellowship 2013-18//Royal Society of Edinburgh (RSE)/ ; }, mesh = {Bacteria/genetics ; Genes, Plant/genetics ; *Hordeum/genetics ; *Microbiota/genetics ; Plant Roots/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.}, }
@article {pmid35710651, year = {2022}, author = {Zhou, L and Huang, S and Gong, J and Xu, P and Huang, X}, title = {500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {310}, pmid = {35710651}, issn = {2052-4463}, mesh = {China ; Estuaries ; *Genome, Microbial ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {As a unique geographical transition zone, the estuary is considered as a model environment to decipher the diversity, functions and ecological processes of microbial communities, which play important roles in the global biogeochemical cycle. Here we used surface water metagenomic sequencing datasets to construct metagenome-assembled genomes (MAGs) from 30 subtropical estuaries at a large scale along South China. In total, 500 dereplicated MAGs with completeness ≥ 50% and contamination ≤ 10% were obtained, among which more than one-thirds (n = 207 MAGs) have a completeness ≥ 70%. These MAGs are dominated by taxa assigned to the phylum Proteobacteria (n = 182 MAGs), Bacteroidota (n = 110) and Actinobacteriota (n = 104). These draft genomes can be used to study the diversity, phylogenetic history and metabolic potential of microbiota in the estuary, which should help improve our understanding of the structure and function of these microorganisms and how they evolved and adapted to extreme conditions in the estuarine ecosystem.}, }
@article {pmid35584918, year = {2022}, author = {He, T and Zhu, C and Li, Z and Ai, L and Hu, D and Wang, C and Li, F and Yang, X and Lv, H and Chen, W and Qian, H and Tan, W and Wang, C}, title = {Virome analysis of ticks in Zhoushan Archipelago, China.}, journal = {The Journal of veterinary medical science}, volume = {84}, number = {6}, pages = {847-854}, doi = {10.1292/jvms.22-0058}, pmid = {35584918}, issn = {1347-7439}, mesh = {Animals ; China/epidemiology ; *Phlebovirus ; Phylogeny ; *Tick-Borne Diseases/veterinary ; *Ticks ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Ticks are an important group of arthropod vectors. Ticks pose a profound risk to public health by transmitting many types of microorganisms that are human and animal pathogens. With the development of next-generation sequencing (NGS) technology and viral metagenomics, numerous novel viruses have been discovered in ticks and tick-related hosts. To fully understand the virus spectrum in ticks in the Zhoushan Archipelago of Zhejiang province in China, ticks were collected from Qushan Island, Zhoushan Island, and Daishan Island in the Zhoushan Archipelago in June 2016. NGS performed to investigate the diversity of tick-associated viruses identified 21 viral sequences. Twelve were pathogenic to humans and animals. Trough verification by polymerase chain reaction (PCR) revealed the existence of three tick-associated viruses with extensive homology with Dabieshan, MG22, and Odaw virus. Other NGS-detected sequences that could not be amplified by PCR were highly homologous (92-100%) with known pathogenic viruses that included hepatitis B virus, papillomavirus, and human mastadenovirus C. This is the first study to systematically apply high throughput sequencing technology to explore the spectrum of viruses carried by ticks in the Zhoushan Archipelago. The findings are fundamental knowledge of the diversity of tick-associated viruses in this region and will inform strategies to monitor and prevent the spread of tick-borne diseases.}, }
@article {pmid35536051, year = {2022}, author = {Seitz, VA and McGivern, BB and Daly, RA and Chaparro, JM and Borton, MA and Sheflin, AM and Kresovich, S and Shields, L and Schipanski, ME and Wrighton, KC and Prenni, JE}, title = {Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {11}, pages = {e0022622}, doi = {10.1128/aem.00226-22}, pmid = {35536051}, issn = {1098-5336}, support = {1750189//National Science Foundation (NSF)/ ; DE-SC0019746//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; P30CA046934//CU | Anschutz Medical Campus, University of Colorado (CU Anschutz)/ ; DE-SC0014395//U.S. Department of Energy (DOE)/ ; }, mesh = {Exudates and Transudates ; *Microbiota/physiology ; Plant Growth Regulators/metabolism ; Plant Roots/metabolism ; Plants/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Rhizosphere ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. IMPORTANCE Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites. Together, these findings demonstrate the tractability of high-resolution multiomics tools to investigate soil microbiomes and provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.}, }
@article {pmid35378331, year = {2022}, author = {Gonzalez, CG and Mills, RH and Kordahi, MC and Carrillo-Terrazas, M and Secaira-Morocho, H and Widjaja, CE and Tsai, MS and Mittal, Y and Yee, BA and Vargas, F and Weldon, K and Gauglitz, JM and Delaroque, C and Sauceda, C and Rossitto, LA and Ackermann, G and Humphrey, G and Swafford, AD and Siegel, CA and Buckey, JC and Raffals, LE and Sadler, C and Lindholm, P and Fisch, KM and Valaseck, M and Suriawinata, A and Yeo, GW and Ghosh, P and Chang, JT and Chu, H and Dorrestein, P and Zhu, Q and Chassaing, B and Knight, R and Gonzalez, DJ and Dulai, PS}, title = {The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {14}, number = {1}, pages = {35-53}, doi = {10.1016/j.jcmgh.2022.03.008}, pmid = {35378331}, issn = {2352-345X}, mesh = {Animals ; *Colitis, Ulcerative/therapy ; Humans ; *Hyperbaric Oxygenation ; Interleukin-10 ; Mice ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND &amp; AIMS: Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy.<br><br>METHODS: Pre- and post-intervention mucosal biopsies, tissue, and fecal samples were collected from HBOT phase 2 clinical trials. Biopsies and fecal samples were subjected to shotgun metaproteomics, metabolomics, 16s rRNA sequencing, and metagenomics. Tissue was subjected to bulk RNA sequencing and digital spatial profiling (DSP) for single-cell RNA and protein analysis, and immunohistochemistry was performed. Fecal samples were also used for colonization experiments in IL10-/- germ-free UC mouse models.<br><br>RESULTS: Proteomics identified negative associations between HBOT response and neutrophil azurophilic granule abundance. DSP identified an HBOT-specific reduction of neutrophil STAT3, which was confirmed by immunohistochemistry. HBOT decreased microbial diversity with a proportional increase in Firmicutes and a secondary bile acid lithocholic acid. A major source of the reduction in diversity was the loss of mucus-adherent taxa, resulting in increased MUC2 levels post-HBOT. Targeted database searching revealed strain-level associations between Akkermansia muciniphila and HBOT response status. Colonization of IL10-/- with stool obtained from HBOT responders resulted in lower colitis activity compared with non-responders, with no differences in STAT3 expression, suggesting complementary but independent host and microbial responses.<br><br>CONCLUSIONS: HBOT reduces host neutrophil STAT3 and azurophilic granule activity in UC patients and changes in microbial composition and metabolism in ways that improve colitis activity. Intestinal microbiota, especially strain level variations in A muciniphila, may contribute to HBOT non-response.}, }
@article {pmid35705722, year = {2022}, author = {Di Chiacchio, IM and Gómez-Abenza, E and Paiva, IM and de Abreu, DJM and Rodríguez-Vidal, JF and Carvalho, EEN and Carvalho, SM and Solis-Murgas, LD and Mulero, V}, title = {Bee pollen in zebrafish diet affects intestinal microbiota composition and skin cutaneous melanoma development.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9998}, pmid = {35705722}, issn = {2045-2322}, support = {88881.189191/2018-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; BIO2017-84702-R//Ministerio de Ciencia e Innovación/ ; }, mesh = {Animals ; Bees ; Diet ; *Gastrointestinal Microbiome ; *Melanoma/etiology ; Pollen ; *Skin Neoplasms/etiology ; Zebrafish ; }, abstract = {Bee pollen is recommended as dietary supplement due to immunostimulating functions including antioxidant, anti-inflammatory and anti-carcinogenic properties. Nevertheless, the effectiveness of such properties is still not well understood. As diet can be associated with animal performance, microbiota modulation and potentially factor for cancer, this study aimed to analyze if bee pollen could influence growth, gut microbial and skin cutaneous melanoma development in zebrafish. Control diets based on commercial flakes and Artemia were compared with the same diet supplemented with bee pollen. Fish weight gain, increased length, intestinal bacteria metagenomics analysis, serum amyloid A gene expression and cutaneous melanoma transplantation assays were performed. Bee pollen affected microbiota composition and melanoma development. Differential abundance revealed higher abundance in the control group for Aeromonadaceae family, Aeromonas and Pseudomonas genus, A. sobria, A. schubertii, A. jandaei and P. alcaligenes species compared with pollen diet group. Pollen group presented higher abundance for Chromobacterium genus and for Gemmobacter aquaticus, Flavobacterium succinicans and Bifidobacterium breve compared with control group. Unexpectedly, fish fed with bee pollen showed higher tumor growth rate and larger tumor size than control group. This is the first study to report intestinal microbial changes and no protective cancer properties after bee pollen administration.}, }
@article {pmid35705309, year = {2022}, author = {Prekrasna, I and Pavlovska, M and Miryuta, N and Dzhulai, A and Dykyi, E and Convey, P and Kozeretska, I and Bedernichek, T and Parnikoza, I}, title = {Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function.}, journal = {Microbes and environments}, volume = {37}, number = {2}, pages = {}, doi = {10.1264/jsme2.ME21069}, pmid = {35705309}, issn = {1347-4405}, mesh = {*Actinobacteria/genetics ; Antarctic Regions ; Bacteria/genetics ; Lignin ; *Microbiota/genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C. quitensis had markedly lower diversity. The majority of bacteria in the rhizosphere communities of the hairgrass were affiliated to Proteobacteria, Bacteroidetes, and Actinobacteria. The rhizosphere of C. quitensis was dominated by Actinobacteria. All microbial communities included high proportions of unique amplicon sequence variants (ASVs) and there was high heterogeneity between samples at the ASV level. The soil parameters examined did not explain this heterogeneity. Bacteria belonging to Actinobacteria, Bacteroidetes, and Proteobacteria were sensitive to fluctuations in the soil surface temperature. The values of the United Soil Surface Temperature Influence Index (UTII, Iti) showed that variations in most microbial communities from Galindez Island were associated with microscale variations in temperature. Metabolic predictions in silico using PICRUSt 2.0, based on the taxonomically affiliated part of the microbiomes, showed similarities with the rhizosphere community of D. antarctica in terms of the predicted functional repertoire. The results obtained indicate that these communities are involved in the primary processes of soil development (particularly the degradation of lignin and lignin-derived compounds) in the central maritime Antarctic and may be beneficial for the growth of Antarctic vascular plants. However, due to the limitations associated with interpreting PICRUSt 2.0 outputs, these predictions need to be verified experimentally.}, }
@article {pmid35588986, year = {2022}, author = {Murali, A and Giri, V and Cameron, HJ and Sperber, S and Zickgraf, FM and Haake, V and Driemert, P and Walk, T and Kamp, H and Rietjens, IM and van Ravenzwaay, B}, title = {Investigating the gut microbiome and metabolome following treatment with artificial sweeteners acesulfame potassium and saccharin in young adult Wistar rats.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {165}, number = {}, pages = {113123}, doi = {10.1016/j.fct.2022.113123}, pmid = {35588986}, issn = {1873-6351}, mesh = {Animals ; Bile Acids and Salts ; Body Weight ; Feces/chemistry ; Female ; *Gastrointestinal Microbiome ; Male ; Metabolome ; Metabolomics ; Rats ; Rats, Wistar ; Saccharin ; Sweetening Agents/analysis ; Thiazines ; }, abstract = {To elucidate if artificial sweeteners modify fecal bacterial composition and the fecal and plasma metabolomes, Wistar rats from both sexes were treated for 28 days with acesulfame potassium (40 and 120 mg/kg body weight) and saccharin (20 and 100 mg/kg body weight). Targeted MS-based metabolome profiling (plasma and feces) and fecal 16S gene sequencing were conducted. Both sweeteners exhibited only minor effects on the fecal metabolome and microbiota. Saccharin treatment significantly altered amino acids, lipids, energy metabolism and specifically, bile acids in the plasma metabolome. Additionally, sex-specific differences were observed for conjugated primary and secondary bile acids. Acesulfame potassium treated male rats showed larger alterations in glycine conjugated primary and secondary bile-acids than females. Other changes in the plasma metabolome were more profound for saccharin than acesulfame potassium, for both sexes. Changes in conjugated bile-acids in plasma, which are often associated with microbiome changes, and the absence of similarly large changes in microbiota suggest an adaptative change of the latter, rather than toxicity. Further studies with a high resolution 16S sequencing data and/or metagenomics approach, with particular emphasis on bile acids, will be required to explore the mechanisms driving this metabolic outcome of saccharin in Wistar rats.}, }
@article {pmid35584752, year = {2022}, author = {Singh, R and Pal, DB and Alkhanani, MF and Almalki, AH and Areeshi, MY and Haque, S and Srivastava, N}, title = {Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {155966}, doi = {10.1016/j.scitotenv.2022.155966}, pmid = {35584752}, issn = {1879-1026}, mesh = {*Biofuels ; Biomass ; Lignin/metabolism ; *Microbiota ; Soil ; }, abstract = {Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural &amp; functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.}, }
@article {pmid35703559, year = {2022}, author = {Churcheward, B and Millet, M and Bihouée, A and Fertin, G and Chaffron, S}, title = {MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0043222}, doi = {10.1128/msystems.00432-22}, pmid = {35703559}, issn = {2379-5077}, abstract = {Metagenome-assembled genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyze uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAG reconstruction but also emphasized several limitations, such as the nonbinning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used; however, it still remains unclear which assembly strategy, in combination with which binning approach, offers the best performance for MAG recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to coassemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto. IMPORTANCE Genome-resolved metagenomics has led to the discovery of previously untapped biodiversity within the microbial world. As the development of computational methods for the recovery of genomes from metagenomes continues, existing strategies need to be evaluated and compared to eventually lead to standardized computational workflows. In this study, we compared commonly used assembly and binning strategies and assessed their performance using both simulated and real metagenomic data sets. We propose a novel approach to automate coassembly, avoiding the requirement for a priori knowledge to combine metagenomic information. The comparison against a previous coassembly approach demonstrates a strong impact of this step on genome binning results, but also the benefits of informing coassembly for improving the quality of recovered genomes. MAGNETO integrates complementary assembly-binning strategies to optimize genome reconstruction and provides a complete reads-to-genomes workflow for the growing microbiome research community.}, }
@article {pmid35696554, year = {2022}, author = {Han, Y and Quan, X and Chuang, Y and Liang, Q and Li, Y and Yuan, Z and Bian, Y and Wei, L and Wang, J and Zhao, Y}, title = {A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao.}, journal = {Clinical and translational medicine}, volume = {12}, number = {6}, pages = {e909}, doi = {10.1002/ctm2.909}, pmid = {35696554}, issn = {2001-1326}, mesh = {Aged ; *Gastrointestinal Microbiome ; Humans ; Macau ; Metagenomics/methods ; Neurocognitive Disorders ; *Proteomics/methods ; }, abstract = {BACKGROUND: Due to the increasing ageing population, neurocognitive disorders (NCDs) have been a global public health issue, and its prevention and early diagnosis are crucial. Our previous study demonstrated that there is a significant correlation between specific populations and NCDs, but the biological characteristics of the vulnerable group predispose to NCDs are unclear. The purpose of this study is to investigate the predictors for the vulnerable group by a multi-omics analysis.<br><br>METHODS: Multi-omics approaches, including metagenomics, metabolomic and proteomic, were used to detect gut microbiota, faecal metabolites and urine exosome of 8 normal controls and 13 vulnerable elders after a rigorous screening of 400 elders in Macao. The multi-omics data were analysed using R and Bioconductor. The two-sided Wilcoxon's rank-sum test, Kruskal-Wallis rank sum test and the linear discriminant analysis effective size were applied to investigate characterized features. Moreover, a 2-year follow-up was conducted to evaluate cognitive function change of the elderly.<br><br>RESULTS: Compared with the control elders, the metagenomics of gut microbiota showed that Ruminococcus gnavus, Lachnospira eligens, Escherichia coli and Desulfovibrio piger were increased significantly in the vulnerable group. Carboxylates, like alpha-ketoglutaric acid and d-saccharic acid, and levels of vitamins had obvious differences in the faecal metabolites. There was a distinct decrease in the expression of eukaryotic translation initiation factor 2 subunit 1 (eIF2α) and amine oxidase A (MAO-A) according to the proteomic results of the urine exosomes. Moreover, the compound annual growth rate of neurocognitive scores was notably decreased in vulnerable elders.<br><br>CONCLUSIONS: The multi-omics characteristics of disturbed glyoxylate and dicarboxylate metabolism (bacteria), vitamin digestion and absorption and tricarboxylic acid cycle in vulnerable elders can serve as predictors of NCDs risk among the elderly of Macao. Intervention with them may be effective therapeutic approaches for NCDs, and the underlying mechanisms merit further exploration.}, }
@article {pmid35643020, year = {2022}, author = {Smith, SE and Huang, W and Tiamani, K and Unterer, M and Khan Mirzaei, M and Deng, L}, title = {Emerging technologies in the study of the virome.}, journal = {Current opinion in virology}, volume = {54}, number = {}, pages = {101231}, doi = {10.1016/j.coviro.2022.101231}, pmid = {35643020}, issn = {1879-6265}, mesh = {*Bacteriophages/genetics ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Virome ; *Viruses/genetics ; }, abstract = {Despite the growing interest in the microbiome in recent years, the study of the virome, the major part of which is made up of bacteriophages, is relatively underdeveloped compared with their bacterial counterparts. This is due in part to the lack of a universally conserved marker such as the 16S rRNA gene. For this reason, the development of metagenomic approaches was a major milestone in the study of the viruses in the microbiome or virome. However, it has become increasingly clear that these wet-lab methods have not yet been able to detect the full range of viruses present, and our understanding of the composition of the virome remains incomplete. In recent years, a range of new technologies has been developed to further our understanding. Direct RNA-Seq technologies bypass the need for cDNA synthesis, thus avoiding biases subjected to this step, which further expands our understanding of RNA viruses. The new generation of amplification methods could solve the low biomass issue relevant to most virome samples while reducing the error rate and biases caused by whole genome amplification. The application of long-read sequencing to virome samples can resolve the shortcomings of short-read sequencing in generating complete viral genomes and avoid the biases introduced by the assembly. Novel experimental methods developed to measure viruses' host range can help overcome the challenges of assigning hosts to many phages, specifically unculturable ones.}, }
@article {pmid35686590, year = {2022}, author = {Jiang, S and Nie, J and Chen, YX and Wang, XY and Chen, F}, title = {Structure and Composition of Candidate Phyla Radiation in Supragingival Plaque of Caries Patients.}, journal = {The Chinese journal of dental research : the official journal of the Scientific Section of the Chinese Stomatological Association (CSA)}, volume = {25}, number = {2}, pages = {107-118}, doi = {10.3290/j.cjdr.b3086339}, pmid = {35686590}, issn = {1867-5646}, mesh = {Bacteria ; Capnocytophaga ; *Dental Caries ; Dental Caries Susceptibility ; *Dental Deposits ; *Dental Plaque/microbiology ; Humans ; *Microbiota ; Mouth/microbiology ; }, abstract = {OBJECTIVE: To investigate the composition and abundance of candidate phyla radiation (CPR) in the oral cavity in caries patients and a healthy population.<br><br>METHODS: The raw macrogenomic sequencing data for a total of 88 subjects were downloaded from the National Centre for Biotechnology Sequence Read Archive (NCBI SRA) public database according to the public data usage specifications. Trimmomatic (Department for Metabolic Networks, Potsdam, Germany) and Bowtie 2 (University of Maryland, College Park, MD, USA) were used to quality control and dehost the host sequences. Species annotation was made using Kraken2 (Johns Hopkins University, Baltimore, MD, USA) and Bracken (Johns Hopkins University) based on the reference database. According to the results of the species annotation, the species-significant differences and species correlation of caries and healthy oral microbiota in species composition and microbiota diversity were analysed to study the distribution and abundance differences of CPR in the oral environment.<br><br>RESULTS: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria were the main components. The relative abundance of TM7 (Candidatus Saccharibacteria) and GN02 (Candidatus Gracilibacteria) of CPR is second only to the aforementioned five bacteria, indicating that CPR is an important part of the oral microbiota. TM7 and GN02 were common to both the caries patients and healthy patients and were detected in all samples, suggesting that CPR is the 'core microbiome'. There was a correlation between CPR and a variety of oral microbiota, among which the positive correlation with Capnocytophaga was the strongest, suggesting that Capnocytophaga might be the potential host bacteria of CPR.<br><br>CONCLUSION: CPR is an indispensable part of the oral microbiota. It is the 'core microflora' of the oral cavity and may play an important role in the stability and function of the oral microecological environment. Capnocytophaga may be the potential host bacteria of CPR.}, }
@article {pmid35681493, year = {2022}, author = {Das De, T and Sharma, P and Tevatiya, S and Chauhan, C and Kumari, S and Yadav, P and Singla, D and Srivastava, V and Rani, J and Hasija, Y and Pandey, KC and Kajla, M and Dixit, R}, title = {Bidirectional Microbiome-Gut-Brain-Axis Communication Influences Metabolic Switch-Associated Responses in the Mosquito Anopheles culicifacies.}, journal = {Cells}, volume = {11}, number = {11}, pages = {}, doi = {10.3390/cells11111798}, pmid = {35681493}, issn = {2073-4409}, support = {Health-NIMR-2017-01-03/AP/db//Tata Trusts/ ; No.3/1/3/ICRMR-VFS/HRD/2/2016//Indian Council of Medical Research/ ; 3/1/3/PDF(18)/2018-HRD//Indian Council of Medical Research/ ; }, mesh = {Animals ; *Anopheles ; Bacteria/genetics ; Brain/metabolism ; Communication ; Female ; *Gastrointestinal Microbiome/physiology ; }, abstract = {The periodic ingestion of a protein-rich blood meal by adult female mosquitoes causes a drastic metabolic change in their innate physiological status, which is referred to as a 'metabolic switch'. While understanding the neural circuits for host-seeking is modestly attended, how the gut 'metabolic switch' modulates brain functions, and resilience to physiological homeostasis, remains unexplored. Here, through a comparative brain RNA-Seq study, we demonstrate that the protein-rich diet induces the expression of brain transcripts related to mitochondrial function and energy metabolism, possibly causing a shift in the brain's engagement to manage organismal homeostasis. A dynamic mRNA expression pattern of neuro-signaling and neuro-modulatory genes in both the gut and brain likely establishes an active gut-brain communication. The disruption of this communication through decapitation does not affect the modulation of the neuro-modulator receptor genes in the gut. In parallel, an unusual and paramount shift in the level of neurotransmitters (NTs), from the brain to the gut after blood feeding, further supports the idea of the gut's ability to serve as a 'second brain'. After blood-feeding, a moderate enrichment of the gut microbial population, and altered immunity in the gut of histamine receptor-silenced mosquitoes, provide initial evidence that the gut-microbiome plays a crucial role in gut-brain-axis communication. Finally, a comparative metagenomics evaluation of the gut microbiome highlighted that blood-feeding enriches the family members of the Morganellaceae and Pseudomonadaceae bacterial communities. The notable observation of a rapid proliferation of Pseudomonas bacterial sp. and tryptophan enrichment in the gut correlates with the suppression of appetite after blood-feeding. Additionally, altered NTs dynamics of naïve and aseptic mosquitoes provide further evidence that gut-endosymbionts are key modulators for the synthesis of major neuroactive molecules. Our data establish a new conceptual understanding of microbiome-gut-brain-axis communication in mosquitoes.}, }
@article {pmid35678705, year = {2022}, author = {Sun, J and Prabhu, A and Aroney, STN and Rinke, C}, title = {Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials.}, journal = {Microbial genomics}, volume = {8}, number = {6}, pages = {}, doi = {10.1099/mgen.0.000842}, pmid = {35678705}, issn = {2057-5858}, mesh = {Animals ; *Coleoptera/metabolism ; Larva/metabolism ; *Microbiota/genetics ; Plastics/metabolism ; Polystyrenes/metabolism ; }, abstract = {Plastics are inexpensive and widely used organic polymers, but their high durability hinders biodegradation. Polystyrene, including extruded polystyrene (also known as styrofoam), is among the most commonly produced plastics worldwide and is recalcitrant to microbial degradation. In this study, we assessed changes in the gut microbiome of superworms (Zophobas morio) reared on bran, polystyrene or under starvation conditions over a 3 weeks period. Superworms on all diets were able to complete their life cycle to pupae and imago, although superworms reared on polystyrene had minimal weight gains, resulting in lower pupation rates compared to bran reared worms. The change in microbial gut communities from baseline differed considerably between diet groups, with polystyrene and starvation groups characterized by a loss of microbial diversity and the presence of opportunistic pathogens. Inferred microbial functions enriched in the polystyrene group included transposon movements, membrane restructuring and adaptations to oxidative stress. We detected several encoded enzymes with reported polystyrene and styrene degradation abilities, supporting previous reports of polystyrene-degrading bacteria in the superworm gut. By recovering metagenome-assembled genomes (MAGs) we linked phylogeny and functions and identified genera including Pseudomonas, Rhodococcus and Corynebacterium that possess genes associated with polystyrene degradation. In conclusion, our results provide the first metagenomic insights into the metabolic pathways used by the gut microbiome of superworms to degrade polystyrene. Our results also confirm that superworms can survive on polystyrene feed, but this diet has considerable negative impacts on host gut microbiome diversity and health.}, }
@article {pmid35689184, year = {2022}, author = {Van der Jeugt, F and Maertens, R and Steyaert, A and Verschaffelt, P and De Tender, C and Dawyndt, P and Mesuere, B}, title = {UMGAP: the Unipept MetaGenomics Analysis Pipeline.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {433}, pmid = {35689184}, issn = {1471-2164}, support = {1164420N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; 1174621N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; 1512619N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; 12I5220N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; }, abstract = {BACKGROUND: Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availability of fast, accurate and user-friendly biodiversity analysis tools.<br><br>RESULTS: Because environmental samples may contain strains and species that are not covered in reference databases and because protein sequences are more conserved than the genes encoding them, we explore the alternative route of taxonomic profiling based on protein coding regions translated from the shotgun metagenomics reads, instead of directly processing the DNA reads. We therefore developed the Unipept MetaGenomics Analysis Pipeline (UMGAP), a highly versatile suite of open source tools that are implemented in Rust and support parallelization to achieve optimal performance. Six preconfigured pipelines with different performance trade-offs were carefully selected, and benchmarked against a selection of state-of-the-art shotgun metagenomics taxonomic profiling tools.<br><br>CONCLUSIONS: UMGAP's protein space detour for taxonomic profiling makes it competitive with state-of-the-art shotgun metagenomics tools. Despite our design choices of an extra protein translation step, a broad spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, and a highly configurable non-monolithic design, UMGAP achieves low runtime, manageable memory footprint and high accuracy. Its interactive visualizations allow for easy exploration and comparison of complex communities.}, }
@article {pmid35680904, year = {2022}, author = {Bruce, SA and Aytur, SA and Andam, CP and Bucci, JP}, title = {Metagenomics to characterize sediment microbial biodiversity associated with fishing exposure within the Stellwagen Bank National Marine Sanctuary.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9499}, pmid = {35680904}, issn = {2045-2322}, abstract = {Microbes in marine sediments constitute a large percentage of the global marine ecosystem and function to maintain a healthy food web. In continental shelf habitats such as the Gulf of Maine (GoM), relatively little is known of the microbial community abundance, biodiversity, and natural product potential. This report is the first to provide a time-series assessment (2017-2020) of the sediment microbial structure in areas open and closed to fishing within the Stellwagen Bank National Marine Sanctuary (SBNMS). A whole metagenome sequencing (WMS) approach was used to characterize the sediment microbial community. Taxonomic abundance was calculated across seven geographic sites with 14 individual sediment samples collected during the summer and fall seasons. Bioinformatics analyses identified more than 5900 different species across multiple years. Non-metric multidimensional scaling methods and generalized linear models demonstrated that species richness was inversely associated with fishing exposure levels and varied by year. Additionally, the discovery of 12 unique biosynthetic gene clusters (BGCs) collected across sites confirmed the potential for medically relevant natural product discovery in the SBNMS. This study provides a practical assessment of how fishing exposure and temporal trends may affect microbial community structure in a coastal marine sanctuary.}, }
@article {pmid35676509, year = {2022}, author = {Gharechahi, J and Sarikhan, S and Han, JL and Ding, XZ and Salekdeh, GH}, title = {Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {46}, pmid = {35676509}, issn = {2055-5008}, support = {2021-YWF-ZX-02//CSC | Chinese Government Scholarship/ ; }, mesh = {Animals ; Camelus/microbiology ; Lignin ; *Microbiota/genetics ; Phylogeny ; *Rumen/microbiology ; }, abstract = {Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.}, }
@article {pmid35676264, year = {2022}, author = {Chen, L and Zhao, N and Cao, J and Liu, X and Xu, J and Ma, Y and Yu, Y and Zhang, X and Zhang, W and Guan, X and Yu, X and Liu, Z and Fan, Y and Wang, Y and Liang, F and Wang, D and Zhao, L and Song, M and Wang, J}, title = {Short- and long-read metagenomics expand individualized structural variations in gut microbiomes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3175}, pmid = {35676264}, issn = {2041-1723}, support = {91857101//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Metabolome/genetics ; Metagenome ; Metagenomics ; *Nanopores ; }, abstract = {In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome.}, }
@article {pmid35672613, year = {2022}, author = {Berntson, L and Öman, A and Engstrand, L and Dicksved, J}, title = {A Pilot Study Investigating Faecal Microbiota After Two Dietary Interventions in Children with Juvenile Idiopathic Arthritis.}, journal = {Current microbiology}, volume = {79}, number = {7}, pages = {215}, pmid = {35672613}, issn = {1432-0991}, support = {R-657931//Reumatikerförbundet/ ; R-744331//Reumatikerförbundet/ ; R-848441//Reumatikerförbundet/ ; }, mesh = {Adolescent ; *Arthritis, Juvenile/therapy ; Child ; Feces/microbiology ; Humans ; *Microbiota/genetics ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {There is evidence for an impact of the gut microbiota on the immune system, which has consequences for inflammatory diseases. Exclusive enteral nutrition (EEN) and the specific carbohydrate diet (SCD) have been demonstrated as effective anti-inflammatory treatments for children with Crohn's disease. We have previously shown an anti-inflammatory effect from these nutritional treatments in children with juvenile idiopathic arthritis (JIA). The aim of this study was to investigate if improved clinical symptoms after EEN or SCD treatment in children with JIA could be linked to changes in faecal microbiota. We included sixteen patients with JIA (age 7-17 years), six for treatment with EEN and ten with SCD. EEN was given for 3-5 weeks and SCD for 4-5 weeks, with clinical and laboratory status assessed before and after treatment. Faecal samples were analysed for microbiota diversity and composition using 16S rRNA gene sequencing. Analyses of the faecal microbiota showed an effect on the overall composition with both interventions; the most striking result was a decreased relative abundance of the genus Faecalibacterium from EEN and of Bifidobacterium from SCD. The α-diversity decreased significantly from SCD (P = 0.04), but not from EEN (P = 0.22). Despite the study cohorts being small, both EEN and SCD were shown to impact the faecal microbiota. Future larger studies with a focus on metagenomics or metabolomics could possibly reveal a link and clarify the clinical effects of those nutritional regimens.}, }
@article {pmid35300964, year = {2022}, author = {Sharma, P and Singh, SP and Iqbal, HMN and Tong, YW}, title = {Omics approaches in bioremediation of environmental contaminants: An integrated approach for environmental safety and sustainability.}, journal = {Environmental research}, volume = {211}, number = {}, pages = {113102}, doi = {10.1016/j.envres.2022.113102}, pmid = {35300964}, issn = {1096-0953}, mesh = {Biodegradation, Environmental ; *Environmental Pollutants/metabolism ; Genomics/methods ; Humans ; Metabolomics/methods ; *Microbiota ; Proteomics/methods ; }, abstract = {Non-degradable pollutants have emerged as a result of industrialization, population growth, and lifestyle changes, endangering human health and the environment. Bioremediation is the process of clearing hazardous contaminants with the help of microorganisms, and cost-effective approach. The low-cost and environmentally acceptable approach to removing environmental pollutants from ecosystems is microbial bioremediation. However, to execute these different bioremediation approaches successfully, this is imperative to have a complete understanding of the variables impacting the development, metabolism, dynamics, and native microbial communities' activity in polluted areas. The emergence of new technologies like next-generation sequencing, protein and metabolic profiling, and advanced bioinformatic tools have provided critical insights into microbial communities and underlying mechanisms in environmental contaminant bioremediation. These omics approaches are meta-genomics, meta-transcriptomics, meta-proteomics, and metabolomics. Moreover, the advancements in these technologies have greatly aided in determining the effectiveness and implementing microbiological bioremediation approaches. At Environmental Protection Agency (EPA)-The government placed special emphasis on exploring how molecular and "omic" technologies may be used to determine the nature, behavior, and functions of the intrinsic microbial communities present at pollution containment systems. Several omics techniques are unquestionably more informative and valuable in elucidating the mechanism of the process and identifying the essential player's involved enzymes and their regulatory elements. This review provides an overview and description of the omics platforms that have been described in recent reports on omics approaches in bioremediation and that demonstrate the effectiveness of integrated omics approaches and their novel future use.}, }
@article {pmid35661258, year = {2022}, author = {Brandau, L and Jacksch, S and Weis, S and Schnell, S and Egert, M}, title = {Minority report: small-scale metagenomic analysis of the non-bacterial kitchen sponge microbiota.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {363}, pmid = {35661258}, issn = {1432-072X}, support = {13FH197PX6//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; *Porifera/genetics ; }, abstract = {Kitchen sponges are particularly well known to harbor a high number and diversity of bacteria, including pathogens. Viruses, archaea, and eukaryotes in kitchen sponges, however, have not been examined in detail so far. To increase knowledge on the non-bacterial kitchen sponge microbiota and its potential hygienic relevance, we investigated five used kitchen sponges by means of metagenomic shot-gun sequencing. Viral particles were sought to be enriched by a filter step during DNA extraction from the sponges. Data analysis revealed that ~ 2% of the sequences could be assigned to non-bacterial taxa. Each sponge harbored different virus (phage) species, while the present archaea were predominantly affiliated with halophilic taxa. Among the eukaryotic taxa, besides harmless algae, or amoebas, mainly DNA from food-left-overs was found. The presented work offers new insights into the complex microbiota of used kitchen sponges and contributes to a better understanding of their hygienic relevance.}, }
@article {pmid35489490, year = {2022}, author = {Sanseverino, I and Gómez, L and Navarro, A and Cappelli, F and Niegowska, M and Lahm, A and Barbiere, M and Porcel-Rodríguez, E and Valsecchi, S and Pedraccini, R and Crosta, S and Lettieri, T}, title = {Holistic approach to chemical and microbiological quality of aquatic ecosystems impacted by wastewater effluent discharges.}, journal = {The Science of the total environment}, volume = {835}, number = {}, pages = {155388}, doi = {10.1016/j.scitotenv.2022.155388}, pmid = {35489490}, issn = {1879-1026}, mesh = {Bacteria ; Environmental Monitoring/methods ; *Microbiota ; Rivers/chemistry ; Waste Disposal, Fluid/methods ; Waste Water/chemistry ; *Water Pollutants, Chemical/analysis ; *Water Purification ; }, abstract = {Wastewater treatment plants (WWTPs) collect wastewater from various sources and use different treatment processes to reduce the load of pollutants in the environment. Since the removal of many chemical pollutants and bacteria by WWTPs is incomplete, they constitute a potential source of contaminants. The continuous release of contaminants through WWTP effluents can compromise the health of the aquatic ecosystems, even if they occur at very low concentrations. The main objective of this work was to characterize, over a period of four months, the treatment steps starting from income to the effluent and 5 km downstream to the receiving river. In this context, the efficiency removal of chemical pollutants (e.g. hormones and pharmaceuticals, including antibiotics) and bacteria was assessed in a WWTP case study by using a holistic approach. It embraces different chemical and biological-based methods, such as pharmaceutical analysis by HPLC-MSMS, growth rate inhibition in algae, ligand binding estrogen receptor assay, microbial community study by 16S and shotgun sequencing along with relative quantification of resistance genes by quantitative polymerase chain reaction. Although both, chemical and biological-based methods showed a significant reduction of the pollutant burden in effluent and surface waters compared to the influent of the WWTP, no complete removal of pollutants, pathogens and antibiotic resistance genes was observed.}, }
@article {pmid35460297, year = {2022}, author = {Geraerts, M and Vangestel, C and Artois, T and Fernandes, JMO and Jorissen, MWP and Chocha Manda, A and Danadu Mizani, C and Smeets, K and Snoeks, J and Sonet, G and Tingbao, Y and Van Steenberge, M and Vreven, E and Lunkayilakio Wamuini, S and Vanhove, MPM and Huyse, T}, title = {Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources.}, journal = {Molecular ecology}, volume = {31}, number = {12}, pages = {3304-3322}, doi = {10.1111/mec.16479}, pmid = {35460297}, issn = {1365-294X}, support = {683210//European Research Council project/ ; S1_RDC_TILAPIA//OCA type II project/ ; //Belgian Directorate-General for Development Cooperation and Humanitarian Aid/ ; 250548/F20//Research Council of Norway/ ; GOH3817N//European Marine Biological Resource Centre Belgium/ ; //Mbisa Congo project (2013-2018)/ ; 7NI02//Bijzonder Onderzoeksfonds/ ; BOF20TT06//Bijzonder Onderzoeksfonds/ ; K220314N//Fonds Wetenschappelijk Onderzoek/ ; ZRDC2014MP084//VLIR-UOS South Initiative/ ; P505/12/G112//European Centre of Ichtyoparasitology/ ; BR/132/PI/TILAPIA//Belgian Federal Science Policy Office/ ; }, mesh = {Animals ; Aquaculture ; *Cichlids/genetics ; Democratic Republic of the Congo ; Introduced Species ; Metagenomics ; }, abstract = {During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced into non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focusing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridization. Using RAD sequencing (27,611 single nucleotide polymorphisms), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, reflecting their ability to interbreed and the potential threat they pose to the genetic integrity of native tilapias. Nile tilapia populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity to Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge avoiding further introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.}, }
@article {pmid35257467, year = {2022}, author = {Han, Y and Kim, G and Ahn, E and Jung, S and Jung, Y and Kim, Y and Ha, E and Heo, Y and Ryu, DH and Park, H and Hwang, GS}, title = {Integrated metagenomics and metabolomics analysis illustrates the systemic impact of the gut microbiota on host metabolism after bariatric surgery.}, journal = {Diabetes, obesity &amp; metabolism}, volume = {24}, number = {7}, pages = {1224-1234}, doi = {10.1111/dom.14689}, pmid = {35257467}, issn = {1463-1326}, support = {C270200//Korea Basic Science Institute/ ; 2019M3A9D5A01102796//National Research Foundation of Korea/ ; NRF-2020R1A2C200783//National Research Foundation of Korea/ ; HC15C1322//Ministry of HEalth &amp; Welfare/ ; }, mesh = {*Bariatric Surgery ; Bile Acids and Salts ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metabolomics/methods ; Metagenomics ; Obesity/surgery ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIM: To explore how bariatric surgery (BS) modified the obesity-associated gut microbiome, the host metabolome, and their interactions in obese Korean patients.<br><br>MATERIALS AND METHODS: Stool and fasting blood samples were obtained before and 1, 3, 6, and 12 months after BS from 52 patients enrolled in the Korean Obesity Surgical Treatment Study. We analysed the gut microbiome by 16S rRNA gene sequencing and the serum metabolome, including bile acids, by nuclear magnetic resonance spectroscopy and ultrahigh-performance liquid chromatography/triple quadrupole mass spectrometry.<br><br>RESULTS: Stool metagenomics showed that 27 microbiota were enriched and 14 microbiota were reduced after BS, whereas the abundances and diversity of observed features were increased. The levels of branched-chain amino acids and metabolites of energy metabolism in serum were decreased after surgery, whereas the levels of metabolites related to microbial metabolism, including dimethyl sulphone, glycine, and secondary bile acids, were increased in the serum samples. In addition, we found notable mutual associations among metabolites and gut microbiome changes attributed to BS.<br><br>CONCLUSIONS: Changes in the gut microbiome community and systemic levels of amino acids and sugars were directly derived from anatomical changes in the gastrointestinal tract after BS. We hypothesized that the observed increases in microbiome-related serum metabolites were a result of complex and indirect changes derived from BS. Ethnic-specific environmental or genetic factors could affect Korean-specific postmetabolic modification in obese patients who undergo BS.}, }
@article {pmid35007400, year = {2022}, author = {Zhang, J and Zhang, F and Tay, WT and Robin, C and Shi, Y and Guan, F and Yang, Y and Wu, Y}, title = {Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm.}, journal = {Molecular ecology resources}, volume = {22}, number = {5}, pages = {1875-1891}, doi = {10.1111/1755-0998.13581}, pmid = {35007400}, issn = {1755-0998}, support = {31930093//National Natural Science Foundation of China/ ; BP0719029//The SAFEA of China/ ; }, mesh = {Animals ; Biodiversity ; Gossypium ; *Insecticides ; Larva/genetics ; Metagenomics ; *Moths/genetics ; Temperature ; }, abstract = {The cotton bollworm Helicoverpa armigera is a cosmopolitan pest and its diverse habitats plausibly contribute to the formation of diverse lineages. Despite the significant threat it poses to economic crops worldwide, its evolutionary history and genetic basis of local adaptation are poorly understood. In this study, we de novo assembled a high-quality chromosome-level reference genome of H. a. armigera (contig N50 = 7.34 Mb), with 99.13% of the HaSCD2 assembly assigned to 31 chromosomes (Z-chromosome + 30 autosomes). We constructed an ultradense variation map across 14 cotton bollworm populations and identified a novel lineage in northwestern China. Historical inference showed that effective population size changes coincided with global temperature fluctuation. We identified nine differentiated genes in the three H. armigera lineages (H. a. armigera, H. a. conferta and the new northwestern Chinese lineage), of which per and clk genes are involved in circadian rhythm. Selective sweep analyses identified a series of Gene Ontology categories related to climate adaptation, feeding behaviour and insecticide tolerance. Our findings reveal fundamental knowledge of the local adaptation of different cotton bollworm lineages and will guide the formulation of cotton bollworm management measures at different scales.}, }
@article {pmid33315571, year = {2022}, author = {Liu, F and Miao, Y and Liu, Y and Hou, T}, title = {RNN-VirSeeker: A Deep Learning Method for Identification of Short Viral Sequences From Metagenomes.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {19}, number = {3}, pages = {1840-1849}, doi = {10.1109/TCBB.2020.3044575}, pmid = {33315571}, issn = {1557-9964}, mesh = {*Deep Learning ; Humans ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; *Viruses/genetics ; }, abstract = {Viruses are the most abundant biological entities on earth, and play vital roles in many aspects of microbial communities. As major human pathogens, viruses have caused huge mortality and morbidity to human society in history. Metagenomic sequencing methods could capture all microorganisms from microbiota, with sequences of viruses mixed with these of other species. Therefore, it is necessary to identify viral sequences from metagenomes. However, existing methods perform poorly on identifying short viral sequences. To solve this problem, a deep learning based method, RNN-VirSeeker, is proposed in this paper. RNN-VirSeeker was trained by sequences of 500bp sampled from known Virus and Host RefSeq genomes. Experimental results on the testing set have shown that RNN-VirSeeker exhibited AUROC of 0.9175, recall of 0.8640 and precision of 0.9211 for sequences of 500bp, and outperformed three widely used methods, VirSorter, VirFinder, and DeepVirFinder, on identifying short viral sequences. RNN-VirSeeker was also used to identify viral sequences from a CAMI dataset and a human gut metagenome. Compared with DeepVirFinder, RNN-VirSeeker identified more viral sequences from these metagenomes and achieved greater values of AUPRC and AUROC. RNN-VirSeeker is freely available at https://github.com/crazyinter/RNN-VirSeeker.}, }
@article {pmid35663881, year = {2022}, author = {Vidal, P and Martínez-Martínez, M and Fernandez-Lopez, L and Roda, S and Méndez-García, C and Golyshina, OV and Guallar, V and Peláez, AI and Ferrer, M}, title = {Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {868839}, doi = {10.3389/fmicb.2022.868839}, pmid = {35663881}, issn = {1664-302X}, abstract = {Acid mine drainage (AMD) systems are extremely acidic and are metal-rich formations inhabited by relatively low-complexity communities of acidophiles whose enzymes remain mostly uncharacterized. Indeed, enzymes from only a few AMD sites have been studied. The low number of available cultured representatives and genome sequences of acidophiles inhabiting AMDs makes it difficult to assess the potential of these environments for enzyme bioprospecting. In this study, using naïve and in silico metagenomic approaches, we retrieved 16 esterases from the α/β-hydrolase fold superfamily with the closest match from uncultured acidophilic Acidobacteria, Actinobacteria (Acidithrix, Acidimicrobium, and Ferrimicrobium), Acidiphilium, and other Proteobacteria inhabiting the Los Rueldos site, which is a unique AMD formation in northwestern Spain with a pH of ∼2. Within this set, only two polypeptides showed high homology (99.4%), while for the rest, the pairwise identities ranged between 4 and 44.9%, suggesting that the diversity of active polypeptides was dominated not by a particular type of protein or highly similar clusters of proteins, but by diverse non-redundant sequences. The enzymes exhibited amino acid sequence identities ranging from 39 to 99% relative to homologous proteins in public databases, including those from other AMDs, thus indicating the potential novelty of proteins associated with a specialized acidophilic community. Ten of the 16 hydrolases were successfully expressed in Escherichia coli. The pH for optimal activity ranged from 7.0 to 9.0, with the enzymes retaining 33-68% of their activities at pH 5.5, which was consistent with the relative frequencies of acid residues (from 54 to 67%). The enzymes were the most active at 30-65°C, retaining 20-61% of their activity under the thermal conditions characterizing Los Rueldos (13.8 ± 0.6°C). The analysis of the substrate specificity revealed the capacity of six hydrolases to efficiently degrade (up to 1,652 ± 75 U/g at pH 8.0 and 30°C) acrylic- and terephthalic-like [including bis(2-hydroxyethyl)-terephthalate, BHET] esters, and these enzymes could potentially be of use for developing plastic degradation strategies yet to be explored. Our assessment uncovers the novelty and potential biotechnological interest of enzymes present in the microbial populations that inhibit the Los Rueldos AMD system.}, }
@article {pmid35655185, year = {2022}, author = {Ziko, L and AbdelRaheem, O and Nabil, M and Aziz, RK and Siam, R}, title = {Bioprospecting the microbiome of Red Sea Atlantis II brine pool for peptidases and biosynthetic genes with promising antibacterial activity.}, journal = {Microbial cell factories}, volume = {21}, number = {1}, pages = {109}, pmid = {35655185}, issn = {1475-2859}, mesh = {Anti-Bacterial Agents/pharmacology ; Bioprospecting ; *Enterococcus faecium ; Humans ; Indian Ocean ; *Microbiota ; Peptide Hydrolases ; Salts ; }, abstract = {BACKGROUND: The search for novel antimicrobial agents is crucial as antibiotic-resistant pathogens continue to emerge, rendering the available antibiotics no longer effective. Likewise, new anti-cancer drugs are needed to combat the emergence of multi-drug resistant tumors. Marine environments are wealthy sources for natural products. Additionally, extreme marine environments are interesting niches to search for bioactive natural compounds. In the current study, a fosmid library of metagenomic DNA isolated from Atlantis II Deep Lower Convective Layer (ATII LCL), was functionally screened for antibacterial activity as well as anticancer effects.<br><br>RESULTS: Two clones exhibited antibacterial effects against the marine Bacillus Cc6 strain, namely clones 102-5A and 88-1G and they were further tested against eleven other challenging strains, including six safe relatives of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), a safe relative to Mycobacterium tuberculosis and four resistant clinical isolates. Clone 88-1G resulted in clear zones of inhibition against eight bacterial strains, while clone 102-5A resulted in zones of inhibition against five bacterial strains. The whole cell lysates of clone 88-1G showed 15% inhibition of Mtb ClpP protease -Mycobacterium tuberculosis drug target-, while whole cell lysates of clone 102-5A showed 19% inhibition of Mtb ClpP protease. Whole cell lysates from the selected clones exhibited anticancer effects against MCF-7 breast cancer cells (cell viability at 50% v/v was 46.2% ± 9.9 for 88-1G clone and 38% ± 7 for 102-5A clone), U2OS osteosarcoma cells (cell viability at 50% v/v was 64.6% ± 12.3 for 88-1G clone and 28.3% ± 1.7 for 102-5A clone) and 1BR hTERT human fibroblast cells (cell viability at 50% v/v was 74.4% ± 5.6 for 88-1G clone and 57.6% ± 8.9 for 102-5A clone). Sequencing of 102-5A and 88-1G clones, and further annotation detected putative proteases and putative biosynthetic genes in clones 102-5A and 88-1G, respectively.<br><br>CONCLUSIONS: The ATII LCL metagenome hosts putative peptidases and biosynthetic genes that confer antibiotic and anti-cancer effects. The tested clones exhibited promising antibacterial activities against safe relative strains to ESKAPE pathogens and Mycobacterium tuberculosis. Thus, searching the microbial dark matter of extreme environments is a promising approach to identify new molecules with pharmaceutical potential use.}, }
@article {pmid35654877, year = {2022}, author = {Stockdale, SR and Harrington, RS and Shkoporov, AN and Khokhlova, EV and Daly, KM and McDonnell, SA and O'Reagan, O and Nolan, JA and Sheehan, D and Lavelle, A and Draper, LA and Shanahan, F and Ross, RP and Hill, C}, title = {Metagenomic assembled plasmids of the human microbiome vary across disease cohorts.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9212}, pmid = {35654877}, issn = {2045-2322}, support = {SFI/14/SP APC/B3032//Science Foundation Ireland (SFI)/ ; SFI/12/RC/2273_P2//Science Foundation Ireland (SFI)/ ; }, mesh = {Humans ; *Inflammatory Bowel Diseases/genetics/microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Plasmids/genetics ; }, abstract = {We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.}, }
@article {pmid35651033, year = {2022}, author = {Hou, Q and Wang, Y and Cai, W and Ni, H and Zhao, H and Zhang, Z and Liu, Z and Liu, J and Zhong, J and Guo, Z}, title = {Metagenomic and physicochemical analyses reveal microbial community and functional differences between three types of low-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {156}, number = {}, pages = {111167}, doi = {10.1016/j.foodres.2022.111167}, pmid = {35651033}, issn = {1873-7145}, mesh = {Bacteria ; Fermentation ; *Metagenome ; Metagenomics ; *Microbiota ; Temperature ; }, abstract = {Complex microbes of different types of low-temperature Daqu (LTD) play an important role in the formation of flavors and qualities of light-flavor Baijiu during fermentation. However, characterizing the taxonomic and functional diversity of microbiota in three types of LTD (Houhuo, Hongxin, Qingcha) remains a major challenge. The present study combined metagenomic sequencing with culture-based methods and physicochemical analysis to compare the three LTD microbiota and elucidate their function in LFB brewing. The results revealed a high diversity of microbes in LTD, with 1286 genera and 4157 species detected across all studied samples. Bacteria and fungi were the main microbes in LTD, with a bacterial to fungal relative abundance ratio of above 4:1. Bacillus (21.18%) and Bacillus licheniformis (17.45%) were the most abundant microbes in the LTD microbiota at the genus and species levels, respectively. Culture-dependent analysis found the highest abundances of bacteria, fungi, and lactic acid bacteria in Houhuo, while the metagenomic-based microbiota found that the relative abundance of bacteria and fungi were highest in Houhuo and Hongxin among the three types of LTD, respectively. The different production temperatures of LTD had little effect on its microbial variety, but obviously impacted the microbiota structure and metagenomic function of LTD. Although the microbiota of the three types of LTD shared a high commonality, each had specific microbiota and functional metagenomic features, suggesting their different but complementary roles in the LFB fermentation process. The representative dominant microbes in Houhuo were mostly involved in metabolic pathways associated with the production of flavor substances in liquor. In contrast, the enriched microbes in Qingcha and Hongxin were not only capable of producing specific flavor substances but also had a strong ability to degrade macromolecular substances in raw materials, promoting microbial growth. This study has greatly enriched our knowledge of the effect of LTD fermentation temperature on its quality, providing practical and interesting information for future improvement of LTD and light-flavor Baijiu products.}, }
@article {pmid35544980, year = {2022}, author = {Patil, MP and Woo, HE and Lee, IC and Nakashita, S and Kim, K and Kim, JO and Kim, K}, title = {A microcosm study of microbial community profiles during sediment remediation using pyrolyzed oyster shells.}, journal = {Journal of environmental management}, volume = {316}, number = {}, pages = {115229}, doi = {10.1016/j.jenvman.2022.115229}, pmid = {35544980}, issn = {1095-8630}, mesh = {Animals ; Bacteria/genetics ; Geologic Sediments/microbiology ; *Microbiota ; *Ostreidae/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The accumulation of organic and inorganic components in sediments leads to a deterioration in the environment and an imbalance in the coastal ecosystem. Currently, capping is the most effective technology for remediating polluted sediment and restoring ecosystems. A microcosm experiment was designed using pyrolyzed oyster shell (POS). These were mixed in with coastal sediment or added as a capping layer. The results showed that POS effectively decreased pollutants, including PO4-P and NH4-N. Metagenomics analysis was performed using 16S rRNA gene sequencing and the most abundant phyla identified in the POS treated and untreated sediments were Proteobacteria, followed by Firmicutes, Bacteroidetes, Chloroflexi, Fusobacteria, Nitrospirae, and Spirochaetes. The relative abundance of Proteobacteria members of the Class Gammaproteobacteria significantly increased, but Deltaproteobacteria gradually decreased throughout the experiment in POS-covered sediment. This suggests that the POS effectively promoted a shift from anaerobic to facultative anaerobic or aerobic microbial communities in the sediment. Dominant species of facultative anaerobic or microaerophilic bacteria from the order Chromatiales and phylum Nitrospirae were observed in the POS-covered sediment. Based on these study results, it can be concluded that POS is an effective covering material for sediment remediation and restores the microbial communities in sediments.}, }
@article {pmid35526643, year = {2022}, author = {Drovetski, SV and Schmidt, BK and Lai, JE and Gross, MS and Hladik, ML and Matterson, KO and Karouna-Renier, NK}, title = {Exposure to crop production alters cecal prokaryotic microbiota, inflates virulome and resistome in wild prairie grouse.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {306}, number = {}, pages = {119418}, doi = {10.1016/j.envpol.2022.119418}, pmid = {35526643}, issn = {1873-6424}, mesh = {Animals ; Chickens ; Crop Production ; *Grassland ; *Microbiota ; Quail ; }, abstract = {Chemically intensive crop production depletes wildlife food resources, hinders animal development, health, survival, and reproduction, and it suppresses wildlife immune systems, facilitating emergence of infectious diseases with excessive mortality rates. Gut microbiota is crucial for wildlife's response to environmental stressors. Its composition and functionality are sensitive to diet changes and environmental pollution associated with modern crop production. In this study we use shotgun metagenomics (median 8,326,092 sequences/sample) to demonstrate that exposure to modern crop production detrimentally affects cecal microbiota of sharp-tailed grouse (Tympanuchus phasianellus: 9 exposed, 18 unexposed and greater prairie chickens (T. cupido; 11, 11). Exposure to crop production had greater effect on microbiota richness (t = 6.675, P < 0.001) and composition (PERMANOVA r2 = 0.212, P = 0.001) than did the host species (t = 4.762, P < 0.001; r2 = 0.070, P = 0.001) or their interaction (t = 3.449; r2 = 0.072, both P = 0.001), whereas sex and age had no effect. Although microbiota richness was greater in exposed (T. cupido chao1 = 152.8 ± 20.5; T. phasianellus 115.3 ± 17.1) than in unexposed (102.9 ± 15.1 and 101.1 ± 17.2, respectively) birds, some beneficial bacteria dropped out of exposed birds' microbiota or declined and were replaced by potential pathogens. Exposed birds also had higher richness and load of virulome (mean ± standard deviation; T. cupido 24.8 ± 10.0 and 10.1 ± 5.5, respectively; T. phasianellus 13.4 ± 6.8/4.9 ± 2.8) and resistome (T. cupido 46.8 ± 11.7/28.9 ± 10.2, T. phasianellus 38.3 ± 16.7/18.9 ± 14.2) than unexposed birds (T. cupido virulome: 14.2 ± 13.5, 4.5 ± 4.2; T. cupido resistome: 31.6 ± 20.2 and 13.1 ± 12.0; T. phasianellus virulome: 5.2 ± 4.7 and 1.4 ± 1.5; T. phasianellus resistome: 13.7 ± 16.1 and 4.0 ± 6.4).}, }
@article {pmid35504350, year = {2022}, author = {Wang, X and Liu, X and Xiao, S and Zhang, Z and Wu, L and Cheng, Y and Tan, Y and Zhang, G and Jiang, C}, title = {Comparison of gut microbiota compositions and corresponding genetic and metabolic features between guttate and plaque psoriasis by metagenomic sequencing.}, journal = {Microbial pathogenesis}, volume = {167}, number = {}, pages = {105560}, doi = {10.1016/j.micpath.2022.105560}, pmid = {35504350}, issn = {1096-1208}, mesh = {*Epstein-Barr Virus Infections ; *Gastrointestinal Microbiome/genetics ; Herpesvirus 4, Human ; Humans ; Metagenomics ; *Psoriasis ; }, abstract = {BACKGROUND: Guttate psoriasis (GP) and psoriasis plaques (PP) are common subtypes of psoriasis. Previous studies have fully researched the association between psoriasis and gut microbiota. However, the differences in gut microbiota between GPs and PPs are still unknown.<br><br>METHODS: Fecal samples were collected from 30 psoriatic patients (15 GP and 15 PP) and 15 healthy subjects. Metagenomic sequencing was then used to compare gut microbiota compositions and corresponding genetic and metabolic features between GP and PP.<br><br>RESULTS: We found that the genus Megamonas was increased in PP and reduced in GP. The genus Eubacterium was increased in GP and decreased in PP. Ten KEGG pathway were significantly enriched in GP: bacterial secretion system, ribosome, sphingolipid signaling pathway, steroid hormone biosynthesis, complement and coagulation cascades, proteoglycans in cancer, FOXO signaling pathway, cGMP-PKG signaling pathway, insulin resistance, and Epstein-Barr virus infection. Ten metabolites were significantly differentially abundant between GP and PP. Among them, thiamine, biotin, butylamine, phenylethylamine, folic acid, 1,2-propanediol, and 4-aminobutyrate were enriched in PP and l-glutamate, l-glutamine, and propanoate were enriched in GP.<br><br>CONCLUSIONS: These results provide a theoretical basis for the microbiome-guided stratification of patients with psoriasis.}, }
@article {pmid35421499, year = {2022}, author = {Haque, S and Srivastava, N and Pal, DB and Alkhanani, MF and Almalki, AH and Areeshi, MY and Naidu, R and Gupta, VK}, title = {Functional microbiome strategies for the bioremediation of petroleum-hydrocarbon and heavy metal contaminated soils: A review.}, journal = {The Science of the total environment}, volume = {833}, number = {}, pages = {155222}, doi = {10.1016/j.scitotenv.2022.155222}, pmid = {35421499}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Humans ; Hydrocarbons ; *Metals, Heavy/analysis ; *Microbiota ; *Petroleum/metabolism ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Petroleum hydrocarbons and heavy metals are the two major soil contaminants that are released into the environment in the forms of industrial effluents. These contaminants exert serious impacts on human health and the sustainability of the environment. In this context, remediation of these pollutants via a biological approach can be effective, low-cost, and eco-friendly approach. The implementation of microorganisms and metagenomics are regarded as the advanced solution for remediating such pollutants. Further, microbiomes can overcome this issue via adopting specific structural, functional and metabolic pathways involved in the microbial community to degrade these pollutants. Genomic sequencing and library can effectively channelize the degradation of these pollutants via microbiomes. Nevertheless, more advanced technology and reliable strategies are required to develop. The present review provides insights into the role of microbiomes to effectively remediate/degrade petroleum hydrocarbons and heavy metals in contaminated soil. The possible degradation mechanisms of these pollutants have also been discussed in detail along with their existing limitations. Finally, prospects of the bioremediation strategies using microbiomes are discussed.}, }
@article {pmid35421490, year = {2022}, author = {Hu, J and Liu, G and Li, H and Luo, H and Zhang, R}, title = {Synergistic effect of bioanode and biocathode on nitrobenzene removal: Microbial community structure and functions.}, journal = {The Science of the total environment}, volume = {833}, number = {}, pages = {155190}, doi = {10.1016/j.scitotenv.2022.155190}, pmid = {35421490}, issn = {1879-1026}, mesh = {*Bioelectric Energy Sources ; Electricity ; Electrodes ; Glucose ; *Microbiota ; Nitrobenzenes/metabolism ; }, abstract = {This study aimed to reveal the synergistic effect of bioanode and biocathode on nitrobenzene (NB) removal with different microbial community structures and functions. Single-chamber bioelectrochemical reactors were constructed and operated with different initial concentrations of NB and glucose as the substrate. With the synergistic effect of biocathode and bioanode, NB was completely removed within 8 h at a kinetic rate constant of 0.8256 h-1, and high conversion rate from NB to AN (92%) was achieved within 18 h. The kinetic rate constant of NB removal was linearly correlated with the maximum current density and total coulombs (R2 > 0.95). Increase of glucose and NB concentrations had significantly positive and negative effects, respectively, on the NB removal kinetics (R2 > 0.97 and R2 > 0.93, respectively). Geobacter sp. and Enterococcus sp. dominated in the bioanode and biocathode, respectively. The presence of Klebsiella pneumoniae in the bioanode was beneficial for Geobacter species to produce electricity and to alleviate the NB inhibition. As one of the dominant species at the biocathode, Methanobacterium formicicum has the ability of nitroaromatics degradation according to KEGG analysis, which played a crucial role for NB reduction. Fermentative bacteria converted glucose into volatile fatty acids or H2, to provide energy sources to other species (e.g., Geobacter sulfurreducens and Methanobacterium formicicum). The information from this study is useful to optimize the bioelectrocatalytic system for nitroaromatic compound removal.}, }
@article {pmid35398777, year = {2022}, author = {Zhang, Z and Jiao, Q and Zhang, Y and Liu, B and Wang, Y and Li, J}, title = {OTUCD: Unsupervised GCN based metagenomics non-overlapping community detection.}, journal = {Computational biology and chemistry}, volume = {98}, number = {}, pages = {107670}, doi = {10.1016/j.compbiolchem.2022.107670}, pmid = {35398777}, issn = {1476-928X}, mesh = {Algorithms ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Metagenomics is a discipline that studies the genetic material of all tiny organisms in the biological environment. In recent years, the interaction between metagenomic microbial communities, the transfer of horizontal genes, and the dynamic changes of microbial ecosystems have attracted more and more attention. It is of great significance to use the community detection algorithm to divide the metagenomic microbes into modules, and it has a positive guiding role for the follow-up research on human, drug, microbial interaction study and drug prediction and development. At present, there are challenges in mining the effective information hidden in large-scale microbial sequence data. The non-linear characteristics and non-scalability of microbial sequence data still bother people. This paper proposes an end-to-end unsupervised GCN learning model OTUCD (Operational Classification Unit Community Detection), which divides large-scale metagenomic sequence data into potential gene modules. We construct an OTU network, and then performs subsequent nonoverlapping community detection task with graph convolutional networks. Experimental scores show that the community detection effect of this method is better than other latest metagenomic algorithms.}, }
@article {pmid33607296, year = {2021}, author = {Yang, Y and Wang, X and Xie, K and Zhu, C and Chen, N and Chen, T}, title = {kLDM: Inferring Multiple Metagenomic Association Networks Based on the Variation of Environmental Factors.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {19}, number = {5}, pages = {834-847}, doi = {10.1016/j.gpb.2020.06.015}, pmid = {33607296}, issn = {2210-3244}, mesh = {Algorithms ; Computational Biology/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Identification of significant biological relationships or patterns is central to many metagenomic studies. Methods that estimate association networks have been proposed for this purpose; however, they assume that associations are static, neglecting the fact that relationships in a microbial ecosystem may vary with changes in environmental factors (EFs), which can result in inaccurate estimations. Therefore, in this study, we propose a computational model, called the k-Lognormal-Dirichlet-Multinomial (kLDM) model, which estimates multiple association networks that correspond to specific environmental conditions, and simultaneously infers microbe-microbe and EF-microbe associations for each network. The effectiveness of the kLDM model was demonstrated on synthetic data, a colorectal cancer (CRC) dataset, the Tara Oceans dataset, and the American Gut Project dataset. The results revealed that the widely-used Spearman's rank correlation coefficient method performed much worse than the other methods, indicating the importance of separating samples by environmental conditions. Cancer fecal samples were then compared with cancer-free samples, and the estimation achieved by kLDM exhibited fewer associations among microbes but stronger associations between specific bacteria, especially five CRC-associated operational taxonomic units, indicating gut microbe translocation in cancer patients. Some EF-dependent associations were then found within a marine eukaryotic community. Finally, the gut microbial heterogeneity of inflammatory bowel disease patients was detected. These results demonstrate that kLDM can elucidate the complex associations within microbial ecosystems. The kLDM program, R, and Python scripts, together with all experimental datasets, are accessible at https://github.com/tinglab/kLDM.git.}, }
@article {pmid35641634, year = {2022}, author = {Le Bras, A}, title = {Studying the murine gut resistome.}, journal = {Lab animal}, volume = {51}, number = {6}, pages = {156}, doi = {10.1038/s41684-022-00990-5}, pmid = {35641634}, issn = {1548-4475}, mesh = {Animals ; *Gastrointestinal Microbiome ; Metagenomics ; Mice ; Research ; }, }
@article {pmid35637399, year = {2022}, author = {Salih, H and Karaynir, A and Yalcin, M and Oryasin, E and Holyavkin, C and Basbulbul, G and Bozdogan, B}, title = {Metagenomic analysis of wastewater phageome from a University Hospital in Turkey.}, journal = {Archives of microbiology}, volume = {204}, number = {6}, pages = {353}, pmid = {35637399}, issn = {1432-072X}, mesh = {*Bacteriophages/genetics ; Ecosystem ; Hospitals ; Humans ; *Podoviridae/genetics ; Turkey ; Virome ; Waste Water ; }, abstract = {Phage DNA analysis gives opportunity to understand living ecosystem of the environment where the samples are taken. In the present study, we analyzed phage DNA obtained from wastewater sample of university hospital sewage. After filtration, long high-speed centrifugation was done to collect phages. DNA was extracted from pellet by phenol chloroform extraction and used for NGS sequencing. The host profile, taxonomic and functional analyses were performed using MG-RAST, and ResFinder program was used for resistance gene detection. High amounts of reads belong to bacteriophage groups (~ 95%) from our DNA sample were obtained and all bacteriophage reads were found belonging to Caudovirales order and Myoviridae (56%), Siphoviridae (43%), and Podoviridae (0.02%) families. The most common host genera were Escherichia (88.20%), Salmonella (5.49%) and Staphylococcus (5.19%). SEED subsystems hits were mostly structural parts and KEGG Orthology hits were nucleotide- and carbohydrate metabolism-related genes. No anti-microbial resistance genes were detected. Our bacteriophage DNA purification method is favorable for phage metagenomic studies. Dominance of coliphages may explain infrequent Podoviridae. Dominancy of structural genes and auxiliary genes is probably due to abundance of lytic phages in our sample. Absence of antibiotic resistance genes even in hospital environment phages indicates that phages are not important carrier of resistance genes.}, }
@article {pmid35190727, year = {2022}, author = {Metwaly, A and Reitmeier, S and Haller, D}, title = {Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {19}, number = {6}, pages = {383-397}, pmid = {35190727}, issn = {1759-5053}, mesh = {Biomarkers ; *Diabetes Mellitus, Type 2/microbiology ; Dysbiosis/microbiology ; Humans ; *Metabolic Diseases ; *Microbiota ; }, abstract = {The intestine harbours a complex array of microorganisms collectively known as the gut microbiota. The past two decades have witnessed increasing interest in studying the gut microbiota in health and disease, largely driven by rapid innovation in high-throughput multi-omics technologies. As a result, microbial dysbiosis has been linked to many human pathologies, including type 2 diabetes mellitus and inflammatory bowel disease. Integrated analyses of multi-omics data, including metagenomics and metabolomics along with measurements of host response and cataloguing of bacterial isolates, have identified many bacteria and bacterial products that are correlated with disease. Nevertheless, insight into the mechanisms through which microbes affect intestinal health requires going beyond correlation to causation. Current understanding of the contribution of the gut microbiota to disease causality remains limited, largely owing to the heterogeneity of microbial community structures, interindividual differences in disease evolution and incomplete understanding of the mechanisms that integrate microbiota-derived signals into host signalling pathways. In this Review, we provide a broad insight into the microbiome signatures linked to inflammatory and metabolic disorders, discuss outstanding challenges in this field and propose applications of multi-omics technologies that could lead to an improved mechanistic understanding of microorganism-host interactions.}, }
@article {pmid35632601, year = {2022}, author = {Litov, AG and Zueva, AI and Tiunov, AV and Van Thinh, N and Belyaeva, NV and Karganova, GG}, title = {Virome of Three Termite Species from Southern Vietnam.}, journal = {Viruses}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/v14050860}, pmid = {35632601}, issn = {1999-4915}, support = {0837-2019-0007//Ministry of Science and Higher Education of Russia/ ; АААА-А19-119073090024-0//Ministry of Science and Higher Education of Russia/ ; }, mesh = {Animals ; Ecosystem ; Forests ; *Isoptera ; *RNA Viruses ; Vietnam ; Virome ; }, abstract = {Modern metagenomic approaches enable the effective discovery of novel viruses in previously unexplored organisms. Termites are significant ecosystem converters and influencers. As with the majority of tropical forest insects, termites are studied insufficiently, and termite virome remains especially understudied. Here, we studied the virome of lichenophagous and mycophagous termites (Hospitalitermes bicolor, Macrotermes carbonarius and Odontotermes wallonensis) collected in the Cat Tien National Park (Vietnam). We assembled four full genomes of novel viruses related to Solemoviridae, Lispiviridae, Polycipiviridae and Kolmioviridae. We also found several contigs with relation to Chuviridae and Deltaflexiviridae that did not correspond to complete virus genomes. All the novel viruses clustered phylogenetically with previously identified viruses of the termites. Deltaflexi-like contigs were identified in the fungi-cultivating M. carbonarius and showed homology with viruses recently discovered in the edible basidiomycete mushrooms.}, }
@article {pmid35627235, year = {2022}, author = {Silva, I and Alves, M and Malheiro, C and Silva, ARR and Loureiro, S and Henriques, I and González-Alcaraz, MN}, title = {Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation.}, journal = {Genes}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/genes13050850}, pmid = {35627235}, issn = {2073-4425}, support = {PTDC/CTA-AMB/29557/2017//Fundação para a Ciência e Tecnologia/ ; UIDP/50017/2020+UIDB/50017/2020 + LA/P/0094/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/04004/2020//Fundação para a Ciência e Tecnologia/ ; PD/BD/135577/2018//Fundação para a Ciência e Tecnologia/ ; Saavedra Fajardo//Fundación Seneca/ ; MICROCLIM//French National Centre for Scientific Research/ ; 704332//European Union Horizon 2020 - Marie Sklodowska-Curie/ ; }, mesh = {Bacteria/genetics ; DNA, Ribosomal ; *Microbiota ; *Soil/chemistry ; Temperature ; Ultraviolet Rays ; Water ; }, abstract = {We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community's response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 °C + 50% water holding capacity (WHC)); increased air temperature (15-25 °C or 20-30 °C + 50% WHC); flood (20 °C + 75% WHC); drought (20 °C + 25% WHC); and ultraviolet radiation (UV) (20 °C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community's physiological profile and the bacterial community's structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20-30 °C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome-invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.}, }
@article {pmid35624491, year = {2022}, author = {Arora, J and Kinjo, Y and Šobotník, J and Buček, A and Clitheroe, C and Stiblik, P and Roisin, Y and Žifčáková, L and Park, YC and Kim, KY and Sillam-Dussès, D and Hervé, V and Lo, N and Tokuda, G and Brune, A and Bourguignon, T}, title = {The functional evolution of termite gut microbiota.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {78}, pmid = {35624491}, issn = {2049-2618}, support = {20-20548S//Czech Science Foundation/ ; CULS (20213112)//Czech University of Life Sciences/ ; 17H01510//Japan Society for the Promotion of Science/ ; DC2 grant//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Isoptera ; Metagenome ; Phylogeny ; Soil ; }, abstract = {BACKGROUND: Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of termite gut microbiota.<br><br>RESULTS: We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that essential nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways.<br><br>CONCLUSIONS: Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ~ 150 million years ago. Therefore, the "world's smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception. Video Abstract.}, }
@article {pmid35382951, year = {2022}, author = {Orbe-Orihuela, YC and Godoy-Lozano, EE and Lagunas-Martínez, A and Castañeda-Márquez, AC and Murga-Garrido, S and Díaz-Benítez, CE and Ochoa-Leyva, A and Cornejo-Granados, F and Cruz, M and Estrada, K and Bermúdez-Morales, VH and Sanchez-Flores, A and Burguete-García, AI}, title = {Association of Gut Microbiota with Dietary-dependent Childhood Obesity.}, journal = {Archives of medical research}, volume = {53}, number = {4}, pages = {407-415}, doi = {10.1016/j.arcmed.2022.03.007}, pmid = {35382951}, issn = {1873-5487}, mesh = {Body Mass Index ; Carbohydrates ; Child ; Cross-Sectional Studies ; Diet ; *Gastrointestinal Microbiome ; Humans ; *Pediatric Obesity/epidemiology/etiology ; }, abstract = {AIM: To evaluate the taxonomic profile of the gut microbiota using metagenomics and the association with diet-dependent childhood obesity.<br><br>METHODS: A cross-sectional study of a subsample of 46 children was conducted. The children were classified as normal-weight, overweight, and obese according to their age and sex and the World Health Organization (WHO) guidelines. Dietary patterns were determined through principal component analysis. The profile of the human gut microbiota was determined by bioinformatic analysis using whole metagenome shotgun sequencing. The association of gut microbiota and z-BMI, waist circumference and hip circumference, and the possible modifying effect of diet were analyzed using multiple regression models.<br><br>RESULTS: Children with an abundance of Holdemania spp. and high protein and complex carbohydrate consumption had a lower z-BMI (β -19.06, p = 0.011), waist circumference (β -171.92, p = 0.003), and hip circumference (β -157.57, p = 0.004). In contrast, observed a positive association between Coprococcus catus and the low intake of this dietary pattern with hip circumference (β 147.87, p = 0.025). Furthermore, the presence of Bilophila spp. and Paraprevotella xylaniphila with high saturated fat and simple carbohydrate consumption we observed a positive association between z-BMI (β 47.5, p = 0.002), hip circumference (β 44.54, p = 0.025), and waist circumference (β 44.34, p = 0.004).<br><br>CONCLUSION: We suggest that the synergism between diet and the profile of children's gut microbiota can be a factor that could be associated with the development of obesity and its complications in childhood.}, }
@article {pmid35613310, year = {2022}, author = {Luo, T and Guo, Z and Liu, D and Guo, Z and Wu, Q and Li, Q and Lin, R and Chen, P and Ou, C and Chen, M}, title = {Deficiency of PSRC1 accelerates atherosclerosis by increasing TMAO production via manipulating gut microbiota and flavin monooxygenase 3.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2077602}, doi = {10.1080/19490976.2022.2077602}, pmid = {35613310}, issn = {1949-0984}, mesh = {Animals ; Apolipoproteins E/genetics ; *Atherosclerosis/genetics/microbiology ; Bacteria/genetics/metabolism ; Flavins ; *Gastrointestinal Microbiome/physiology ; Methylamines/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mixed Function Oxygenases ; *Plaque, Atherosclerotic ; }, abstract = {Maladaptive inflammatory and immune responses are responsible for intestinal barrier integrity and function dysregulation. Proline/serine-rich coiled-coil protein 1 (PSRC1) critically contributes to the immune system, but direct data on the gut microbiota and the microbial metabolite trimethylamine N-oxide (TMAO) are lacking. Here, we investigated the impact of PSRC1 deletion on TMAO generation and atherosclerosis. We first found that PSRC1 deletion in apoE-/- mice accelerated atherosclerotic plaque formation, and then the gut microbiota and metabolites were detected using metagenomics and untargeted metabolomics. Our results showed that PSRC1 deficiency enriched trimethylamine (TMA)-producing bacteria and functional potential for TMA synthesis and accordingly enhanced plasma betaine and TMAO production. Furthermore, PSRC1 deficiency resulted in a proinflammatory colonic phenotype that was significantly associated with the dysregulated bacteria. Unexpectedly, hepatic RNA-seq indicated upregulated flavin monooxygenase 3 (FMO3) expression following PSRC1 knockout. Mechanistically, PSRC1 overexpression inhibited FMO3 expression in vitro, while an ERα inhibitor rescued the downregulation. Consistently, PSRC1-knockout mice exhibited higher plasma TMAO levels with a choline-supplemented diet, which was gut microbiota dependent, as evidenced by antibiotic treatment. To investigate the role of dysbiosis induced by PSRC1 deletion in atherogenesis, apoE-/- mice were transplanted with the fecal microbiota from either apoE-/- or PSRC1-/-apoE-/- donor mice. Mice that received PSRC1-knockout mouse feces showed an elevation in TMAO levels, as well as plaque lipid deposition and macrophage accumulation, which were accompanied by increased plasma lipid levels and impaired hepatic cholesterol transport. Overall, we identified PSRC1 as an atherosclerosis-protective factor, at least in part, attributable to its regulation of TMAO generation via a multistep pathway. Thus, PSRC1 holds great potential for manipulating the gut microbiome and alleviating atherosclerosis.}, }
@article {pmid35612791, year = {2022}, author = {Fong, SB and Boyer, E and Bonnaure-Mallet, M and Meuric, V}, title = {Microbiota in Periodontitis: Advances in the Omic Era.}, journal = {Advances in experimental medicine and biology}, volume = {1373}, number = {}, pages = {19-43}, pmid = {35612791}, issn = {0065-2598}, mesh = {Bacteria/genetics ; Biofilms ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; *Periodontitis/microbiology ; }, abstract = {The complexity of the oral microbiome continues to astound researchers even with the advancement of multi-disciplinary strategies being used to study these microorganisms in relation to the human body. There is extensive literature available that explains how oral bacterial communities exist within the biofilm and maintains a balance with the host immune system, but when this balance is tipped disease can occur. The purpose of this review is to highlight the subgingival microbial compositions during health and periodontal disease using next generation sequencing techniques, as well as determining the types of functional activities that partake during these states. The subgingival microbiota is a fluid structure that can adapt accordingly to the environment and the identification of signature biomarkers may aid in the assessment of risk and disease severity in an individual to complement clinical diagnosis in the future.}, }
@article {pmid35608941, year = {2022}, author = {Otake-Kasamoto, Y and Kayama, H and Kishikawa, T and Shinzaki, S and Tashiro, T and Amano, T and Tani, M and Yoshihara, T and Li, B and Tani, H and Liu, L and Hayashi, A and Okuzaki, D and Motooka, D and Nakamura, S and Okada, Y and Iijima, H and Takeda, K and Takehara, T}, title = {Lysophosphatidylserines derived from microbiota in Crohn's disease elicit pathological Th1 response.}, journal = {The Journal of experimental medicine}, volume = {219}, number = {7}, pages = {}, doi = {10.1084/jem.20211291}, pmid = {35608941}, issn = {1540-9538}, support = {//Core Research for Evolutional Science and TechnologyPRIME/ ; 19gm1010004//Japan Agency for Medical Research and Development/ ; //Osaka University Graduate School of Medicine/ ; //Immunology Frontier Research Center/ ; 17H04159//Grant-in-Aid for Scientific Research/ ; }, mesh = {Animals ; *Colitis/pathology ; *Crohn Disease/etiology ; Dysbiosis/complications ; Humans ; Inflammation/pathology ; Intestinal Mucosa/metabolism ; Lysophospholipids ; Mice ; *Microbiota ; Th1 Cells/metabolism ; }, abstract = {Microbiota alteration and IFN-γ-producing CD4+ T cell overactivation are implicated in Crohn's disease (CD) pathogenesis. However, it remains unclear how dysbiosis enhances Th1 responses, leading to intestinal inflammation. Here, we identified key metabolites derived from dysbiotic microbiota that induce enhanced Th1 responses and exaggerate colitis in mouse models. Patients with CD showed elevated lysophosphatidylserine (LysoPS) concentration in their feces, accompanied by a higher relative abundance of microbiota possessing a gene encoding the phospholipid-hydrolyzing enzyme phospholipase A. LysoPS induced metabolic reprogramming, thereby eliciting aberrant effector responses in both human and mouse IFN-γ-producing CD4+ T cells. Administration of LysoPS into two mouse colitis models promoted large intestinal inflammation. LysoPS-induced aggravation of colitis was impaired in mice lacking P2ry10 and P2ry10b, and their CD4+ T cells were hyporesponsive to LysoPS. Thus, our findings elaborate on the mechanism by which metabolites elevated in patients with CD harboring dysbiotic microbiota promote Th1-mediated intestinal pathology.}, }
@article {pmid35595870, year = {2022}, author = {Shi, H and Nelson, JW and Phillips, S and Petrosino, JF and Bryan, RM and Durgan, DJ}, title = {Alterations of the gut microbial community structure and function with aging in the spontaneously hypertensive stroke prone rat.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8534}, pmid = {35595870}, issn = {2045-2322}, support = {T32 GM008231/NH/NIH HHS/United States ; R01NS102594/NS/NINDS NIH HHS/United States ; R01HL134838/HL/NHLBI NIH HHS/United States ; DK56338//U.S. Public Health Service/ ; 16SDG29970000//American Heart Association/ ; }, mesh = {Aging ; Animals ; Blood Pressure/physiology ; Dysbiosis ; *Gastrointestinal Microbiome ; *Hypertension ; Rats ; Rats, Inbred SHR ; Rats, Inbred WKY ; *Stroke ; Tryptophan ; }, abstract = {Gut dysbiosis, a pathological imbalance of bacteria, has been shown to contribute to the development of hypertension (HT), systemic- and neuro-inflammation, and blood-brain barrier (BBB) disruption in spontaneously hypertensive stroke prone rats (SHRSP). However, to date individual species that contribute to HT in the SHRSP model have not been identified. One potential reason, is that nearly all studies of the SHRSP gut microbiota have analyzed samples from rats with established HT. The goal of this study was to examine the SHRSP gut microbiota before, during, and after the onset of hypertension, and in normotensive WKY control rats over the same age range. We hypothesized that we could identify key microbes involved in the development of HT by comparing WKY and SHRSP microbiota during the pre-hypertensive state and longitudinally. Systolic blood pressure (SBP) was measured by tail-cuff plethysmography and fecal microbiota analyzed by16S rRNA gene sequencing. SHRSP showed significant elevations in SBP, as compared to WKY, beginning at 8 weeks of age (p < 0.05 at each time point). Bacterial community structure was significantly different between WKY and SHRSP as early as 4 weeks of age, and remained different throughout the study (p = 0.001-0.01). At the phylum level we observed significantly reduced Firmicutes and Deferribacterota, and elevated Bacteroidota, Verrucomicrobiota, and Proteobacteria, in pre-hypertensive SHRSP, as compared to WKY. At the genus level we identified 18 bacteria whose relative abundance was significantly different in SHRSP versus WKY at the pre-hypertensive ages of 4 or 6 weeks. In an attempt to further refine bacterial candidates that might contribute to the SHRSP phenotype, we compared the functional capacity of WKY versus SHRSP microbial communities. We identified significant differences in amino acid metabolism. Using untargeted metabolomics we found significant reductions in metabolites of the tryptophan-kynurenine pathway and increased indole metabolites in SHRSP versus WKY plasma. Overall, we provide further evidence that gut dysbiosis contributes to hypertension in the SHRSP model, and suggest for the first time the potential involvement of tryptophan metabolizing microbes.}, }
@article {pmid35595857, year = {2022}, author = {Gao, S and Khan, MI and Kalsoom, F and Liu, Z and Chen, Y and Chen, Z}, title = {Role of gene regulation and inter species interaction as a key factor in gut microbiota adaptation.}, journal = {Archives of microbiology}, volume = {204}, number = {6}, pages = {342}, pmid = {35595857}, issn = {1432-072X}, mesh = {Acclimatization ; Adaptation, Physiological/genetics ; Animals ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; }, abstract = {Gut microbiota is a class of microbial flora present in various eukaryotic multicellular complex animals such as human beings. Their community's growth and survival are greatly influenced by various factors such as host-pathogen, pathogen-environment and genetic regulation. Modern technologies like metagenomics have particularly extended our capacity to uncover the microbial treasures in challenging conditions like communities surviving at high altitude. Molecular characterizations by newly developed sequencing tools have shown that this complex interaction greatly influences microbial adaptation to the environment. Literature shows that gut microbiota alters the genetic expression and switches to an alternative pathway under the influence of unfavorable conditions. The remarkable adaptability of microbial genetic regulatory networks enables them to survive and expand in tough and energy-limited conditions. Variable prevalence of species in various regions has strengthened this initial evidence. In view of the interconnection of the world in the form of a global village, this phenomenon must be explored more clearly. In this regard, recently there has been significant addition of knowledge to the field of microbial adaptation. This review summarizes and shed some light on mechanisms of microbial adaptation via gene regulation and species interaction in gut microbiota.}, }
@article {pmid35526357, year = {2022}, author = {Parente, E and Zotta, T and Ricciardi, A}, title = {FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities.}, journal = {International journal of food microbiology}, volume = {372}, number = {}, pages = {109696}, doi = {10.1016/j.ijfoodmicro.2022.109696}, pmid = {35526357}, issn = {1879-3460}, mesh = {*Bacteria/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {With the availability of high-throughput sequencing techniques our knowledge of the structure and dynamics of food microbial communities has made a quantum leap. However, this knowledge is dispersed in a large number of papers and hard data are only partly available through powerful on-line databases and tools such as QIITA, MGnify and the Integrated Microbial Next Generation Sequencing platform, whose annotation is not optimized for foods. Here, we present the 4th iteration of FoodMicrobionet, a database of the composition of bacterial microbial communities of foods and food environments. With 180 studies and 10,151 samples belonging to 8 major food groups FoodMicrobionet 4.1.2 is arguably the largest and best annotated database on food bacterial communities. This version includes 1684 environmental samples and 8467 food samples, belonging to 16 L1 categories and 196 L6 categories of the EFSA FoodEx2 classification and is approximately 4 times larger than previous version (3.1, https://doi.org/10.1016/j.ijfoodmicro.2019.108249). As a representative case study among the many potential applications of FoodMicrobionet, we confirm that taxonomic assignment at the genus level can be performed confidently for the majority of amplicon sequence variants using the most commonly used 16S RNA gene target regions (V1-V3, V3-V4, V4), with best results with higher quality sequences and longer fragment lengths, but that care should be exercised in confirming the assignment at species level. Both FoodMicrobionet and related data and software conform to FAIR (findable, accessible, interoperable, reusable/reproducible) criteria for scientific data and software and are freely available on public repositories (GitHub, Mendeley data). Even if FoodMicrobionet does not have the sophistication of QIITA, IMNGS and MGnify, we feel that this iteration, due to its size and diversity, provides a valuable asset for both the scientific community and industrial and regulatory stakeholders.}, }
@article {pmid35504157, year = {2022}, author = {Hegarty, B and Dai, Z and Raskin, L and Pinto, A and Wigginton, K and Duhaime, M}, title = {A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use.}, journal = {Water research}, volume = {218}, number = {}, pages = {118484}, doi = {10.1016/j.watres.2022.118484}, pmid = {35504157}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Chlorine ; *Disinfectants/pharmacology ; *Drinking Water ; Metagenomics ; Virome ; *Viruses/genetics ; *Water Purification ; }, abstract = {Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.}, }
@article {pmid35266150, year = {2022}, author = {Carrell, AA and Lawrence, TJ and Cabugao, KGM and Carper, DL and Pelletier, DA and Lee, JH and Jawdy, SS and Grimwood, J and Schmutz, J and Hanson, PJ and Shaw, AJ and Weston, DJ}, title = {Habitat-adapted microbial communities mediate Sphagnum peatmoss resilience to warming.}, journal = {The New phytologist}, volume = {234}, number = {6}, pages = {2111-2125}, doi = {10.1111/nph.18072}, pmid = {35266150}, issn = {1469-8137}, support = {DE-AC02-05CH11231//Biological and Environmental Research/ ; DE-AC05-00OR22725//Biological and Environmental Research/ ; DEB-1737899//National Science Foundation (NSF), USA/ ; 1928514//National Science Foundation (NSF), USA/ ; //Office of Science/ ; DE-AC05-00OR22725//US Department of Energy (DOE)/ ; DE-AC02-05CH11231//US Department of Energy (DOE)/ ; }, mesh = {Carbon ; Ecosystem ; Metagenome ; *Microbiota ; *Sphagnopsida/physiology ; Temperature ; }, abstract = {Sphagnum peatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long-term storage of atmospheric carbon. Warming threatens Sphagnum mosses and is known to alter the composition of their associated microbiome. Here, we use a microbiome transfer approach to test if microbiome thermal origin influences host plant thermotolerance. We leveraged an experimental whole-ecosystem warming study to collect field-grown Sphagnum, mechanically separate the associated microbiome and then transfer onto germ-free laboratory Sphagnum for temperature experiments. Host and microbiome dynamics were assessed with growth analysis, Chla fluorescence imaging, metagenomics, metatranscriptomics and 16S rDNA profiling. Microbiomes originating from warming field conditions imparted enhanced thermotolerance and growth recovery at elevated temperatures. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure in a manner that induced the plant heat shock response, especially the HSP70 family and jasmonic acid production. The heat shock response was induced even without warming treatment in the laboratory, suggesting that the warm-microbiome isolated from the field provided the host plant with thermal preconditioning. Our results demonstrate that microbes, which respond rapidly to temperature alterations, can play key roles in host plant growth response to rapidly changing environments.}, }
@article {pmid35589762, year = {2022}, author = {Szóstak, N and Szymanek, A and Havránek, J and Tomela, K and Rakoczy, M and Samelak-Czajka, A and Schmidt, M and Figlerowicz, M and Majta, J and Milanowska-Zabel, K and Handschuh, L and Philips, A}, title = {The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8470}, pmid = {35589762}, issn = {2045-2322}, support = {POIR.04.01.02-00-0025/17-00//Narodowe Centrum Badań i Rozwoju/ ; }, mesh = {DNA ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {In recent years, the number of metagenomic studies increased significantly. Wide range of factors, including the tremendous community complexity and variability, is contributing to the challenge in reliable microbiome community profiling. Many approaches have been proposed to overcome these problems making hardly possible to compare results of different studies. The significant differences between procedures used in metagenomic research are reflected in a variation of the obtained results. This calls for the need for standardisation of the procedure, to reduce the confounding factors originating from DNA isolation, sequencing and bioinformatics analyses in order to ensure that the differences in microbiome composition are of a true biological origin. Although the best practices for metagenomics studies have been the topic of several publications and the main aim of the International Human Microbiome Standard (IHMS) project, standardisation of the procedure for generating and analysing metagenomic data is still far from being achieved. To highlight the difficulties in the standardisation of metagenomics methods, we thoroughly examined each step of the analysis of the human gut microbiome. We tested the DNA isolation procedure, preparation of NGS libraries for next-generation sequencing, and bioinformatics analysis, aimed at identifying microbial taxa. We showed that the homogenisation time is the leading factor impacting sample diversity, with the recommendation for a shorter homogenisation time (10 min). Ten minutes of homogenisation allows for better reflection of the bacteria gram-positive/gram-negative ratio, and the obtained results are the least heterogenous in terms of beta-diversity of samples microbial composition. Besides increasing the homogenisation time, we observed further potential impact of the library preparation kit on the gut microbiome profiling. Moreover, our analysis revealed that the choice of the library preparation kit influences the reproducibility of the results, which is an important factor that has to be taken into account in every experiment. In this study, a tagmentation-based kit allowed for obtaining the most reproducible results. We also considered the choice of the computational tool for determining the composition of intestinal microbiota, with Kraken2/Bracken pipeline outperforming MetaPhlAn2 in our in silico experiments. The design of an experiment and a detailed establishment of an experimental protocol may have a serious impact on determining the taxonomic profile of the intestinal microbiome community. Results of our experiment can be helpful for a wide range of studies that aim to better understand the role of the gut microbiome, as well as for clinical purposes.}, }
@article {pmid35585088, year = {2022}, author = {Yan, J and Liao, C and Taylor, BP and Fontana, E and Amoretti, LA and Wright, RJ and Littmann, ER and Dai, A and Waters, N and Peled, JU and Taur, Y and Perales, MA and Siranosian, BA and Bhatt, AS and van den Brink, MRM and Pamer, EG and Schluter, J and Xavier, JB}, title = {A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {219}, pmid = {35585088}, issn = {2052-4463}, support = {R01 AI137269/AI/NIAID NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; R01 AI137269/AI/NIAID NIH HHS/United States ; }, mesh = {Feces/microbiology ; *Hematopoietic Stem Cell Transplantation ; Humans ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and associated metadata, but we had limited that analysis to taxonomic composition of bacteria from 16S rRNA gene sequencing. Here we augment those data with shotgun metagenomics. The compilation amounts to a nested subset of 395 samples compiled from different studies at Memorial Sloan Kettering. Shotgun metagenomics describes the microbiome at the functional level, particularly in antimicrobial resistances and virulence factors. We provide accession numbers that link each sample to the paired-end sequencing files deposited in a public repository, which can be directly accessed by the online services of PATRIC to be analyzed without the users having to download or transfer the files. Then, we show how shotgun sequencing enables the assembly of genomes from metagenomic data. The new data, combined with the metadata published previously, enables new functional studies of the microbiomes of patients with cancer receiving bone marrow transplantation.}, }
@article {pmid35239207, year = {2022}, author = {de Souza Colombo, G and Viana Mendes, I and de Morais Souto, B and Chaves Barreto, C and Assis Serra, L and Ferreira Noronha, E and Skorupa Parachin, N and Moreira de Almeida, JR and Ferraz Quirino, B}, title = {Identification and functional expression of a new xylose isomerase from the goat rumen microbiome in Saccharomyces cerevisiae.}, journal = {Letters in applied microbiology}, volume = {74}, number = {6}, pages = {941-948}, doi = {10.1111/lam.13689}, pmid = {35239207}, issn = {1472-765X}, support = {//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Fundação de Amparo à Pesquisa do Distrito Federal/ ; }, mesh = {Aldose-Ketose Isomerases ; Animals ; Fermentation ; Goats ; *Microbiota ; Phylogeny ; Rumen ; *Saccharomyces cerevisiae/metabolism ; Xylose/metabolism ; }, abstract = {The current climate crisis demands replacement of fossil energy sources with sustainable alternatives. In this scenario, second-generation bioethanol, a product of lignocellulosic biomass fermentation, represents a more sustainable alternative. However, Saccharomyces cerevisiae cannot metabolize pentoses, such as xylose, present as a major component of lignocellulosic biomass. Xylose isomerase (XI) is an enzyme that allows xylose consumption by yeasts, because it converts xylose into xylulose, which is further converted to ethanol by the pentose-phosphate pathway. Only a few XI were successfully expressed in S. cerevisiae strains. This work presents a new bacterial XI, named GR-XI 1, obtained from a Brazilian goat rumen metagenomic library. Phylogenetic analysis confirmed the bacterial origin of the gene, which is related to Firmicutes XIs. After codon optimization, this enzyme, renamed XySC1, was functionally expressed in S. cerevisiae, allowing growth in media with xylose as sole carbon source. Overexpression of XySC1 in S. cerevisiae allowed the recombinant strain to efficiently consume and metabolize xylose under aerobic conditions.}, }
@article {pmid35158407, year = {2022}, author = {Besaury, L and Rémond, C}, title = {Culturable and metagenomic approaches of wheat bran and wheat straw phyllosphere's highlight new lignocellulolytic microorganisms.}, journal = {Letters in applied microbiology}, volume = {74}, number = {6}, pages = {840-850}, doi = {10.1111/lam.13676}, pmid = {35158407}, issn = {1472-765X}, support = {//French Region Grand Est, Grand Reims and the European Regional Development Fund./ ; }, mesh = {Bacteria ; *Dietary Fiber/metabolism ; Ecosystem ; *Metagenome ; Metagenomics ; Microbial Consortia/genetics ; }, abstract = {The phyllosphere, defined as the aerial parts of plants, is one of the most prevalent microbial habitats on earth. The microorganisms present on the phyllosphere can have several interactions with the plant. The phyllosphere represents then a unique niche where microorganisms have evolved through time in that stressful environment and may have acquired the ability to degrade lignocellulosic plant cell walls in order to survive to oligotrophic conditions. The dynamic lignocellulolytic potential of two phyllospheric microbial consortia (wheat straw and wheat bran) has been studied. The microbial diversity rapidly changed between the native phyllospheres and the final degrading microbial consortia after 48 h of culture. Indeed, the initial microbial consortia was dominated by the Ralstonia (35·8%) and Micrococcus (75·2%) genera for the wheat bran and wheat straw whereas they were dominated by Candidatus phytoplasma (59%) and Acinetobacter (31·8%) in the final degrading microbial consortia respectively. Culturable experiments leading to the isolation of several new lignocellulolytic isolates (belonging to Moraxella and Atlantibacter genera) and metagenomic reconstruction of the microbial consortia highlighted the existence of an unpredicted microbial diversity involved in lignocellulose fractionation but also the existence of new pathways in known genera (presence of CE2 for Acinetobacter, several AAs for Pseudomonas and several GHs for Bacillus in different metagenomes-assembled genomes). The phyllosphere from agricultural co-products represents then a new niche as a lignocellulolytic degrading ecosystem.}, }
@article {pmid35579554, year = {2022}, author = {Sim, M and Lee, J and Wy, S and Park, N and Lee, D and Kwon, D and Kim, J}, title = {Generation and application of pseudo-long reads for metagenome assembly.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, doi = {10.1093/gigascience/giac044}, pmid = {35579554}, issn = {2047-217X}, support = {2014M3C9A3063544//Konkuk University Researcher Fund/ ; 2019R1F1A1042018//Ministry of Science and ICT of Korea/ ; PJ01334302//Ministry of Education of Korea/ ; //Rural Development Administration of Korea/ ; }, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads.<br><br>RESULTS: In this study, we present a new method called PLR-GEN. It creates pseudo-long reads from metagenomic short reads based on given reference genome sequences by considering small sequence variations existing in individual genomes of the same or different species. When applied to a mock community data set in the Human Microbiome Project, PLR-GEN dramatically extended short reads in length of 101 bp to pseudo-long reads with N50 of 33 Kbp and 0.4% error rate. The use of these pseudo-long reads generated by PLR-GEN resulted in an obvious improvement of metagenomic assembly in terms of the number of sequences, assembly contiguity, and prediction of species and genes.<br><br>CONCLUSIONS: PLR-GEN can be used to generate artificial long read sequences without spending extra sequencing cost, thus aiding various studies using metagenomes.}, }
@article {pmid35574962, year = {2022}, author = {Goh, CE and Bohn, B and Marotz, C and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Rosenbaum, M and Yuzefpolskaya, M and Colombo, PC and Desvarieux, M and Papapanou, PN and Jacobs, DR and Knight, R and Demmer, RT}, title = {Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS.}, journal = {Journal of the American Heart Association}, volume = {11}, number = {10}, pages = {e023038}, doi = {10.1161/JAHA.121.023038}, pmid = {35574962}, issn = {2047-9980}, mesh = {Adult ; Bacteria/genetics/metabolism ; *Cardiovascular Diseases/diagnosis/epidemiology/genetics ; Female ; Humans ; Male ; *Microbiota ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitrites ; Nitrogen ; Nitrogen Dioxide/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Background The enterosalivary nitrate-nitrite-nitric oxide (NO3-NO2-NO) pathway generates NO following oral microbiota-mediated production of salivary nitrite, potentially linking the oral microbiota to reduced cardiometabolic risk. Nitrite depletion by oral bacteria may also be important for determining the net nitrite available systemically. We examine if higher abundance of oral microbial genes favoring increased oral nitrite generation and decreased nitrite depletion is associated with a better cardiometabolic profile cross-sectionally. Methods and Results This study includes 764 adults (mean [SD] age 32 [9] years, 71% women) enrolled in ORIGINS (Oral Infections, Glucose Intolerance, and Insulin Resistance Study). Microbial DNA from subgingival dental plaques underwent 16S rRNA gene sequencing; PICRUSt2 was used to estimate functional gene profiles. To represent the different components and pathways of nitrogen metabolism in bacteria, predicted gene abundances were operationalized to create summary scores by (1) bacterial nitrogen metabolic pathway or (2) biochemical product (NO2, NO, or ammonia [NH3]) formed by the action of the bacterial reductases encoded. Finally, nitrite generation-to-depletion ratios of gene abundances were created from the above summary scores. A composite cardiometabolic Z score was created from cardiometabolic risk variables, with higher scores associated with worse cardiometabolic health. We performed multivariable linear regression analysis with cardiometabolic Z score as the outcome and the gene abundance summary scores and ratios as predictor variables, adjusting for sex, age, race, and ethnicity in the simple adjusted model. A 1 SD higher NO versus NH3 summary ratio was inversely associated with a -0.10 (false discovery rate q=0.003) lower composite cardiometabolic Z score in simple adjusted models. Higher NH3 summary score (suggestive of nitrite depletion) was associated with higher cardiometabolic risk, with a 0.06 (false discovery rate q=0.04) higher composite cardiometabolic Z score. Conclusions Increased net capacity for nitrite generation versus depletion by oral bacteria, assessed through a metagenome estimation approach, is associated with lower levels of cardiometabolic risk.}, }
@article {pmid34980911, year = {2022}, author = {Bickhart, DM and Kolmogorov, M and Tseng, E and Portik, DM and Korobeynikov, A and Tolstoganov, I and Uritskiy, G and Liachko, I and Sullivan, ST and Shin, SB and Zorea, A and Andreu, VP and Panke-Buisse, K and Medema, MH and Mizrahi, I and Pevzner, PA and Smith, TPL}, title = {Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.}, journal = {Nature biotechnology}, volume = {40}, number = {5}, pages = {711-719}, pmid = {34980911}, issn = {1546-1696}, support = {R44AI162570//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R44 AI150008/AI/NIAID NIH HHS/United States ; 5090-31000-026-00-D//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 1947/19//Israel Science Foundation (ISF)/ ; 1715911//National Science Foundation (NSF)/ ; R44AI150008//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 3040-31000-100-00D//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; R44 AI162570/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Feces ; *Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Sheep ; }, abstract = {Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Using existing methods, we sequenced the sheep fecal metagenome and identified 428 MAGs with more than 90% completeness, including 44 MAGs in single circular contigs. To resolve closely related strains (lineages), we developed MAGPhase, which separates lineages of related organisms by discriminating variant haplotypes across hundreds of kilobases of genomic sequence. MAGPhase identified 220 lineage-resolved MAGs in our dataset. The ability to resolve closely related microbes in complex microbial communities improves the identification of biosynthetic gene clusters and the precision of assigning mobile genetic elements to host genomes. We identified 1,400 complete and 350 partial biosynthetic gene clusters, most of which are novel, as well as 424 (298) potential host-viral (host-plasmid) associations using Hi-C data.}, }
@article {pmid35572506, year = {2022}, author = {Porto, BN}, title = {Insights Into the Role of the Lung Virome During Respiratory Viral Infections.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {885341}, doi = {10.3389/fimmu.2022.885341}, pmid = {35572506}, issn = {1664-3224}, mesh = {Child ; Humans ; Lung ; Metagenomics ; Virome ; *Virus Diseases ; *Viruses/genetics ; }, abstract = {The virome constitutes the viral component of the microbiome and it consists of the genomes of all the viruses that inhabit a particular region of the human body, including those that cause acute, persistent or latent infection, and retroviral elements integrated to host chromosomes. The human virome is composed by eukaryotic viruses, bacteriophages and archaeal viruses. The understanding of the virome composition and role on human health has been delayed by the absence of specific tools and techniques to accurately characterize viruses. However, more recently, advanced methods for viral diagnostics, such as deep sequencing and metagenomics, have allowed a better understanding of the diverse viral species present in the human body. Previous studies have shown that the respiratory virome modulates the host immunity and that, since childhood, the human lung is populated by viruses for whom there is no disease association. Whether these viruses are potentially pathogenic and the reason for their persistence remain elusive. Increased respiratory viral load can cause exacerbation of chronic pulmonary diseases, including COPD, cystic fibrosis, and asthma. Moreover, the presence of resident viral populations may contribute to the pathogenesis of community-acquired respiratory virus infections. In this mini review, I will discuss the recent progress on our understanding of the human lung virome and summarize the up-to-date knowledge on the relationships among community-acquired respiratory viruses, the lung virome and the immune response to better understand disease pathophysiology and the factors that may lead to viral persistence.}, }
@article {pmid35572406, year = {2022}, author = {Diao, Z and Han, D and Zhang, R and Li, J}, title = {Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections.}, journal = {Journal of advanced research}, volume = {38}, number = {}, pages = {201-212}, doi = {10.1016/j.jare.2021.09.012}, pmid = {35572406}, issn = {2090-1224}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Respiratory Tract Infections/diagnosis ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has changed the diagnosis landscape of lower respiratory tract infections (LRIs). With the development of newer sequencing assays, it is now possible to assess all microorganisms in a sample using a single mNGS analysis. The applications of mNGS for LRIs span a wide range of areas including LRI diagnosis, airway microbiome analyses, human host response analyses, and prediction of drug resistance. mNGS is currently in an exciting transitional period; however, before implementation in a clinical setting, there are several barriers to overcome, such as the depletion of human nucleic acid, discrimination between colonization and infection, high costs, and so on. Aim of Review: In this review, we summarize the potential applications and challenges of mNGS in the diagnosis of LRIs to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting. Key Scientific Concepts of Review: Once its analytical validation, clinical validation and clinical utility been demonstrated, mNGS will become an important tool in the field of infectious disease diagnosis.}, }
@article {pmid35565868, year = {2022}, author = {Yu, X and Xing, Y and Liu, H and Chang, Y and You, Y and Dou, Y and Liu, B and Wang, Q and Ma, D and Chen, L and Tong, X}, title = {Effects of a Formula with scGOS/lcFOS (9:1) and Glycomacropeptide (GMP) Supplementation on the Gut Microbiota of Very Preterm Infants.}, journal = {Nutrients}, volume = {14}, number = {9}, pages = {}, pmid = {35565868}, issn = {2072-6643}, support = {NO. S160004//Natural Science Foundation of Beijing/ ; 2021YFC2700700//National Key Research and Development Program of China/ ; No. BYSYLXHG2019005//Peking University Third Hospital Research Fund for outstanding overseas returnees/ ; }, mesh = {Caseins ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Infant, Newborn ; Infant, Premature ; Oligosaccharides/pharmacology ; Peptide Fragments ; Prebiotics/analysis ; }, abstract = {Microbial colonization of very preterm (VPT) infants is detrimentally affected by the complex interplay of physiological, dietary, medical, and environmental factors. The aim of this study was to evaluate the effects of an infant formula containing the specific prebiotic mixture of scGOS/lcFOS (9:1) and glycomacropeptide (GMP) on the composition and function of VPT infants' gut microbiota. Metagenomic analysis was performed on the gut microbiota of VPT infants sampled at four time points: 24 h before the trial and 7, 14, and 28 days after the trial. Functional profiling was aggregated into gut and brain modules (GBMs) and gut metabolic modules (GMMs) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Enterococcus faecium, Escherichia coli, Klebsiella aerogenes, and Klebsiella pneumoniae were dominant species in both the test group and the control group. After the 4-week intervention, the abundance of Bifidobacterium in the test group was significantly increased. We found two GBMs (quinolinic acid synthesis and kynurenine degradation) and four GMMs (glutamine degradation, glyoxylate bypass, dissimilatory nitrate reduction, and preparatory phase of glycolysis) were significantly enriched in the test group, respectively. The results of this study suggested that formula enriched with scGOS/lcFOS (9:1) and GPM is beneficial to the intestinal microecology of VPT infants.}, }
@article {pmid35565725, year = {2022}, author = {Hernandez, AR and Kemp, KM and Burke, SN and Buford, TW and Carter, CS}, title = {Influence of Aging, Macronutrient Composition and Time-Restricted Feeding on the Fischer344 x Brown Norway Rat Gut Microbiota.}, journal = {Nutrients}, volume = {14}, number = {9}, pages = {}, pmid = {35565725}, issn = {2072-6643}, support = {T32HD071866/NH/NIH HHS/United States ; P2CHD086851/NH/NIH HHS/United States ; R01AG054538/NH/NIH HHS/United States ; K02AG062498/NH/NIH HHS/United States ; RF1AG060977//National Institute of Health/ ; K12GM088010/NH/NIH HHS/United States ; }, mesh = {Aging ; Animals ; Cytokines ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases ; Nutrients ; Rats ; }, abstract = {Both ketogenic diets (KD) and time-restricted feeding (TRF) regimens have the ability to influence several parameters of physical health, including gut microbiome composition and circulating cytokine concentration. Moreover, both of these dietary interventions prevent common impairments associated with the aging process. However, significantly altering macronutrient intake, which is required for a KD, may be unappealing to individuals and decrease compliance to dietary treatments. In contrast to a KD, TRF allows individuals to continue eating the foods they are used to, and only requires a change in the time of day at which they eat. Therefore, we investigated both a KD and a diet with a more Western-like macronutrient profile in the context of TRF, and compared both diets to animals allowed access to standard chow ad libitum in young adult and aged rats. While limited effects on cytokine levels were observed, both methods of microbiome analysis (16S sequencing and metagenomics) indicate that TRF and KDs significantly altered the gut microbiome in aged rats. These changes were largely dependent on changes to feeding paradigm (TRF vs. ad libitum) alone regardless of macronutrient content for many gut microbiota, but there were also macronutrient-specific changes. Specifically, functional analysis indicates significant differences in several pathways, including those involved in the tricarboxylic acid (TCA) cycle, carbohydrate metabolism and neurodegenerative disease. These data indicate that age- and disease-related gut dysbiosis may be ameliorated through the use of TRF with both standard diets and KDs.}, }
@article {pmid35549618, year = {2022}, author = {Chen, L and Zheng, T and Yang, Y and Chaudhary, PP and Teh, JPY and Cheon, BK and Moses, D and Schuster, SC and Schlundt, J and Li, J and Conway, PL}, title = {Integrative multiomics analysis reveals host-microbe-metabolite interplays associated with the aging process in Singaporeans.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2070392}, doi = {10.1080/19490976.2022.2070392}, pmid = {35549618}, issn = {1949-0984}, mesh = {Adult ; Aged ; Aging ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolome ; Metagenomics ; Singapore ; Young Adult ; }, abstract = {The age-associated alterations in microbiomes vary across populations due to the influence of genetics and lifestyles. To the best of our knowledge, the microbial changes associated with aging have not yet been investigated in Singapore adults. We conducted shotgun metagenomic sequencing of fecal and saliva samples, as well as fecal metabolomics to characterize the gut and oral microbial communities of 62 healthy adult male Singaporeans, including 32 young subjects (age, 23.1 ± 1.4 years) and 30 elderly subjects (age, 69.0 ± 3.5 years). We identified 8 gut and 13 oral species that were differentially abundant in elderly compared to young subjects. By combining the gut and oral microbiomes, 25 age-associated oral-gut species connections were identified. Moreover, oral bacteria Acidaminococcus intestine and Flavonifractor plautii were less prevalent/abundant in elderly gut samples than in young gut samples, whereas Collinsella aerofaciens and Roseburia hominis showed the opposite trends. These results indicate the varied gut-oral communications with aging. Subsequently, we expanded the association studies on microbiome, metabolome and host phenotypic parameters. In particular, Eubacterium eligens increased in elderly compared to young subjects, and was positively correlated with triglycerides, which implies that the potential role of E. eligens in lipid metabolism is altered during the aging process. Our results demonstrated aging-associated changes in the gut and oral microbiomes, as well as the connections between metabolites and host-microbe interactions, thereby deepening the understanding of alterations in the human microbiome during the aging process in a Singapore population.}, }
@article {pmid35546409, year = {2022}, author = {Liu, S and Moon, CD and Zheng, N and Huws, S and Zhao, S and Wang, J}, title = {Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {76}, pmid = {35546409}, issn = {2049-2618}, support = {(CAAS-ZDXT2019004)//The Scientific Research Project for Major Achievements of The Agricultural Science and Technology Innovation Program/ ; (ASTIP-IAS12)//Modern Agro-Industry Technology Research System of the PR China, and the Agricultural Science and Technology Innovation Program/ ; }, mesh = {Bacteria/genetics ; Genomics ; *Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract.}, }
@article {pmid35545042, year = {2022}, author = {Russell, A and Copio, JN and Shi, Y and Kang, S and Franklin, CL and Ericsson, AC}, title = {Reduced housing density improves statistical power of murine gut microbiota studies.}, journal = {Cell reports}, volume = {39}, number = {6}, pages = {110783}, doi = {10.1016/j.celrep.2022.110783}, pmid = {35545042}, issn = {2211-1247}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Housing ; Mice ; Mice, Inbred C57BL ; }, abstract = {The gut microbiome of humans and animals is critical to host health. Mice are used to investigate the microbiome and its influences; however, the predictive value of such studies is hindered by cage effects due to coprophagy. Our objectives were to evaluate the influence of cage density on the statistical power to detect treatment-dependent effects of a selective pressure on microbiome composition. C57BL/6 mice were separated into groups of 2 or 4 mice per cage and then assigned to groups receiving enrofloxacin, broad-spectrum antibiotics, or control. Fecal samples were collected at weeks 0, 1, and 4, along with contents of the jejunum and cecum. Bacterial DNA analysis examined microbiome richness, diversity, and variability within and between cages. Statistical analyses reveal that reduced housing density consistently results in comparable susceptibility to antibiotics, reduced cage effects, and increased statistical power to detect treatment-associated effects, justifying the practice of reduced housing density.}, }
@article {pmid35544065, year = {2022}, author = {Tsitsiklis, A and Osborne, CM and Kamm, J and Williamson, K and Kalantar, K and Dudas, G and Caldera, S and Lyden, A and Tan, M and Neff, N and Soesanto, V and Harris, JK and Ambroggio, L and Maddux, AB and Carpenter, TC and Reeder, RW and Locandro, C and Simões, EAF and Leroue, MK and Hall, MW and Zuppa, AF and Carcillo, J and Meert, KL and Sapru, A and Pollack, MM and McQuillen, PS and Notterman, DA and Dean, JM and Zinter, MS and Wagner, BD and DeRisi, JL and Mourani, PM and Langelier, CR}, title = {Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics.}, journal = {The Lancet. Microbe}, volume = {3}, number = {4}, pages = {e284-e293}, doi = {10.1016/S2666-5247(21)00304-9}, pmid = {35544065}, issn = {2666-5247}, mesh = {Bacteria/genetics ; Child ; Cohort Studies ; Critical Illness ; Haemophilus influenzae ; Humans ; Metagenomics ; Moraxella catarrhalis ; Prospective Studies ; Respiration, Artificial ; *Respiratory Syncytial Virus, Human ; *Respiratory Tract Infections/diagnosis ; United States ; }, abstract = {BACKGROUND: Lower respiratory tract infections (LRTI) are a leading cause of critical illness and mortality in mechanically ventilated children; however, the pathogenic microbes frequently remain unknown. We combined traditional diagnostics with metagenomic next generation sequencing (mNGS) to evaluate the cause of LRTI in critically ill children.<br><br>METHODS: We conducted a prospective, multicentre cohort study of critically ill children aged 31 days to 17 years with respiratory failure requiring mechanical ventilation (>72 h) in the USA. By combining bacterial culture and upper respiratory viral PCR testing with mNGS of tracheal aspirate collected from all patients within 24 h of intubation, we determined the prevalence, age distribution, and seasonal variation of viral and bacterial respiratory pathogens detected by either method in children with or without LRTI.<br><br>FINDINGS: Between Feb 26, 2015, and Dec 31, 2017, of the 514 enrolled patients, 397 were eligible and included in the study (276 children with LRTI and 121 with no evidence of LRTI). A presumptive microbiological cause was identified in 255 (92%) children with LRTI, with respiratory syncytial virus (127 [46%]), Haemophilus influenzae (70 [25%]), and Moraxella catarrhalis (65 [24%]) being most prevalent. mNGS identified uncommon pathogens including Ureaplasma parvum and Bocavirus. Co-detection of viral and bacterial pathogens occurred in 144 (52%) patients. Incidental carriage of potentially pathogenic microbes occurred in 82 (68%) children without LRTI, with rhinovirus (30 [25%]) being most prevalent. Respiratory syncytial virus (p<0·0001), H influenzae (p=0·0006), and M catarrhalis (p=0·0002) were most common in children younger than 5 years. Viral and bacterial LRTI occurred predominantly during winter months.<br><br>INTERPRETATION: These findings demonstrate that respiratory syncytial virus, H influenzae, and M catarrhalis contribute disproportionately to severe paediatric LRTI, co-infections are common, and incidental carriage of potentially pathogenic microbes occurs frequently. Further, we provide a framework for future epidemiological and emerging pathogen surveillance studies, highlighting the potential for metagenomics to enhance clinical diagnosis.<br><br>FUNDING: US National Institutes of Health and CZ Biohub.}, }
@article {pmid35538082, year = {2022}, author = {Shin, J and Noh, JR and Choe, D and Lee, N and Song, Y and Cho, S and Kang, EJ and Go, MJ and Ha, SK and Kim, JH and Kim, YH and Kim, KS and Kim, BC and Lee, CH and Cho, BK}, title = {Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {197}, pmid = {35538082}, issn = {2052-4463}, support = {2019M3A9F3065867//National Research Foundation of Korea (NRF)/ ; 2018M3A9H3024759//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Aging/genetics ; Animals ; Disease Models, Animal ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Mice ; *RNA, Ribosomal, 16S/genetics ; Rejuvenation ; }, abstract = {The gut microbiota is associated with the health and longevity of the host. A few methods, such as fecal microbiota transplantation and oral administration of probiotics, have been applied to alter the gut microbiome and promote healthy aging. The changes in host microbiomes still remain poorly understood. Here, we characterized both the changes in gut microbial communities and their functional potential derived from colon samples in mouse models during aging. We achieved this through four procedures including co-housing, serum injection, parabiosis, and oral administration of Akkermansia muciniphila as probiotics using bacterial 16 S rRNA sequencing and shotgun metagenomic sequencing. The dataset comprised 16 S rRNA sequencing (36,249,200 paired-end reads, 107 sequencing data) and metagenomic sequencing data (307,194,369 paired-end reads, 109 sequencing data), characterizing the taxonomy of bacterial communities and their functional potential during aging and rejuvenation. The generated data expand the resources of the gut microbiome related to aging and rejuvenation and provide a useful dataset for research on developing therapeutic strategies to achieve healthy active aging.}, }
@article {pmid35524899, year = {2022}, author = {You, HS and Lee, SH and Lee, YJ and Lee, H and Kang, SS and Hyun, SH}, title = {Next-Generation Sequencing Results Vary Between Cultured and Uncultured Microbes.}, journal = {Current microbiology}, volume = {79}, number = {6}, pages = {187}, pmid = {35524899}, issn = {1432-0991}, support = {PA-I000001//korean national police agency/ ; }, mesh = {Bacteria/genetics ; Firmicutes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Next-generation sequencing (NGS) technology has led to innovations in environmental metagenomics and investigations involving humans and microbes. However, it is necessary to analyze the components that will affect analysis of the method upon processing a large amount of information. In particular, the processing method after sample collection affects the NGS results, and it is necessary to check for inaccurate results. Here, we show that the microbial communities obtained from fingertip samples differ from those obtained from fingertips remaining on mobile phones and desks, when cultured or not for 24 h. We also confirmed changes in microbial communities in fingertip samples from desks incubated for 2, 4, 8, 16, and 24 h. Samples of prints from mobile phones that are considerably vulnerable to external factors were not analyzed. Ratios of Firmicutes and Bacillus were, respectively, increased in cultures at the phylum and species levels. Collectively, we identified bacterial species that can aid in determining whether a sample has been cultured. In addition, although microbial communities differed depending on sample types, we confirmed changes after culture for 4 and 8 h. However, since this study is a sample limited to three types, it is necessary to analyze other types of samples in the same way and check whether they are applicable to all types. This strategy can verify the suitability of samples for deriving informative results from cultured or uncultured bacterial communities.}, }
@article {pmid35515981, year = {2022}, author = {Cobos, M and Estela, SL and Rodríguez, HN and Castro, CG and Grandez, M and Castro, JC}, title = {Soil microbial diversity and functional profiling of a tropical rainforest of a highly dissected low hill from the upper Itaya river basin revealed by analysis of shotgun metagenomics sequencing data.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108205}, pmid = {35515981}, issn = {2352-3409}, abstract = {The tropical rainforest of a highly dissected low hill from the upper Itaya river basin belongs to the western Amazonia region. Some investigations on the biodiversity of these rainforests were more focused on animals and plants diversity. The soils of this region are composed of moderately fertile sediments deposited recently from the initiation of the Andean orogenesis in the Miocene until now. However, scientific information about the soil microbial and functional diversity is still missing. This report presents shotgun metagenomics sequencing data from soils of this rainforest type. A composite loamy soil sample was collected from a primary forest, and metagenomic DNA was purified with standardized methods. Furthermore, libraries were prepared and paired-end sequenced on the Illumina NextSeq 550 platform. Raw Illumina paired-end reads have been uploaded and analysed in the Metagenomics RAST server (MG-RAST). The raw sequence data in fastq format is available at NCBI's Sequence Read Archive (SRA) with accession number SRX12846710.}, }
@article {pmid35515005, year = {2022}, author = {Sheehy, L and Cutler, J and Weedall, GD and Rae, R}, title = {Microbiome Analysis of Malacopathogenic Nematodes Suggests No Evidence of a Single Bacterial Symbiont Responsible for Gastropod Mortality.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {878783}, pmid = {35515005}, issn = {1664-3224}, mesh = {Animals ; *Microbiota ; *Nematoda ; *Rhabditoidea/microbiology ; Snails ; Soil ; }, abstract = {Nematodes and bacteria are prevalent in soil ecosystems, and some have evolved symbiotic relationships. In some cases, symbionts carry out highly specialized functions: a prime example being entomopathogenic nematodes (EPNs), which vector bacteria (Xenorhabdus or Photorhabdus) into insect hosts, killing them to provide a food source for the nematodes. It is thought that the commercially available malacopathogenic (kills slugs and snails) biocontrol nematode Phasmarhabditis hermaphrodita vectors a bacterium (Moraxella osloensis) into slugs to kill them. To investigate this further we used a metagenomic approach to profile the bacteria present in the commercial strain of P. hermaphrodita, a wild strain of P. hermaphrodita and two other Phasmarhabditis species (P. californica and P. neopapillosa), after they had killed their slug host (Deroceras invadens). We show that these nematodes do not exclusively associate with one bacterium but a range of species, with members of the phyla Pseudomonadota, Bacillota, Actinobacteriota and Bacteroidota the most prevalent. The commercial strain of P. hermaphrodita had the least diverse bacterial community. Furthermore, we found that the bacterium P. hermaphrodita has been cultured on for 25 years is not the expected species M. osloensis but is Psychrobacter spp. and the only strain of the Phasmarhabditis species to associate with Psychrobacter spp. was the commercial strain of P. hermaphrodita. In summary, we found no evidence to show that P. hermaphrodita rely exclusively on one bacterium to cause host mortality but found variable and diverse bacterial communities associated with these nematodes in their slug hosts.}, }
@article {pmid35503723, year = {2022}, author = {Pronk, LJU and Medema, MH}, title = {Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure.}, journal = {Microbial genomics}, volume = {8}, number = {5}, pages = {}, doi = {10.1099/mgen.0.000823}, pmid = {35503723}, issn = {2057-5858}, mesh = {Bacteria/genetics ; Eukaryota/genetics ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Metagenomics has become a prominent technology to study the functional potential of all organisms in a microbial community. Most studies focus on the bacterial content of these communities, while ignoring eukaryotic microbes. Indeed, many metagenomics analysis pipelines silently assume that all contigs in a metagenome are prokaryotic, likely resulting in less accurate annotation of eukaryotes in metagenomes. Early detection of eukaryotic contigs allows for eukaryote-specific gene prediction and functional annotation. Here, we developed a classifier that distinguishes eukaryotic from prokaryotic contigs based on foundational differences between these taxa in terms of gene structure. We first developed Whokaryote, a random forest classifier that uses intergenic distance, gene density and gene length as the most important features. We show that, with an estimated recall, precision and accuracy of 94, 96 and 95 %, respectively, this classifier with features grounded in biology can perform almost as well as the classifiers EukRep and Tiara, which use k-mer frequencies as features. By retraining our classifier with Tiara predictions as an additional feature, the weaknesses of both types of classifiers are compensated; the result is Whokaryote+Tiara, an enhanced classifier that outperforms all individual classifiers, with an F1 score of 0.99 for both eukaryotes and prokaryotes, while still being fast. In a reanalysis of metagenome data from a disease-suppressive plant endospheric microbial community, we show how using Whokaryote+Tiara to select contigs for eukaryotic gene prediction facilitates the discovery of several biosynthetic gene clusters that were missed in the original study. Whokaryote (+Tiara) is wrapped in an easily installable package and is freely available from https://github.com/LottePronk/whokaryote.}, }
@article {pmid35501856, year = {2022}, author = {Mesnage, R and Bowyer, RCE and El Balkhi, S and Saint-Marcoux, F and Gardere, A and Ducarmon, QR and Geelen, AR and Zwittink, RD and Tsoukalas, D and Sarandi, E and Paramera, EI and Spector, T and Steves, CJ and Antoniou, MN}, title = {Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins.}, journal = {Environmental health : a global access science source}, volume = {21}, number = {1}, pages = {46}, pmid = {35501856}, issn = {1476-069X}, mesh = {Adult ; Dietary Exposure/analysis ; *Herbicides/analysis ; Humans ; *Insecticides/analysis ; *Microbiota ; Organophosphorus Compounds ; *Pesticide Residues/analysis ; *Pesticides ; Vegetables/chemistry ; }, abstract = {BACKGROUND: Dietary habits have a profound influence on the metabolic activity of gut microorganisms and their influence on health. Concerns have been raised as to whether the consumption of foodstuffs contaminated with pesticides can contribute to the development of chronic disease by affecting the gut microbiome. We performed the first pesticide biomonitoring survey of the British population, and subsequently used the results to perform the first pesticide association study on gut microbiome composition and function from the TwinsUK registry.<br><br>METHODS: Dietary exposure of 186 common insecticide, herbicide, or fungicide residues and the faecal microbiome in 65 twin pairs in the UK was investigated. We evaluated if dietary habits, geographic location, or the rural/urban environment, are associated with the excretion of pesticide residues. The composition and metabolic activity of faecal microbiota was evaluated using shotgun metagenomics and metabolomics respectively. We performed a targeted urine metabolomics analysis in order to evaluate whether pesticide urinary excretion was also associated with physiological changes.<br><br>RESULTS: Pyrethroid and/or organophosphorus insecticide residues were found in all urine samples, while the herbicide glyphosate was found in 53% of individuals. Food frequency questionnaires showed that residues from organophosphates were higher with increased consumption of fruit and vegetables. A total of 34 associations between pesticide residue concentrations and faecal metabolite concentrations were detected. Glyphosate excretion was positively associated with an overall increased bacterial species richness, as well as to fatty acid metabolites and phosphate levels. The insecticide metabolite Br2CA, reflecting deltamethrin exposure, was positively associated with the phytoestrogens enterodiol and enterolactone, and negatively associated with some N-methyl amino acids. Urine metabolomics performed on a subset of samples did not reveal associations with the excretion of pesticide residues.<br><br>CONCLUSIONS: The consumption of conventionally grown fruit and vegetables leads to higher ingestion of pesticides with unknown long-term health consequences. Our results highlight the need for future dietary intervention studies to understand effects of pesticide exposure on the gut microbiome and possible health consequences.}, }
@article {pmid35501694, year = {2022}, author = {Jiang, C and Zhu, S and Feng, J and Shui, W}, title = {Slope aspect affects the soil microbial communities in karst tiankeng negative landforms.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {54}, pmid = {35501694}, issn = {2730-7182}, support = {41871198//National Natural Science Foundation of China/ ; }, mesh = {Bacteria ; Biodiversity ; Humans ; *Microbiota ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {BACKGROUND: Karst tiankeng is a large-scale negative surface terrain, and slope aspects affect the soil conditions, vegetation and microbial flora in the tiankeng. However, the influence of the slope aspect on the soil microbial community in tiankeng has not been elucidated.<br><br>METHODS: In this study, metagenomic sequencing technology was used to analyze the soil microbial community structure and functional potentials on the shady and sunny slopes of karst tiankeng.<br><br>RESULTS: The Shannon-Wiener diversity of microbial communities on shady slope (SHS) was significantly higher than that on sunny slope (SUS). Although the composition of dominant phyla on shady slope (SHS) and sunny slope (SUS) was similar, there were significant differences in beta-diversity. The linear discriminate analysis (LDA) results showed that biomarkers mainly belongs to Actinobacteria, Chloroflexi and Proteobacteria. Functional pathways and CAZy (Carbohydrate-Active Enzymes) genes also had a remarkable response to slope aspect change. LEfSe results indicated several biomarker pathways in sunny slope involved in human disease. Moreover, the abundance of CAZy genes was higher in shady slope and had stronger ability in decomposing litter. The microbial communities were mainly correlation with the vegetation characteristics (species richness and coverage) and soil properties (SOC and pH).<br><br>CONCLUSIONS: These results indicate slope aspect has a pronounced influence on microbial community composition, structure and function at karst tiankeng. In the future, the conservation of karst tiankeng biodiversity should pay more attention to topographical factors.}, }
@article {pmid35484115, year = {2022}, author = {Pan, S and Zhu, C and Zhao, XM and Coelho, LP}, title = {A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2326}, pmid = {35484115}, issn = {2041-1723}, support = {61932008//National Natural Science Foundation of China (National Science Foundation of China)/ ; 61772368//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31950410544//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2018SHZDZX01//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; }, mesh = {Algorithms ; *Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Neural Networks, Computer ; }, abstract = {Metagenomic binning is the step in building metagenome-assembled genomes (MAGs) when sequences predicted to originate from the same genome are automatically grouped together. The most widely-used methods for binning are reference-independent, operating de novo and enable the recovery of genomes from previously unsampled clades. However, they do not leverage the knowledge in existing databases. Here, we introduce SemiBin, an open source tool that uses deep siamese neural networks to implement a semi-supervised approach, i.e. SemiBin exploits the information in reference genomes, while retaining the capability of reconstructing high-quality bins that are outside the reference dataset. Using simulated and real microbiome datasets from several different habitats from GMGCv1 (Global Microbial Gene Catalog), including the human gut, non-human guts, and environmental habitats (ocean and soil), we show that SemiBin outperforms existing state-of-the-art binning methods. In particular, compared to other methods, SemiBin returns more high-quality bins with larger taxonomic diversity, including more distinct genera and species.}, }
@article {pmid35482264, year = {2022}, author = {Paranhos, AGO and Pereira, AR and da Fonseca, YA and de Queiroz Silva, S and de Aquino, SF}, title = {Tylosin in anaerobic reactors: degradation kinetics, effects on methane production and on the microbial community.}, journal = {Biodegradation}, volume = {33}, number = {3}, pages = {283-300}, pmid = {35482264}, issn = {1572-9729}, support = {2510001557612017-21//National Health Fundation - FUNASA/ ; 423101/2018-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ-02701-18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; }, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Bioreactors/microbiology ; Kinetics ; Methane/metabolism ; *Microbiota ; *Tylosin/pharmacology ; }, abstract = {Tylosin eliminated in animal waste, during therapeutic treatment, can be efficiently removed in anaerobic systems. The present study investigated the influence of tylosin concentration and assessed its degradation kinetics and the microorganisms involved in each stage of its anaerobic digestion (hydrolysis/acidogenesis; acetogenesis; methanogenesis). The results showed a stimulating effect on methane production with increasing tylosin concentration in the poultry litter up to 80 mg kg-1 tylosin (232.9 NL CH4 kg SV-1). As for tylosin degradation, greater removal of antibiotics was observed in the methanogenic phase (88%), followed by acetogenic (84%) and hydrolytic/acidogenic (76%) phases. The higher rate of tylosin degradation obtained in the methanogenic step, is mainly related to the co-metabolic effect exerted by the presence of acetate and its degradation by acetoclastic methanogens. Indeed, metagenomic analyses suggested a syntrophic action between archaea of ​​the genus Methanobacterium, and bacteria such as Clostridium and Flexilinea, which seemed decisive for tylosin degradation.}, }
@article {pmid35477737, year = {2022}, author = {Wang, H and Yang, GX and Hu, Y and Lam, P and Sangha, K and Siciliano, D and Swenerton, A and Miller, R and Tilley, P and Von Dadelszen, P and Kalyan, S and Tang, P and Patel, MS}, title = {Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6875}, pmid = {35477737}, issn = {2045-2322}, support = {130494/CAPMC/CIHR/Canada ; KRZ28015//BC Children's Hospital Foundation Telethon/ ; KRZ75069//Circle of Care/ ; }, mesh = {Amniotic Fluid ; Female ; Humans ; Metagenomics ; *Microbiota/genetics ; *Nucleic Acids ; Uterus ; }, abstract = {As metagenomic approaches for detecting infectious agents have improved, each tissue that was once thought to be sterile has been found to harbor a variety of microorganisms. Controversy still exists over the status of amniotic fluid, which is part of an immunologically privileged zone that is required to prevent maternal immune system rejection of the fetus. Due to this privilege, the exclusion of microbes has been proposed to be mandatory, leading to the sterile womb hypothesis. Since nucleic acid yields from amniotic fluid are very low, contaminating nucleic acid found in water, reagents and the laboratory environment frequently confound attempts to address this hypothesis. Here we present metagenomic criteria for microorganism detection and a metagenomic method able to be performed with small volumes of starting material, while controlling for exogenous contamination, to circumvent these and other pitfalls. We use this method to show that human mid-gestational amniotic fluid has no detectable virome or microbiome, supporting the sterile womb hypothesis.}, }
@article {pmid35467501, year = {2022}, author = {Zhu, Y and Ma, L and Wei, W and Li, X and Chang, Y and Pan, Z and Gao, H and Yang, R and Bi, Y and Ding, L}, title = {Metagenomics analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues.}, journal = {Journal of medical microbiology}, volume = {71}, number = {4}, pages = {}, doi = {10.1099/jmm.0.001523}, pmid = {35467501}, issn = {1473-5644}, mesh = {Bacteria/genetics ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics ; }, abstract = {Introduction. Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and environment. Of these, the role of the gut microbiota in cancer biology is increasingly recognized.Hypothesis/Gap Statement. Micro-organisms have been widely detected in stool samples, but few mucosal samples have been detected and sequenced in depth.Aim. Analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues with metagenomics sequencing.Methodology. Twenty-eight paired tumour and non-tumour tissues from 14 patients undergoing surgery for CRC were analysed. We removed the influence of eukaryotic cells via culture. The composition of mucosal microbiota in intestinal mucosa were detected and analysed with metagenomic sequencing.Results. Compared with non-cultured mucosal sample, 80 % bacteria species could be detected after culture. Moreover, after culture, additional 30 % bacteria could be detected, compared with non-cultured samples. Since after culture it was difficult to estimate the original abundance of microbiome, we focused on the identification of the CRC tissue-specific species. There were 298 bacterial species, which could only be cultured and detected in CRC tissues. Myroides odoratimimus and Cellulophaga baltica could be isolated from all the tumour samples of 14 CRC patients, suggesting that these species may be related to tumour occurrence and development. Further functional analysis indicated that bacteria from CRC tissues showed more active functions, including basic metabolism, signal transduction and survival activities.Conclusion. We used a new method based on culture to implement information on prokaryotic taxa, and related functions, which samples were from colorectal tissues. This method is suitable for removing eukaryotic contamination and detecting micro-organisms from other tissues.}, }
@article {pmid35456018, year = {2022}, author = {Henry, C and Bassignani, A and Berland, M and Langella, O and Sokol, H and Juste, C}, title = {Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers-Example of Crohn's Disease and Ulcerative Colitis Flare-Ups.}, journal = {Cells}, volume = {11}, number = {8}, pages = {}, pmid = {35456018}, issn = {2073-4409}, support = {ANR-15-CE14-0013-01//AGENCE NATIONALE DE LA RECHERCHE (ANR)/ ; 2016-1212I//FONDATION DE COOPERATION SCIENTIFIQUE CAMPUS PARIS-SACLAY/ ; }, mesh = {Biomarkers/metabolism ; *Colitis, Ulcerative/diagnosis ; *Crohn Disease/diagnosis ; Feces ; Humans ; *Microbiota ; }, abstract = {Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty faecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host-microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes-active ulcerative colitis, or active Crohn's disease either with ileo-colonic or exclusive colonic localization-differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising additional diagnostic tool for IBDs.}, }
@article {pmid35452151, year = {2022}, author = {Lu, JL and Jia, P and Feng, SW and Wang, YT and Zheng, J and Ou, SN and Wu, ZH and Liao, B and Shu, WS and Liang, JL and Li, JT}, title = {Remarkable effects of microbial factors on soil phosphorus bioavailability: A country-scale study.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16213}, pmid = {35452151}, issn = {1365-2486}, support = {2021B1515120039//Guangdong Basic and Applied Basic Research Foundation/ ; 2019B110207001//Key-Area Research and Development Program of Guangdong Province/ ; 41622106//National Natural Science Foundation of China/ ; 42077117//National Natural Science Foundation of China/ ; 42177009//National Natural Science Foundation of China/ ; 2020A1515010937//Natural Science Foundation of Guangdong Province of China/ ; }, abstract = {Low soil phosphorus (P) bioavailability causes the widespread occurrence of P-limited terrestrial ecosystems around the globe. Exploring the factors influencing soil P bioavailability at large spatial scales is critical for managing these ecosystems. However, previous studies have mostly focused on abiotic factors. In this study, we explored the effects of microbial factors on soil P bioavailability of terrestrial ecosystems using a country-scale sampling effort. Our results showed that soil microbial biomass carbon (MBC) and acid phosphatase were important predictors of soil P bioavailability of agro- and natural ecosystems across China although they appeared less important than total soil P. The two microbial factors had a positive effect on soil P bioavailability of both ecosystem types and were able to mediate the effects of several abiotic factors (e.g., mean annual temperature). Meanwhile, we revealed that soil phytase could affect soil P bioavailability at the country scale via ways similar to those of soil MBC and acid phosphatase, a pattern being more pronounced in agroecosystems than in natural ecosystems. Moreover, we obtained evidence for the positive effects of microbial genes encoding these enzymes on soil P bioavailability at the country scale although their effect sizes varied between the two ecosystem types. Taken together, this study demonstrated the remarkable effects of microbial factors on soil P bioavailability at a large spatial scale, highlighting the importance to consider microbial factors in managing the widespread P-limited terrestrial ecosystems.}, }
@article {pmid35444277, year = {2022}, author = {Raina, JB and Lambert, BS and Parks, DH and Rinke, C and Siboni, N and Bramucci, A and Ostrowski, M and Signal, B and Lutz, A and Mendis, H and Rubino, F and Fernandez, VI and Stocker, R and Hugenholtz, P and Tyson, GW and Seymour, JR}, title = {Chemotaxis shapes the microscale organization of the ocean's microbiome.}, journal = {Nature}, volume = {605}, number = {7908}, pages = {132-138}, pmid = {35444277}, issn = {1476-4687}, mesh = {2,5-Dimethoxy-4-Methylamphetamine/metabolism ; Bacteria ; *Chemotaxis ; *Microbiota ; Oceans and Seas ; Phytoplankton/metabolism ; Seawater/microbiology ; }, abstract = {The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry1-3, but has never been examined comprehensively in situ among natural microbial communities. Here, using a field-based microfluidic platform to quantify the behavioural responses of marine bacteria and archaea, we observed significant levels of chemotaxis towards microscale hotspots of phytoplankton-derived dissolved organic matter (DOM) at a coastal field site across multiple deployments, spanning several months. Microscale metagenomics revealed that a wide diversity of marine prokaryotes, spanning 27 bacterial and 2 archaeal phyla, displayed chemotaxis towards microscale patches of DOM derived from ten globally distributed phytoplankton species. The distinct DOM composition of each phytoplankton species attracted phylogenetically and functionally discrete populations of bacteria and archaea, with 54% of chemotactic prokaryotes displaying highly specific responses to the DOM derived from only one or two phytoplankton species. Prokaryotes exhibiting chemotaxis towards phytoplankton-derived compounds were significantly enriched in the capacity to transport and metabolize specific phytoplankton-derived chemicals, and displayed enrichment in functions conducive to symbiotic relationships, including genes involved in the production of siderophores, B vitamins and growth-promoting hormones. Our findings demonstrate that the swimming behaviour of natural prokaryotic assemblages is governed by specific chemical cues, which dictate important biogeochemical transformation processes and the establishment of ecological interactions that structure the base of the marine food web.}, }
@article {pmid35443009, year = {2022}, author = {Lin, PC and Yang, YSH and Lin, SC and Lu, MC and Tsai, YT and Lu, SC and Chen, SH and Chen, SY}, title = {Clinical significance and intestinal microbiota composition in immunocompromised children with norovirus gastroenteritis.}, journal = {PloS one}, volume = {17}, number = {4}, pages = {e0266876}, pmid = {35443009}, issn = {1932-6203}, mesh = {*Caliciviridae Infections/epidemiology ; Child ; Feces ; *Gastroenteritis ; *Gastrointestinal Microbiome/genetics ; Genotype ; Humans ; Infant ; *Norovirus/genetics ; RNA, Viral ; }, abstract = {BACKGROUND: Norovirus (NoV) infection is common in pediatric patients with immunodeficiency and is more likely to cause severe disease. Objective Our study aims to figure out the clinical differences and distribution of intestinal microbiota in immunocompromised children with NoV gastroenteritis.<br><br>METHODS: Pediatric patients admitted to Shang-Ho Hospital with diagnosis of acute gastroenteritis including different immune status were enrolled and their medical records were reviewed. NoV gastroenteritis was validated using RT-PCR molecular methods. Viral shedding period was determined by real-time RT-PCR assays. Intestinal microbiota enrichment analysis was carried out by next generation sequencing after fecal DNA extraction and subsequent Linear Discriminant Analysis (LDA) Effect Size (LEfSe) method.<br><br>RESULTS: Significantly higher frequency of diarrhea [mean, (IQR), 3.8 (3-5) /day] and longer viral shedding time [mean, IQR, 8.5 (5-13) days] was found in immunocompromised NoV infections than in immunocompetent patients without NoV infections (p = 0.013*) and immunocompetent patients with NoV infections (p = 0.030**). The fever prevalence was significantly lower in immunocompromised NoV infections than in different immune or infection status. Intestinal microbiota metagenomics analysis showed no significant community richness difference while the LEfSe analysis showed a significant difference in commensal richness at the phylum level, the family level, and the genus level in patients under different immune status.<br><br>CONCLUSION: We evaluated the clinical significances and microbiota composition in immunocompromised children with norovirus gastroenteritis. This will further facilitate studies of the interaction between the intestinal microbiota in such patients with precise determination of their bacterial infection control and probiotic supplements strategy.}, }
@article {pmid35440640, year = {2022}, author = {Li, C and Luan, Z and Zhao, Y and Chen, J and Yang, Y and Wang, C and Jing, Y and Qi, S and Li, Z and Guo, H and Xu, W and Zhao, B and Wu, C and Wang, S and Yang, Y and Sun, G}, title = {Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {28}, pmid = {35440640}, issn = {2055-5008}, mesh = {Aged, 80 and over ; Bacteria/genetics ; Centenarians ; China ; Health Promotion ; Humans ; Longevity ; *Metagenomics/methods ; *Microbiota ; Young Adult ; }, abstract = {The gut microbes play important roles in human longevity and the gut microbiota profile of centenarians shows some unique features from young adults. Nowadays, most microbial studies on longevity are commonly based on metagenomic sequencing which may lose information about the functional microbes with extremely low abundance. Here, we combined in-depth metagenomic sequencing and large-scale culturomics to reveal the unique gut microbial structure of a Chinese longevity population, and to explore the possible relationship between intestinal microbes and longevity. Twenty-five healthy Hainan natives were enrolled in the study, including 12 centenarians and 13 senior neighbors. An average of 51.1 Gb raw sequencing data were obtained from individual fecal sample. We assembled 1778 non-redundant metagenomic assembled genomes (MAGs), 33.46% of which cannot be classified into known species. Comparison with the ordinary people in Hainan province, the longevous cohort displayed significantly decreased abundance of butyrate-producing bacteria and largely increased proportion of Escherichia coli, Desulfovibrio piger and Methanobrevibacter smithii. These species showed a constant change with aging. We also isolated 8,030 strains from these samples by large-scale culturomics, most of which belonged to 203 known species as identified by MALDI-TOF. Surprisingly, only 42.17% of the isolated species were also detected by metagenomics, indicating obvious complementarity between these two approaches. Combination of two complement methods, in-depth metagenomic sequencing and culturomics, provides deeper insights into the longevity-related gut microbiota. The uniquely enriched gut microbes in Hainan extreme decades population may help to promote health and longevity.}, }
@article {pmid35440042, year = {2022}, author = {Wolf, PG and Cowley, ES and Breister, A and Matatov, S and Lucio, L and Polak, P and Ridlon, JM and Gaskins, HR and Anantharaman, K}, title = {Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {64}, pmid = {35440042}, issn = {2049-2618}, support = {T32GM008692/NH/NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; RO1CA204808/NH/NIH HHS/United States ; T32CA057699/NH/NIH HHS/United States ; NLM 5T15LM007359//U.S. National Library of Medicine/ ; T32 GM140935/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria ; *Carcinoma ; *Colorectal Neoplasms/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Sulfates/metabolism ; Sulfur/metabolism ; Taurine/metabolism ; }, abstract = {BACKGROUND: Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut. Microbial sulfidogenesis produces genotoxic hydrogen sulfide (H2S) in the human colon using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates; however, the majority of studies have focused on sulfate reduction using dissimilatory sulfite reductases (Dsr).<br><br>RESULTS: Here, we show that genes for microbial sulfur metabolism are more abundant and diverse than previously observed and are statistically associated with CRC. Using ~ 17,000 bacterial genomes from publicly available stool metagenomes, we studied the diversity of sulfur metabolic genes in 667 participants across different health statuses: healthy, adenoma, and carcinoma. Sulfidogenic genes were harbored by 142 bacterial genera and both organic and inorganic sulfidogenic genes were associated with carcinoma. Significantly, the anaerobic sulfite reductase (asr) genes were twice as abundant as dsr, demonstrating that Asr is likely a more important contributor to sulfate reduction in the human gut than Dsr. We identified twelve potential pathways for reductive taurine metabolism and discovered novel genera harboring these pathways. Finally, the prevalence of metabolic genes for organic sulfur indicates that these understudied substrates may be the most abundant source of microbially derived H2S.<br><br>CONCLUSIONS: Our findings significantly expand knowledge of microbial sulfur metabolism in the human gut. We show that genes for microbial sulfur metabolism in the human gut are more prevalent than previously known, irrespective of health status (i.e., in both healthy and diseased states). Our results significantly increase the diversity of pathways and bacteria that are associated with microbial sulfur metabolism in the human gut. Overall, our results have implications for understanding the role of the human gut microbiome and its potential contributions to the pathogenesis of CRC. Video abstract.}, }
@article {pmid35439563, year = {2022}, author = {Wang, K and Qaisar, M and Chen, B and Xiao, J and Cai, J}, title = {Metagenomic analysis of microbial community and metabolic pathway of simultaneous sulfide and nitrite removal process exposed to divergent hydraulic retention times.}, journal = {Bioresource technology}, volume = {354}, number = {}, pages = {127186}, doi = {10.1016/j.biortech.2022.127186}, pmid = {35439563}, issn = {1873-2976}, mesh = {Bacteria/genetics/metabolism ; Bioreactors ; Denitrification ; Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; *Nitrites/metabolism ; Nitrogen/metabolism ; Sulfides/metabolism ; }, abstract = {The role of hydraulic retention time (HRT) on S0 production was assessed through metagenomics analyses. Considering comprehensive performance for the tested HRTs (0.25-13.33 h), the optimal HRT was 1 h, while respective sulfide and nitrite loading rate could reach 6.84 kg S/(m3·d) and 1.95 kg N/(m3·d), and total S0 yield was 0.36 kg S/(kg (VSS)·d). Bacterial community richness decreased along the shortening of HRT. Microbacterium, Sulfurimonas, Sulfurovum, Paracoccus and Thauera were highly abundant bacteria. During sulfur metabolism, high expression of sqr gene was the main reason of maintaining high desulfurization load, while lacking soxB caused the continuous increase of S0. Regarding nitrogen metabolism, the rapid decrease of nitrite transporter prevented nitrite to enter in cells, which caused a rapid decrease of nitrite removal under extreme HRT. Adjusting HRT is an effective way to enhance S0 production for the application of the simultaneous sulfide and nitrite removal process.}, }
@article {pmid35437888, year = {2022}, author = {Latz, MAC and Grujcic, V and Brugel, S and Lycken, J and John, U and Karlson, B and Andersson, A and Andersson, AF}, title = {Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13623}, pmid = {35437888}, issn = {1755-0998}, support = {NV-03728-17//Naturvårdsverket/ ; 34442//Villum Fonden/ ; }, abstract = {High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics data sets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.}, }
@article {pmid35436900, year = {2022}, author = {Song, J and Li, T and Zheng, Z and Fu, W and Long, Z and Shi, N and Han, Y and Zhang, L and Yu, Y and Fang, H}, title = {Carbendazim shapes microbiome and enhances resistome in the earthworm gut.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {63}, pmid = {35436900}, issn = {2049-2618}, support = {41877144//National Nature Science Foundation of China/ ; 42177252//National Nature Science Foundation of China/ ; LZ21B070002//Key Program of Natural Science Foundation of Zhejiang Province of China/ ; 2018C02034//Zhejiang Provincial Key Research and Development Program of China/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Benzimidazoles ; Carbamates ; *Fungicides, Industrial ; Genes, Bacterial ; *Microbiota/genetics ; *Oligochaeta ; Soil/chemistry ; }, abstract = {BACKGROUND: It is worrisome that several pollutants can enhance the abundance of antibiotic resistance genes (ARGs) in the environment, including agricultural fungicides. As an important bioindicator for environmental risk assessment, earthworm is still a neglected focus that the effects of the fungicide carbendazim (CBD) residues on the gut microbiome and resistome are largely unknown. In this study, Eisenia fetida was selected to investigate the effects of CBD in the soil-earthworm systems using shotgun metagenomics and qPCR methods.<br><br>RESULTS: CBD could significantly perturb bacterial community and enrich specific bacteria mainly belonging to the phylum Actinobacteria. More importantly, CBD could serve as a co-selective agent to elevate the abundance and diversity of ARGs, particularly for some specific types (e.g., multidrug, glycopeptide, tetracycline, and rifamycin resistance genes) in the earthworm gut. Additionally, host tracking analysis suggested that ARGs were mainly carried in some genera of the phyla Actinobacteria and Proteobacteria. Meanwhile, the level of ARGs was positively relevant to the abundance of mobile genetic elements (MGEs) and some representative co-occurrence patterns of ARGs and MGEs (e.g., cmx-transposase and sul1-integrase) were further found on the metagenome-assembled contigs in the CBD treatments.<br><br>CONCLUSIONS: It can be concluded that the enhancement effect of CBD on the resistome in the earthworm gut may be attributed to its stress on the gut microbiome and facilitation on the ARGs dissemination mediated by MGEs, which may provide a novel insight into the neglected ecotoxicological risk of the widely used agrochemicals on the gut resistome of earthworm dwelling in soil. Video abstract.}, }
@article {pmid35436715, year = {2022}, author = {Liu, Z and Wei, Y and Li, J and Ding, GC}, title = {Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting.}, journal = {Waste management (New York, N.Y.)}, volume = {144}, number = {}, pages = {357-365}, doi = {10.1016/j.wasman.2022.04.013}, pmid = {35436715}, issn = {1879-2456}, mesh = {*Agricultural Inoculants/genetics ; *Composting ; Manure/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can increase the efficiency of composting. Herein, we illustrate an approach that integrate 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria for the development of inoculants to improve manure composting. The 16S rRNA amplicon sequencing analysis revealed that Firmicutes and Actinobacteria were dominant in the composting mixture, and that different microbial hubs succeeded during the thermophilic stage. All isolated thermophilic bacteria were affiliated with the order Bacillales, such as Geobacillus, Bacillus, and Aeribacillus. These isolated thermophilic bacteria were grouped into 11 phylotypes, which shared ＞99% sequence identity to 0.15% to 5.32% of 16S rRNA reads by the amplicon sequencing. Three of these phylotypes transiently enriched during the thermophilic stage. Six thermophilic bacteria were selected from the three phylotypes to obtain seven microbial inoculants. Five out of seven of the microbial inoculants enhanced the thermophilic stage of composting by 16.9% to 52.2%. Three-dimensional excitation emission matrix analysis further revealed that two inoculants (Thermoactinomyces intermedius and Ureibacillus thermophilus) stimulated humification. Additionally, the 16S rRNA amplicon sequencing analysis revealed that inoculation with thermophilic bacteria enhanced the succession of the microbial community during composting. In conclusion, 16S rRNA amplicon metagenomics is a useful tool for the development of microbial inoculants to enhance manure composting.}, }
@article {pmid35435701, year = {2022}, author = {Podowski, JC and Paver, SF and Newton, RJ and Coleman, ML}, title = {Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers.}, journal = {mBio}, volume = {}, number = {}, pages = {e0237921}, doi = {10.1128/mbio.02379-21}, pmid = {35435701}, issn = {2150-7511}, abstract = {Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth's largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) "Candidatus Nitrotoga" and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change. IMPORTANCE Microorganisms play critical roles in Earth's nitrogen cycle. In lakes, microorganisms called nitrifiers derive energy from reduced nitrogen compounds. In doing so, they transform nitrogen into a form that can ultimately be lost to the atmosphere by a process called denitrification, which helps mitigate nitrogen pollution from fertilizer runoff and sewage. Despite their importance, freshwater nitrifiers are virtually unexplored. To understand their diversity and function, we reconstructed genomes of freshwater nitrifiers across some of Earth's largest freshwater lakes, the Laurentian Great Lakes. We discovered several new species of nitrifiers specialized for clear low-nutrient waters and distinct species in comparatively turbid Lake Erie. Surprisingly, one species may be able to harness light energy by using a protein called proteorhodopsin, despite the fact that nitrifiers typically live in deep dark water. Our work reveals the unique biodiversity of the Great Lakes and fills key gaps in our knowledge of an important microbial group, the nitrifiers.}, }
@article {pmid35433497, year = {2022}, author = {Wang, Y and Gao, X and Lv, J and Zeng, Y and Li, Q and Wang, L and Zhang, Y and Gao, W and Wang, J}, title = {Gut Microbiome Signature Are Correlated With Bone Mineral Density Alterations in the Chinese Elders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {827575}, pmid = {35433497}, issn = {2235-2988}, mesh = {Aged ; Bone Density/genetics ; China ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; *Osteoporosis/genetics ; RNA, Ribosomal, 16S/genetics ; *Vitamin D Deficiency ; }, abstract = {Objective: Osteoporosis (OP), clinically featured with a low bone mineral density (BMD) and high risk of bone fracture, has become a major risk factor of disability and death in the elders, especially in postmenopausal women. The gut microbiome (GM) is thought to be implicated in bone metabolism. Herein, we clarified the composition signature and gene functional profile of GM in older people with normal and low BMD.<br><br>Design and Methods: A total of 455 participants underwent the BMD measurement and biochemical detection. GM analysis was further performed on 113 cases of postmenopausal women and men aged over 50, including both 16S rRNA and metagenomic sequencing.<br><br>Results: Generally, the BMD value was significantly lower in the older age groups, especially in the postmenopausal women. Consistently, we observed obvious vitamin D deficiency or insufficiency in females (compared to the male, P < 0.0001). The results from 16S rRNA sequencing revealed higher numbers of OTUs and diversity indexes in females than in males. The abundance in composition of Firmicutes and Clostridiales were correlated with the BMD values in females. LEfSe analysis discovered several enriched bacteria taxons in OP and normal control (NC) subgroups. A positive correlation between the number of genes and BMD values was observed in females based on metagenomic sequencing analysis. Furthermore, we identified the connecting modules among the GM composition - gene functional signature - BMD value/T score in both females and males.<br><br>Conclusions: This study provides evidences upon which to understand the mechanisms of the effects of GM on bone health, consequently revealing the physiology status and potential diagnostic/therapeutic targets based on GM for OP and postmenopausal osteoporosis (PMOP). Besides, the status of vitamin D deficiency or insufficiency need to be concerned and improved in the Chinese people.}, }
@article {pmid35430490, year = {2022}, author = {Zhou, Y and Liu, M and Yang, J}, title = {Recovering metagenome-assembled genomes from shotgun metagenomic sequencing data: Methods, applications, challenges, and opportunities.}, journal = {Microbiological research}, volume = {260}, number = {}, pages = {127023}, doi = {10.1016/j.micres.2022.127023}, pmid = {35430490}, issn = {1618-0623}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Reference genomes are essential for analyzing the metabolic and functional potentials of microbiomes. However, microbial genome resources are limited because most of microorganisms are difficult to culture. Genome binning is a culture-independent approach that can recover a vast number of microbial genomes from short-read high throughput shotgun metagenomic sequencing data. In this review, we summarize methods commonly used for reconstructing metagenome-assembled genomes (MAGs) to provide a reference for researchers to choose propriate software programs among the numerous and complicated tools and pipelines that are available for these analyses. In addition, we discuss application prospects, challenges, and opportunities for recovering MAGs from metagenomic sequencing data.}, }
@article {pmid35421353, year = {2022}, author = {Dsouza, M and Menon, R and Crossette, E and Bhattarai, SK and Schneider, J and Kim, YG and Reddy, S and Caballero, S and Felix, C and Cornacchione, L and Hendrickson, J and Watson, AR and Minot, SS and Greenfield, N and Schopf, L and Szabady, R and Patarroyo, J and Smith, W and Harrison, P and Kuijper, EJ and Kelly, CP and Olle, B and Bobilev, D and Silber, JL and Bucci, V and Roberts, B and Faith, J and Norman, JM}, title = {Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers.}, journal = {Cell host &amp; microbe}, volume = {30}, number = {4}, pages = {583-598.e8}, doi = {10.1016/j.chom.2022.03.016}, pmid = {35421353}, issn = {1934-6069}, mesh = {*Clostridioides difficile ; *Clostridium Infections/microbiology/therapy ; Fecal Microbiota Transplantation/methods ; Healthy Volunteers ; Humans ; *Microbiota ; }, abstract = {Manipulation of the gut microbiota via fecal microbiota transplantation (FMT) has shown clinical promise in diseases such as recurrent Clostridioides difficile infection (rCDI). However, the variable nature of this approach makes it challenging to describe the relationship between fecal strain colonization, corresponding microbiota changes, and clinical efficacy. Live biotherapeutic products (LBPs) consisting of defined consortia of clonal bacterial isolates have been proposed as an alternative therapeutic class because of their promising preclinical results and safety profile. We describe VE303, an LBP comprising 8 commensal Clostridia strains under development for rCDI, and its early clinical development in healthy volunteers (HVs). In a phase 1a/b study in HVs, VE303 is determined to be safe and well-tolerated at all doses tested. VE303 strains optimally colonize HVs if dosed over multiple days after vancomycin pretreatment. VE303 promotes the establishment of a microbiota community known to provide colonization resistance.}, }
@article {pmid35417481, year = {2022}, author = {Lyalina, S and Stepanauskas, R and Wu, F and Sanjabi, S and Pollard, KS}, title = {Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community.}, journal = {PloS one}, volume = {17}, number = {4}, pages = {e0261795}, pmid = {35417481}, issn = {1932-6203}, support = {R21 AI108953/AI/NIAID NIH HHS/United States ; R21 AI134037/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Mammals/genetics ; Metagenome ; Metagenomics ; Mice ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Laboratory mice are widely studied as models of mammalian biology, including the microbiota. However, much of the taxonomic and functional diversity of the mouse gut microbiome is missed in current metagenomic studies, because genome databases have not achieved a balanced representation of the diverse members of this ecosystem. Towards solving this problem, we used flow cytometry and low-coverage sequencing to capture the genomes of 764 single cells from the stool of three laboratory mice. From these, we generated 298 high-coverage microbial genome assemblies, which we annotated for open reading frames and phylogenetic placement. These genomes increase the gene catalog and phylogenetic breadth of the mouse microbiota, adding 135 novel species with the greatest increase in diversity to the Muribaculaceae and Bacteroidaceae families. This new diversity also improves the read mapping rate, taxonomic classifier performance, and gene detection rate of mouse stool metagenomes. The novel microbial functions revealed through our single-cell genomes highlight previously invisible pathways that may be important for life in the murine gastrointestinal tract.}, }
@article {pmid35416715, year = {2022}, author = {Yang, C and Su, Q and Tang, M and Luo, S and Zheng, H and Zhang, X and Zhou, X}, title = {Amplicon Sequencing of Single-Copy Protein-Coding Genes Reveals Accurate Diversity for Sequence-Discrete Microbiome Populations.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0210521}, pmid = {35416715}, issn = {2165-0497}, support = {2018FY100403//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; No. 31772493//National Natural Science Foundation of China (NSFC)/ ; No. 32000346//National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {An in-depth understanding of microbial function and the division of ecological niches requires accurate delineation and identification of microbes at a fine taxonomic resolution. Microbial phylotypes are typically defined using a 97% small subunit (16S) rRNA threshold. However, increasing evidence has demonstrated the ubiquitous presence of taxonomic units of distinct functions within phylotypes. These so-called sequence-discrete populations (SDPs) have used to be mainly delineated by disjunct sequence similarity at the whole-genome level. However, gene markers that could accurately identify and quantify SDPs are lacking in microbial community studies. Here, we developed a pipeline to screen single-copy protein-coding genes that could accurately characterize SDP diversity via amplicon sequencing of microbial communities. Fifteen candidate marker genes were evaluated using three criteria (extent of sequence divergence, phylogenetic accuracy, and conservation of primer regions) and the selected genes were subject to test the efficiency in differentiating SDPs within Gilliamella, a core honeybee gut microbial phylotype, as a proof-of-concept. The results showed that the 16S V4 region failed to report accurate SDP diversities due to low taxonomic resolution and changing copy numbers. In contrast, the single-copy genes recommended by our pipeline were able to successfully quantify Gilliamella SDPs for both mock samples and honeybee guts, with results highly consistent with those of metagenomics. The pipeline developed in this study is expected to identify single-copy protein coding genes capable of accurately quantifying diverse bacterial communities at the SDP level. IMPORTANCE Microbial communities can be distinguished by discrete genetic and ecological characteristics. These sequence-discrete populations are foundational for investigating the composition and functional structures of microbial communities at high resolution. In this study, we screened for reliable single-copy protein-coding marker genes to identify sequence-discrete populations through our pipeline. Using marker gene amplicon sequencing, we could accurately and efficiently delineate the population diversity in microbial communities. These results suggest that single copy protein-coding genes can be an accurate, quantitative, and economical alternative for characterizing population diversity. Moreover, the feasibility of a gene as marker for any bacterial population identification can be quickly evaluated by the pipeline proposed here.}, }
@article {pmid35414589, year = {2022}, author = {Shalon, N and Relman, DA and Yaffe, E}, title = {Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors.}, journal = {Genome research}, volume = {32}, number = {5}, pages = {986-1003}, doi = {10.1101/gr.275894.121}, pmid = {35414589}, issn = {1549-5469}, mesh = {Genotype ; Humans ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Plasmids/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. Their circular genomes correspond to circular walks in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present DomCycle, an algorithm that reconstructs likely circular genomes based on the identification of so-called "dominant" graph cycles. In the implementation, we leverage paired reads to bridge assembly gaps and scrutinize cycles through a nucleotide-level analysis, making the approach robust to misassembly artifacts. We validated the approach using simulated and real sequencing data. Application of DomCycle to 32 publicly available DNA shotgun sequence data sets from diverse natural environments led to the reconstruction of hundreds of circular mobile genomes. Clustering revealed 20 highly prevalent and cryptic plasmids that have clonal population structures with recent common ancestors. This method facilitates the study of microbial communities that evolve through horizontal gene transfer.}, }
@article {pmid35414107, year = {2022}, author = {Martínez-Álvaro, M and Auffret, MD and Duthie, CA and Dewhurst, RJ and Cleveland, MA and Watson, M and Roehe, R}, title = {Bovine host genome acts on rumen microbiome function linked to methane emissions.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {350}, pmid = {35414107}, issn = {2399-3642}, support = {BB/N01720X/1, BB/N016742/1, BB/S006567/1, BB/S006680/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; RESAS_2016-2022_Commission//Rural and Environment Science and Analytical Services Division (Scottish Government's Rural and Environment Science and Analytical Services Division)/ ; }, mesh = {Animals ; Archaea/genetics ; Cattle ; Metagenome ; Methane ; *Microbiota/genetics ; *Rumen ; }, abstract = {Our study provides substantial evidence that the host genome affects the comprehensive function of the microbiome in the rumen of bovines. Of 1,107/225/1,141 rumen microbial genera/metagenome assembled uncultured genomes (RUGs)/genes identified from whole metagenomics sequencing, 194/14/337 had significant host genomic effects (heritabilities ranging from 0.13 to 0.61), revealing that substantial variation of the microbiome is under host genomic control. We found 29/22/115 microbial genera/RUGs/genes host-genomically correlated (|0.59| to |0.93|) with emissions of the potent greenhouse gas methane (CH4), highlighting the strength of a common host genomic control of specific microbial processes and CH4. Only one of these microbial genes was directly involved in methanogenesis (cofG), whereas others were involved in providing substrates for archaea (e.g. bcd and pccB), important microbial interspecies communication mechanisms (ABC.PE.P), host-microbiome interaction (TSTA3) and genetic information processes (RP-L35). In our population, selection based on abundances of the 30 most informative microbial genes provided a mitigation potential of 17% of mean CH4 emissions per generation, which is higher than for selection based on measured CH4 using respiration chambers (13%), indicating the high potential of microbiome-driven breeding to cumulatively reduce CH4 emissions and mitigate climate change.}, }
@article {pmid35413521, year = {2022}, author = {Li, L and Xiao, Y and Wang, C and Olsen, RH and Meng, H and Shi, L}, title = {Exploring the resistome, virulome, mobilome and microbiome along pork production chain using metagenomics.}, journal = {International journal of food microbiology}, volume = {371}, number = {}, pages = {109674}, doi = {10.1016/j.ijfoodmicro.2022.109674}, pmid = {35413521}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Metagenomics ; *Microbiota ; *Pork Meat ; *Red Meat ; Swine ; beta-Lactamases/genetics ; }, abstract = {In order to understand and minimize microbial contaminants spread from animal to raw pork products, we explored the diversity of antibiotic resistance genes (ARGs), virulence factors (VFs), mobile genetic elements (MGEs) and the bacterial community composition in feces of pigs, processing areas as well as the end pork products in a large-scale pig slaughterhouse in China using metagenomics. The abundance and diversity of microbial community was higher in arrival and slaughtering room area and decreased sharply in the end pork products. Furthermore, the relative abundance of some clinically relevant pathogens and opportunity pathogens were greater in the end pork products and cutter samples. We identified 1412 subtypes of ARGs related to 30 antibiotic classes, in which ARGs related to multidrug resistance and β-lactamase were dominant. Resistance determinants to clinically critical important antibiotics, including sequences related to mcr, optrA, poxtA, tetX and β-lactamase genes (i.e. blaOXA, blaVIM, blaIMP, blaGES, blaNDM, blaKPC and blaSME) were detected. More than 42 general virulence features, mainly adherence, secretion system, iron uptake, toxin, antiphagocytosis and immune evasion, were identified. A total of 1922 types of MGEs, mainly plasmids were observed. Most of the ARGs are predicted to be associated with MGEs. The prevalence of ARGs, VFs and MGEs decreased over subsequential processing steps. Most of the remaining ARGs, VFs and MGEs in end pork products were also present on other samples, indicating the flow of these genes through the production line. These results broaden our understanding of the global ARGs, VFs and MGEs diversity along the pork production chain, with the suggestion of implementing improved control measures to reduce the risk of spread of pathogenic bacteria and their associated resistome, virulome and mobilome from animal to the food chain and the surrounding environment.}, }
@article {pmid35412096, year = {2022}, author = {Passarini, MRZ and Ottoni, JR and Costa, PEDS and Hissa, DC and Falcão, RM and Melo, VMM and Balbino, VQ and Mendonça, LAR and Lima, MGS and Coutinho, HDM and Verde, LCL}, title = {Fungal community diversity of heavy metal contaminated soils revealed by metagenomics.}, journal = {Archives of microbiology}, volume = {204}, number = {5}, pages = {255}, pmid = {35412096}, issn = {1432-072X}, support = {DCR-0024-01438.01.00/12//funcap/ ; }, mesh = {Biodegradation, Environmental ; Metagenomics ; *Metals, Heavy/metabolism ; *Mycobiome ; Soil ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.}, }
@article {pmid35410034, year = {2022}, author = {Campobasso, CP and Mastroianni, G and Feola, A and Mascolo, P and Carfora, A and Liguori, B and Zangani, P and Dell'Annunziata, F and Folliero, V and Petrillo, A and Della Pepa, ME and Martora, F and Galdiero, M}, title = {MALDI-TOF Mass Spectrometry Analysis and Human Post-Mortem Microbial Community: A Pilot Study.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {7}, pages = {}, pmid = {35410034}, issn = {1660-4601}, mesh = {Humans ; Metagenomics ; *Microbiota ; Pilot Projects ; Reproducibility of Results ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; }, abstract = {INTRODUCTION: The human post-mortem microbiome (HPM) plays a major role in the decomposition process. Successional changes in post-mortem bacterial communities have been recently demonstrated using high throughput metagenomic sequencing techniques, showing great potential as a post-mortem interval (PMI) predictor. The aim of this study is to verify the application of the mass spectrometry technique, better known as MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), as a cheap and quick method for microbe taxonomic identification and for studying the PM microbiome.<br><br>METHODS: The study was carried out on 18 human bodies, ranging from 4 months to 82 years old and with a PMI range from 24 h up to 15 days. The storage time interval in the coolers was included in the final PMI estimates. Using the PMI, the sample study was divided into three main groups: seven cases with a PMI < 72 h; six cases with a PMI of 72-168 h and five cases with a PMI > 168 h. For each body, microbiological swabs were sampled from five external anatomical sites (eyes, ears, nose, mouth, and rectum) and four internal organs (brain, spleen, liver, and heart).<br><br>RESULTS: The HPM became increasingly different from the starting communities over time in the internal organs as well as at skin sites; the HPM microbiome was mostly dominated by Firmicutes and Proteobacteria phyla; and a PM microbial turnover existed during decomposition, evolving with the PMI.<br><br>CONCLUSIONS: MALDI-TOF is a promising method for PMI estimation, given its sample handling, good reproducibility, and high speed and throughput. Although several intrinsic and extrinsic factors can affect the structure of the HPM, MALDI-TOF can detect the overall microbial community turnover of most prevalent phyla during decomposition. Limitations are mainly related to its sensitivity due to the culture-dependent method and bias in the identification of new isolates.}, }
@article {pmid35409199, year = {2022}, author = {Li, QC and Wang, B and Zeng, YH and Cai, ZH and Zhou, J}, title = {The Microbial Mechanisms of a Novel Photosensitive Material (Treated Rape Pollen) in Anti-Biofilm Process under Marine Environment.}, journal = {International journal of molecular sciences}, volume = {23}, number = {7}, pages = {}, pmid = {35409199}, issn = {1422-0067}, support = {41976126//National Natural Science Foundation of China/ ; 2020B1515120012//Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {*Biofilms ; *Biofouling/prevention &amp; control ; Oxidants/pharmacology ; Pollen ; Seawater/microbiology ; }, abstract = {Marine biofouling is a worldwide problem in coastal areas and affects the maritime industry primarily by attachment of fouling organisms to solid immersed surfaces. Biofilm formation by microbes is the main cause of biofouling. Currently, application of antibacterial materials is an important strategy for preventing bacterial colonization and biofilm formation. A natural three-dimensional carbon skeleton material, TRP (treated rape pollen), attracted our attention owing to its visible-light-driven photocatalytic disinfection property. Based on this, we hypothesized that TRP, which is eco-friendly, would show antifouling performance and could be used for marine antifouling. We then assessed its physiochemical characteristics, oxidant potential, and antifouling ability. The results showed that TRP had excellent photosensitivity and oxidant ability, as well as strong anti-bacterial colonization capability under light-driven conditions. Confocal laser scanning microscopy showed that TRP could disperse pre-established biofilms on stainless steel surfaces in natural seawater. The biodiversity and taxonomic composition of biofilms were significantly altered by TRP (p < 0.05). Moreover, metagenomics analysis showed that functional classes involved in the antioxidant system, environmental stress, glucose-lipid metabolism, and membrane-associated functions were changed after TRP exposure. Co-occurrence model analysis further revealed that TRP markedly increased the complexity of the biofilm microbial network under light irradiation. Taken together, these results demonstrate that TRP with light irradiation can inhibit bacterial colonization and prevent initial biofilm formation. Thus, TRP is a potential nature-based green material for marine antifouling.}, }
@article {pmid35409014, year = {2022}, author = {Jones, KA and Richard, AJ and Salbaum, JM and Newman, S and Carmouche, R and Webb, S and Bruce-Keller, AJ and Stephens, JM and Campagna, SR}, title = {Cross-Omics Analysis of Fenugreek Supplementation Reveals Beneficial Effects Are Caused by Gut Microbiome Changes Not Mammalian Host Physiology.}, journal = {International journal of molecular sciences}, volume = {23}, number = {7}, pages = {}, pmid = {35409014}, issn = {1422-0067}, support = {R01AT010279/AT/NCCIH NIH HHS/United States ; NIH8 1P30GM118430-02/NH/NIH HHS/United States ; NIH 2P30DK072476/NH/NIH HHS/United States ; }, mesh = {Animals ; Cholesterol ; *Diabetes Mellitus, Type 2/drug therapy ; Dietary Supplements ; *Gastrointestinal Microbiome ; Mammals ; Mice ; Plant Extracts/pharmacology/therapeutic use ; *Trigonella ; }, abstract = {Herbal remedies are increasing in popularity as treatments for metabolic conditions such as obesity and Type 2 Diabetes. One potential therapeutic option is fenugreek seeds (Trigonella foenum-graecum), which have been used for treating high cholesterol and Type 2 diabetes. A proposed mechanism for these benefits is through alterations in the microbiome, which impact mammalian host metabolic function. This study used untargeted metabolomics to investigate the fenugreek-induced alterations in the intestinal, liver, and serum profiles of mice fed either a 60% high-fat or low-fat control diet each with or without fenugreek supplementation (2% w/w) for 14 weeks. Metagenomic analyses of intestinal contents found significant alterations in the relative composition of the gut microbiome resulting from fenugreek supplementation. Specifically, Verrucomicrobia, a phylum containing beneficial bacteria which are correlated with health benefits, increased in relative abundance with fenugreek. Metabolomics partial least squares discriminant analysis revealed substantial fenugreek-induced changes in the large intestines. However, it was observed that while the magnitude of changes was less, significant modifications were present in the liver tissues resulting from fenugreek supplementation. Further analyses revealed metabolic processes affected by fenugreek and showed broad ranging impacts in multiple pathways, including carnitine biosynthesis, cholesterol and bile acid metabolism, and arginine biosynthesis. These pathways may play important roles in the beneficial effects of fenugreek.}, }
@article {pmid35406140, year = {2022}, author = {Leeuwendaal, NK and Stanton, C and O'Toole, PW and Beresford, TP}, title = {Fermented Foods, Health and the Gut Microbiome.}, journal = {Nutrients}, volume = {14}, number = {7}, pages = {}, pmid = {35406140}, issn = {2072-6643}, support = {6555//Teagasc - The Irish Agriculture and Food Development Authority/ ; }, mesh = {Diet ; Fermentation ; *Fermented Foods ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Fermented foods have been a part of human diet for almost 10,000 years, and their level of diversity in the 21st century is substantial. The health benefits of fermented foods have been intensively investigated; identification of bioactive peptides and microbial metabolites in fermented foods that can positively affect human health has consolidated this interest. Each fermented food typically hosts a distinct population of microorganisms. Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, which can now be resolved at the species and strain level by metagenomics. Transient or long-term colonization of the gut by fermented food strains or impacts of fermented foods on indigenous gut microbes can therefore be determined. This review considers the primary food fermentation pathways and microorganisms involved, the potential health benefits, and the ability of these foodstuffs to impact the gut microbiome once ingested either through compounds produced during the fermentation process or through interactions with microorganisms from the fermented food that are capable of surviving in the gastro-intestinal transit. This review clearly shows that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet.}, }
@article {pmid35404958, year = {2022}, author = {Grazioli, F and Siarheyeu, R and Alqassem, I and Henschel, A and Pileggi, G and Meiser, A}, title = {Microbiome-based disease prediction with multimodal variational information bottlenecks.}, journal = {PLoS computational biology}, volume = {18}, number = {4}, pages = {e1010050}, pmid = {35404958}, issn = {1553-7358}, mesh = {*Gastrointestinal Microbiome ; Humans ; Machine Learning ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Scientific research is shedding light on the interaction of the gut microbiome with the human host and on its role in human health. Existing machine learning methods have shown great potential in discriminating healthy from diseased microbiome states. Most of them leverage shotgun metagenomic sequencing to extract gut microbial species-relative abundances or strain-level markers. Each of these gut microbial profiling modalities showed diagnostic potential when tested separately; however, no existing approach combines them in a single predictive framework. Here, we propose the Multimodal Variational Information Bottleneck (MVIB), a novel deep learning model capable of learning a joint representation of multiple heterogeneous data modalities. MVIB achieves competitive classification performance while being faster than existing methods. Additionally, MVIB offers interpretable results. Our model adopts an information theoretic interpretation of deep neural networks and computes a joint stochastic encoding of different input data modalities. We use MVIB to predict whether human hosts are affected by a certain disease by jointly analysing gut microbial species-relative abundances and strain-level markers. MVIB is evaluated on human gut metagenomic samples from 11 publicly available disease cohorts covering 6 different diseases. We achieve high performance (0.80 < ROC AUC < 0.95) on 5 cohorts and at least medium performance on the remaining ones. We adopt a saliency technique to interpret the output of MVIB and identify the most relevant microbial species and strain-level markers to the model's predictions. We also perform cross-study generalisation experiments, where we train and test MVIB on different cohorts of the same disease, and overall we achieve comparable results to the baseline approach, i.e. the Random Forest. Further, we evaluate our model by adding metabolomic data derived from mass spectrometry as a third input modality. Our method is scalable with respect to input data modalities and has an average training time of < 1.4 seconds. The source code and the datasets used in this work are publicly available.}, }
@article {pmid35404122, year = {2022}, author = {Hu, Y and Irinyi, L and Hoang, MTV and Eenjes, T and Graetz, A and Stone, EA and Meyer, W and Schwessinger, B and Rathjen, JP}, title = {Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0244421}, pmid = {35404122}, issn = {2150-7511}, support = {FT180100024//Australian Research Council/ ; GNT1121936//Department of Health | National Health and Medical Research Council (NHMRC)/ ; HSF_17_04//Hermon Slade Foundation/ ; }, mesh = {Bacteria/genetics ; Fungi/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiota/genetics ; *Mycobiome ; }, abstract = {The kingdom Fungi is highly diverse in morphology and ecosystem function. Yet fungi are challenging to characterize as they can be difficult to culture and morphologically indistinct. Overall, their description and analysis lag far behind other microbes such as bacteria. Classification of species via high-throughput sequencing is increasingly becoming the norm for pathogen detection, microbiome studies, and environmental monitoring. With the rapid development of sequencing technologies, however, standardized procedures for taxonomic assignment of long sequence reads have not yet been well established. Focusing on nanopore sequencing technology, we compared classification and community composition analysis pipelines using shotgun and amplicon sequencing data generated from mock communities comprising 43 fungal species. We show that regardless of the sequencing methodology used, the highest accuracy of species identification was achieved by sequence alignment against a fungal-specific database. During the assessment of classification algorithms, we found that applying cutoffs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without major data loss. We also generated draft genome assemblies for three fungal species from nanopore data which were absent from genome databases. Our study improves sequence-based classification and estimation of relative sequence abundance using real fungal community data and provides a practical guide for the design of metagenomics analyses focusing on fungi. IMPORTANCE Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes. Although great progress has been made on bacterial community compositions, microbial eukaryotes such as fungi clearly lag behind. Our study provides a detailed breakdown of strategies to improve species identification with immediate relevance to real-world studies. We find that real-life data sets do not always behave as expected, distinct from reports based on simulated data sets.}, }
@article {pmid35402307, year = {2022}, author = {Mudrik-Zohar, H and Carasso, S and Gefen, T and Zalmanovich, A and Katzir, M and Cohen, Y and Paitan, Y and Geva-Zatorsky, N and Chowers, M}, title = {Microbiome Characterization of Infected Diabetic Foot Ulcers in Association With Clinical Outcomes: Traditional Cultures Versus Molecular Sequencing Methods.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {836699}, pmid = {35402307}, issn = {2235-2988}, mesh = {*Diabetes Mellitus ; *Diabetic Foot/complications/microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background: Infected diabetic foot ulcers (IDFU) are a major complication of diabetes mellitus. These potentially limb-threatening ulcers are challenging to treat due to impaired wound healing characterizing diabetic patients and the complex microbial environment of these ulcers.<br><br>Aim: To analyze the microbiome of IDFU in association with clinical outcomes.<br><br>Methods: Wound biopsies from IDFU were obtained from hospitalized patients and were analyzed using traditional microbiology cultures, 16S rRNA sequencing and metagenomic sequencing. Patients' characteristics, culture-based results and sequencing data were analyzed in association with clinical outcomes.<br><br>Results: A total of 31 patients were enrolled. Gram-negative bacteria dominated the IDFU samples (79%, 59% and 54% of metagenomics, 16S rRNA and cultures results, respectively, p<0.001). 16S rRNA and metagenomic sequencing detected significantly more anaerobic bacteria, as compared to conventional cultures (59% and 76%, respectively vs. 26% in cultures, p=0.001). Culture-based results showed that Staphylococcus aureus was more prevalent among patients who were treated conservatively (p=0.048). In metagenomic analysis, the Bacteroides genus was more prevalent among patients who underwent amputation (p<0.001). Analysis of metagenomic-based functional data showed that antibiotic resistance genes and genes related to biofilm production and to bacterial virulent factors were more prevalent in IDFU that resulted in amputation (p<0.001).<br><br>Conclusion: Sequencing tools uncover the complex biodiversity of IDFU and emphasize the high prevalence of anaerobes and Gram-negative bacteria in these ulcers. Furthermore, sequencing results highlight possible associations among certain genera, species, and bacterial functional genes to clinical outcomes.}, }
@article {pmid35402298, year = {2022}, author = {Li, K and Zeng, Z and Liu, J and Pei, L and Wang, Y and Li, A and Kulyar, MF and Shahzad, M and Mehmood, K and Li, J and Qi, D}, title = {Effects of Short-Chain Fatty Acid Modulation on Potentially Diarrhea-Causing Pathogens in Yaks Through Metagenomic Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {805481}, pmid = {35402298}, issn = {2235-2988}, mesh = {Animals ; Bacteria/genetics ; Cattle ; Clostridiales ; Diarrhea/microbiology ; Fatty Acids, Volatile ; Feces ; *Gastrointestinal Microbiome ; *Metagenomics ; }, abstract = {Short-chain fatty acids (SCFA) are principal nutrient substrates of intestinal epithelial cells that regulate the epithelial barrier in yaks. Until now, metagenomics sequencing has not been reported in diarrheal yaks. Scarce information is available regarding the levels of fecal SCFA and diarrhea in yaks. So, our study aims to identify the potential pathogens that cause the emerging diarrhea and explore the potential relationship of short-chain fatty acids in this issue. We estimated diarrhea rate in yaks after collecting an equal number of fecal samples from affected animals. Metagenomics sequencing and quantitative analysis of SCFA were performed, which revealed 15%-25% and 5%-10% prevalence of diarrhea in yak's calves and adults, respectively. Violin box plot also showed a higher degree of dispersion in gene abundance distribution of diarrheal yaks, as compared to normal yaks. We found 366,163 significant differential abundance genes in diarrheal yaks, with 141,305 upregulated and 224,858 downregulated genes compared with normal yaks via DESeq analysis. Metagenomics binning analysis indicated the higher significance of bin 33 (Bacteroidales) (p < 0.05) in diarrheal animals, while bin 10 (p < 0.0001), bin 30 (Clostridiales) (p < 0.05), bin 51 (Lactobacillales) (p < 0.05), bin 8 (Lachnospiraceae) (p < 0.05), and bin 47 (Bacteria) (p < 0.05) were significantly higher in normal yaks. At different levels, a significant difference in phylum (n = 4), class (n = 8), oder (n = 8), family (n = 16), genus (n = 17), and species (n = 30) was noticed, respectively. Compared with healthy yaks, acetic acid (p < 0.01), propionic acid (p < 0.01), butyric acid (p < 0.01), isobutyric acid (p < 0.01), isovaleric acid (p < 0.05), and caproic acid (p < 0.01) were all observed significantly at a lower rate in diarrheal yaks. In conclusion, besides the increased Staphylococcus aureus, Babesia ovata, Anaplasma phagocytophilum, Bacteroides fluxus, viruses, Klebsiella pneumonia, and inflammation-related bacteria, the decrease of SCFA caused by the imbalance of intestinal microbiota was potentially observed in diarrheal yaks.}, }
@article {pmid35398400, year = {2022}, author = {Do, TT and Nolan, S and Hayes, N and O'Flaherty, V and Burgess, C and Brennan, F and Walsh, F}, title = {Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {305}, number = {}, pages = {119271}, doi = {10.1016/j.envpol.2022.119271}, pmid = {35398400}, issn = {1873-6424}, mesh = {Anaerobiosis ; Animals ; Anti-Bacterial Agents/pharmacology ; *Composting ; Manure/analysis ; Metagenome ; *Microbiota/genetics ; Nitrogen/analysis ; Swine ; }, abstract = {Direct application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment.}, }
@article {pmid35397610, year = {2022}, author = {Strehlow, BW and Schuster, A and Francis, WR and Canfield, DE}, title = {Metagenomic data for Halichondria panicea from Illumina and nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts.}, journal = {BMC research notes}, volume = {15}, number = {1}, pages = {135}, pmid = {35397610}, issn = {1756-0500}, support = {16518//Villum Fonden/ ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; *Microbiota ; *Nanopore Sequencing ; *Porifera/genetics ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses.<br><br>DATA DESCRIPTION: These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of Halichondria panicea-one Illumina MiSeq (2 × 300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the 'best' assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.}, }
@article {pmid35394234, year = {2022}, author = {Ayiti, OE and Ayangbenro, AS and Babalola, OO}, title = {Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere.}, journal = {Archives of microbiology}, volume = {204}, number = {5}, pages = {246}, pmid = {35394234}, issn = {1432-072X}, support = {UID123634//National Research Foundation South Africa/ ; UID132595//National Research Foundation South Africa/ ; }, mesh = {*Microbiota ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Zea mays/microbiology ; }, abstract = {The microbial network of rhizosphere is unique as a result of root exudate. Insights into the relationship that exists with the energy metabolic functional groups will help in biofertilizer production. We hypothesize that there exists a relationship between nitrifying microorganisms and other energy metabolic functional microbial groups in the maize rhizosphere across different growth stages. Nucleospin soil DNA extraction kit was used to extract DNA from soil samples collected from maize rhizosphere. The 16S metagenomics sequencing was carried out on Illumina Miseq. The sequence obtained was analyzed on MG-RAST. Nitrospira genera were the most abundant in the nitrifying community. Nitrifying microorganisms were more than each of the studied functional groups except for nitrogen-fixing bacteria. Also, majority of the microorganisms were noticed at the fruiting stage and there was variation in the microbial structure across different growth stages. The result showed that there exists a substantial amount of both negative and positive correlation within the nitrifying microorganisms, and between them and other energy metabolic functional groups. The knowledge obtained from this study will help improve the growth and development of maize through modification of the rhizosphere microbial community structure.}, }
@article {pmid35392807, year = {2022}, author = {Raineri, S and Sherriff, JA and Thompson, KSJ and Jones, H and Pfluger, PT and Ilott, NE and Mellor, J}, title = {Pharmacologically induced weight loss is associated with distinct gut microbiome changes in obese rats.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {91}, pmid = {35392807}, issn = {1471-2180}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteroides ; Female ; *Gastrointestinal Microbiome ; Inflammation ; Obesity/microbiology ; Rats ; Rats, Wistar ; Weight Loss ; }, abstract = {BACKGROUND: Obesity, metabolic disease and some psychiatric conditions are associated with changes to relative abundance of bacterial species and specific genes in the faecal microbiome. Little is known about the impact of pharmacologically induced weight loss on distinct microbiome species and their respective gene programs in obese individuals.<br><br>METHODOLOGY: Using shotgun metagenomics, the composition of the microbiome was obtained for two cohorts of obese female Wistar rats (n = 10-12, total of 82) maintained on a high fat diet before and after a 42-day treatment with a panel of four investigatory or approved anti-obesity drugs (tacrolimus/FK506, bupropion, naltrexone and sibutramine), alone or in combination.<br><br>RESULTS: Only sibutramine treatment induced consistent weight loss and improved glycaemic control in the obese rats. Weight loss was associated with reduced food intake and changes to the faecal microbiome in multiple microbial taxa, genes, and pathways. These include increased β-diversity, increased relative abundance of multiple Bacteroides species, increased Bacteroides/Firmicutes ratio and changes to abundance of genes and species associated with obesity-induced inflammation, particularly those encoding components of the flagellum and its assembly.<br><br>CONCLUSIONS: Sibutramine-induced weight loss in obese rats is associated with improved metabolic health, and changes to the faecal microbiome consistent with a reduction in obesity-induced bacterially-driven inflammation.}, }
@article {pmid35392799, year = {2022}, author = {Behzad, H and Ohyanagi, H and Alharbi, B and Ibarra, M and Alarawi, M and Saito, Y and Duarte, CM and Bajic, V and Mineta, K and Gojobori, T}, title = {A cautionary signal from the Red Sea on the impact of increased dust activity on marine microbiota.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {277}, pmid = {35392799}, issn = {1471-2164}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Dust/analysis ; Indian Ocean ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: Global climate change together with growing desertification is leading to increased dust emissions to the atmosphere, drawing attention to possible impacts on marine ecosystems receiving dust deposition. Since microorganisms play important roles in maintaining marine homeostasis through nutrient cycling and carbon flow, detrimental changes in the composition of marine microbiota in response to increased dust input could negatively impact marine health, particularly so in seas located within the Global Dust Belt. Due to its strategic location between two deserts and unique characteristics, the Red Sea provides an attractive semi-enclosed "megacosm" to examine the impacts of large dust deposition on the vastly diverse microbiota in its exceptionally warm oligotrophic waters.<br><br>RESULTS: We used culture-independent metagenomic approaches to assess temporal changes in the Red Sea microbiota in response to two severe sandstorms, one originated in the Nubian Desert in the summer 2016 and a second one originated in the Libyan Desert in the spring 2017. Despite differences in sandstorm origin and meteorological conditions, both sandstorms shifted bacterial and Archaeal groups in a similar mode. In particular, the relative abundance of autotrophic bacteria declined while those of heterotrophic bacteria, particularly Bacteroidetes, and Archaea increased. The changes peaked within six days from the start of sandstorms, and the community recovered the original assemblage within one month.<br><br>CONCLUSION: Our results suggest that increased dust emission with expanding desertification could lead to undesirable impacts in ocean function, enhancing heterotrophic processes while reducing autotrophic ones, thereby affecting the marine food web in seas receiving dust deposition.}, }
@article {pmid35389162, year = {2022}, author = {Dunn, CM and Jeffries, MA}, title = {The Microbiome in Osteoarthritis: a Narrative Review of Recent Human and Animal Model Literature.}, journal = {Current rheumatology reports}, volume = {24}, number = {5}, pages = {139-148}, pmid = {35389162}, issn = {1534-6307}, support = {K08AR070891/AR/NIAMS NIH HHS/United States ; R61AR078075/AR/NIAMS NIH HHS/United States ; R01AR076440/AR/NIAMS NIH HHS/United States ; P20GM125528/GM/NIGMS NIH HHS/United States ; PR191652//Congressionally Directed Medical Research Programs/ ; K08AR070891/AR/NIAMS NIH HHS/United States ; R61AR078075/AR/NIAMS NIH HHS/United States ; R01AR076440/AR/NIAMS NIH HHS/United States ; P20GM125528/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; Models, Animal ; *Osteoarthritis, Knee ; *Probiotics/therapeutic use ; }, abstract = {PURPOSE OF THE REVIEW: The microbiome has recently emerged as a powerful contributor to health and illness in chronic, systemic disorders. Furthermore, new microbiome niches beyond traditional gut locations are frequently being described. Over the past 5 years, numerous pivotal studies have demonstrated associations between changes in various microbiome niches and the development of osteoarthritis (OA). Herein, we review the most impactful recent literature, including microbiome associations with disease and the potential therapeutic value of microbiome manipulation.<br><br>RECENT FINDINGS: The gut microbiome of human OA patients is enriched in specific bacterial clades, most notably Streptococcus, which correlates with OA pain, Firmicutes, and others. Most studies have focused on knee OA, although one publication demonstrated positive associations with 3 gut microbiome clades in hand OA. OA can be easily distinguished from RA by evaluating differences in oral microbiome composition. Most studies have also demonstrated a reduction in richness of the gut microbiome (alpha diversity) associated with OA. Several studies have identified bacterial signatures within human knee and hip cartilage, synovial fluid, and synovial tissue and have described changes in these patterns occurring with the development of OA. In animal models of OA, high-fat diet-induced obesity has been the most well-studied OA risk factor associated with changes in the microbiome, with numerous bacterial clades changed within the gut microbiome and associated with OA. Also in animal models, various oral supplementations, including dietary fiber, probiotics including Lactobacillus species, and cecal microbiome transplantation have all shown improvements in OA histopathology or cartilage healing. Microbiome changes are strongly associated with the OA disease process and with individual OA risk factors related to both the gut microbiome and the microbial DNA patterns in the joint. Microbiome-directed interventions have the potential to prevent or reduce the progression of OA. Future studies should investigate the mechanistic underpinnings of these microbiome associations and further define the therapeutic potential of microbiome augmentation.}, }
@article {pmid35388735, year = {2022}, author = {Davies, M and Galazzo, G and van Hattem, JM and Arcilla, MS and Melles, DC and de Jong, MD and Schultsz, C and Wolffs, P and McNally, A and Schaik, WV and Penders, J}, title = {Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2060676}, pmid = {35388735}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria ; Bacteroidaceae ; Diarrhea/drug therapy ; Enterobacteriaceae/genetics ; *Enterobacteriaceae Infections/microbiology ; Escherichia coli/genetics ; *Gastrointestinal Microbiome ; Humans ; Travel ; beta-Lactamases/genetics/pharmacology ; }, abstract = {Previous studies have shown high acquisition risks of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) among international travelers visiting antimicrobial resistance (AMR) hotspots. Although antibiotic use and travelers' diarrhea have shown to influence the ESBL-E acquisition risk, it remains largely unknown whether successful colonization of ESBL-E during travel is associated with the composition, functional capacity and resilience of the traveler's microbiome. The microbiome of pre- and post-travel fecal samples from 190 international travelers visiting Africa or Asia was profiled using whole metagenome shotgun sequencing. A metagenomics species concept approach was used to determine the microbial composition, population diversity and functional capacity before travel and how it is altered longitudinally. Eleven travelers were positive for ESBL-E before travel and removed from the analysis. Neither the microbial richness (Chao1), diversity (effective Shannon) and community structure (Bray-Curtis dissimilarity) in pretravel samples nor the longitudinal change of these metrics during travel were predictive for ESBL-E acquisition. A zero-inflated two-step beta-regression model was used to determine how the longitudinal change in both prevalence and abundance of each taxon was related to ESBL acquisition. There were detected increases in both the prevalence and abundance of Citrobacter freundii and two members of the genus Bacteroides, in association with remaining uncolonized by ESBL-E. These results highlight the potential of these individual microbes as a microbial consortium to prevent the acquisition of ESBL-E. The ability to alter a person's colonization resistance to a bacterium could be key to intervention strategies that aim to minimize the spread of MDR bacteria.}, }
@article {pmid35381769, year = {2022}, author = {Bamola, VD and Kapardar, R and Lal, B and Sharma, A and Chaudhry, R}, title = {A metagenomic assessment of gut microbiota in Indian colon cancer patients.}, journal = {Journal of cancer research and therapeutics}, volume = {18}, number = {1}, pages = {96-102}, doi = {10.4103/0973-1482.341139}, pmid = {35381769}, issn = {1998-4138}, mesh = {*Colonic Neoplasms ; Dysbiosis ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background: Gut microbiota plays an important role in the development of different diseases including colorectal cancer. The geography, lifestyle, and dietary habits of Indians are different from Western world, thus microbiome studies of Western population could not be extrapolated to their Indian counterparts.<br><br>Method: Therefore, we have conducted a study on gut microbiota in Indian healthy subjects and patients of colon cancer using 16S ribosomal RNA Amplicon sequencing. Operational taxonomic units were calculated for different bacterial taxon including phylum, class, order, family, and genus level.<br><br>Results: Observed results indicated a considerable difference in the bacterial diversity in both the groups. Phylum Firmicutes was significantly dominated in both the groups followed by Bacteroidetes, Actinobacteria, and Proteobacteria which clearly indicates the dominance of phylum Firmicutes in Indian population. Phylum Firmicutes and Actinobacteria were significantly abundant in the healthy group while phylum Bacteroidetes in the colon cancer group. Bacterial genera Megamonas, Megasphaera, Mitsuokella, and Streptococcus were significantly abundant in the healthy group and Veillonella, Prevotella, and Eubacterium in the colon cancer group. Bacterial genus Bradyrhizobium was present in the healthy group and Alistipes, Coprococcus, Dorea, and Rhodococcus were present in the colon cancer group but absent in the healthy group.<br><br>Conclusion: There was a considerable difference in bacterial diversity in both the study groups indicating dysbiosis in the colon cancer group.}, }
@article {pmid35377222, year = {2022}, author = {Tarracchini, C and Fontana, F and Lugli, GA and Mancabelli, L and Alessandri, G and Turroni, F and Ventura, M and Milani, C}, title = {Investigation of the Ecological Link between Recurrent Microbial Human Gut Communities and Physical Activity.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0042022}, pmid = {35377222}, issn = {2165-0497}, mesh = {Bacteria/genetics ; Butyrates ; Exercise ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Emerging evidence has shown an association between the composition of intestinal microbial communities and host physical activity, suggesting that modifications of the gut microbiota composition may support training, performance, and post-exercise recovery of the host. Nevertheless, investigation of differences in the gut microbiota between athletes and individuals with reduced physical activity is still lacking. In this study, we performed a meta-analysis of 207 publicly available shotgun metagenomics sequencing data of fecal samples from athletes and healthy non-athletes. Accordingly, analysis of species-level fecal microbial profiles revealed three recurring compositional patterns, named HPC1 to 3, that characterize the host based on their commitment to physical activity. Interestingly, the gut microbiome of athletes showed a higher abundance of anti-inflammatory, health-promoting bacteria than that of non-athletic individuals. Moreover, the bacterial species profiled in the gut of professional athletes are short-fatty acid producers, which potentially improve energy production, and therefore sports performances. Intriguingly, microbial interaction network analyses suggested that exercise-induced microbiota adaptation involves the whole microbial community structure, resulting in a complex microbe-microbe interplay driven by positive relationships among the predicted butyrate-producing community members. IMPORTANCE Through metagenomic analyses, this work revealed that athletes have a gut-associated microbial community enriched in butyrate-producing species compared with non-athletes. This evidence can support the existence of a two-way association between the host's lifestyle and the gut microbiota composition, with potential intriguing athletic performance outcomes.}, }
@article {pmid35372129, year = {2022}, author = {Greenbaum, J and Lin, X and Su, KJ and Gong, R and Shen, H and Shen, J and Xiao, HM and Deng, HW}, title = {Integration of the Human Gut Microbiome and Serum Metabolome Reveals Novel Biological Factors Involved in the Regulation of Bone Mineral Density.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {853499}, pmid = {35372129}, issn = {2235-2988}, mesh = {Biological Factors ; Bone Density ; Female ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; *Microbiota ; }, abstract = {While the gut microbiome has been reported to play a role in bone metabolism, the individual species and underlying functional mechanisms have not yet been characterized. We conducted a systematic multi-omics analysis using paired metagenomic and untargeted serum metabolomic profiles from a large sample of 499 peri- and early post-menopausal women to identify the potential crosstalk between these biological factors which may be involved in the regulation of bone mineral density (BMD). Single omics association analyses identified 22 bacteria species and 17 serum metabolites for putative association with BMD. Among the identified bacteria, Bacteroidetes and Fusobacteria were negatively associated, while Firmicutes were positively associated. Several of the identified serum metabolites including 3-phenylpropanoic acid, mainly derived from dietary polyphenols, and glycolithocholic acid, a secondary bile acid, are metabolic byproducts of the microbiota. We further conducted a supervised integrative feature selection with respect to BMD and constructed the inter-omics partial correlation network. Although still requiring replication and validation in future studies, the findings from this exploratory analysis provide novel insights into the interrelationships between the gut microbiome and serum metabolome that may potentially play a role in skeletal remodeling processes.}, }
@article {pmid35372117, year = {2022}, author = {Xiong, Z and Peng, K and Song, S and Zhu, Y and Gu, J and Huang, C and Li, X}, title = {Cerebral Intraparenchymal Hemorrhage Changes Patients' Gut Bacteria Composition and Function.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {829491}, pmid = {35372117}, issn = {2235-2988}, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Hemorrhage/genetics ; Humans ; Metagenome ; Metagenomics ; }, abstract = {Gut bacteria consists of 150 times more genes than humans that are vital for health. Several studies revealed that gut bacteria are associated with disease status and influence human behavior and mentality. Whether human brain injury alters the gut bacteria is yet unclear, we tested 20 fecal samples from patients with cerebral intraparenchymal hemorrhage and corresponding healthy controls through metagenomic shotgun sequencing. The composition of patients' gut bacteria changed significantly at the phylum level; Verrucomicrobiota was the specific phylum colonized in the patients' gut. The functional alteration was observed in the patients' gut bacteria, including high metabolic activity for nutrients or neuroactive compounds, strong antibiotic resistance, and less virulence factor diversity. The changes in the transcription and metabolism of differential species were more evident than those of the non-differential species between groups, which is the primary factor contributing to the functional alteration of patients with cerebral intraparenchymal hemorrhage.}, }
@article {pmid35366955, year = {2022}, author = {Li, PD and Zhu, ZR and Zhang, Y and Xu, J and Wang, H and Wang, Z and Li, H}, title = {The phyllosphere microbiome shifts toward combating melanose pathogen.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {56}, pmid = {35366955}, issn = {2049-2618}, support = {CARS-26//Earmarked Fund for China Agriculture Research System/ ; 2019C02022//Provincial Key R&amp;D Program of Zhejiang/ ; 2017YFD0202000//National Key R&amp;D Program of China/ ; }, mesh = {Bacteria/genetics ; *Melanosis ; *Microbiota ; Plant Leaves/microbiology ; Rhizosphere ; }, abstract = {BACKGROUND: Plants can recruit beneficial microbes to enhance their ability to defend against pathogens. However, in contrast to the intensively studied roles of the rhizosphere microbiome in suppressing plant pathogens, the collective community-level change and effect of the phyllosphere microbiome in response to pathogen invasion remains largely elusive.<br><br>RESULTS: Here, we integrated 16S metabarcoding, shotgun metagenomics and culture-dependent methods to systematically investigate the changes in phyllosphere microbiome between infected and uninfected citrus leaves by Diaporthe citri, a fungal pathogen causing melanose disease worldwide. Multiple microbiome features suggested a shift in phyllosphere microbiome upon D. citri infection, highlighted by the marked reduction of community evenness, the emergence of large numbers of new microbes, and the intense microbial network. We also identified the microbiome features from functional perspectives in infected leaves, such as enriched microbial functions for iron competition and potential antifungal traits, and enriched microbes with beneficial genomic characteristics. Glasshouse experiments demonstrated that several bacteria associated with the microbiome shift could positively affect plant performance under D. citri challenge, with reductions in disease index ranging from 65.7 to 88.4%. Among them, Pantoea asv90 and Methylobacterium asv41 identified as "recruited new microbes" in the infected leaves, exhibited antagonistic activities to D. citri both in vitro and in vivo, including inhibition of spore germination and/or mycelium growth. Sphingomonas spp. presented beneficial genomic characteristics and were found to be the main contributor for the functional enrichment of iron complex outer membrane receptor protein in the infected leaves. Moreover, Sphingomonas asv20 showed a stronger suppression ability against D. citri in iron-deficient conditions than iron-sufficient conditions, suggesting a role of iron competition during their antagonistic action.<br><br>CONCLUSIONS: Overall, our study revealed how phyllosphere microbiomes differed between infected and uninfected citrus leaves by melanose pathogen, and identified potential mechanisms for how the observed microbiome shift might have helped plants cope with pathogen pressure. Our findings provide novel insights into understanding the roles of phyllosphere microbiome responses during pathogen challenge. Video abstract.}, }
@article {pmid35365192, year = {2022}, author = {Papaiakovou, M and Littlewood, DTJ and Doyle, SR and Gasser, RB and Cantacessi, C}, title = {Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics.}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {118}, pmid = {35365192}, issn = {1756-3305}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract ; Metabolomics ; Metagenomics ; *Microbiota ; }, abstract = {Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance.}, }
@article {pmid35362813, year = {2022}, author = {Sharma, P and Singh, SP}, title = {Identification and profiling of microbial community from industrial sludge.}, journal = {Archives of microbiology}, volume = {204}, number = {4}, pages = {234}, pmid = {35362813}, issn = {1432-072X}, mesh = {Metagenome ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; }, abstract = {The purpose of this study is to identify microbial communities in pulp and paper industry sludge and their metagenomic profiling on the basis of; phylum, class, order, family, genus and species level. Results revealed that the dominant phyla in 16S rRNA Illumina Miseq analysis inside sludge were Anaerolinea, Pseudomonas, Clostridia, Bacteriodia, Gammaproteobacteria, Spirochetia, Deltaproteobacteria, Spirochaetaceae, Prolixibacteraceae and some unknown microbial strains are also dominant. Metagenomics is a molecular biology-based technology that uses bioinformatics to evaluate huge gene sequences extracted from environmental samples to assess the composition and function of microbiota. The results of metabarcoding of the V3-V4 16S rRNA regions acquired from paired-end Illumina MiSeq sequencing were used to analyze bacterial communities and structure. The present work demonstrates the potential approach to sludge treatment in the open environment via the naturally adapted microorganism, which could be an essential addition to the disposal site. In summary, these investigations indicate that the indigenous microbial community is an acceptable bioresource for remediation or detoxification following secondary treatment. This research aims at understanding the structure of microbial communities and their diversity (%) in highly contaminated sludge to perform in situ bioremediation.}, }
@article {pmid35362479, year = {2022}, author = {Wensel, CR and Pluznick, JL and Salzberg, SL and Sears, CL}, title = {Next-generation sequencing: insights to advance clinical investigations of the microbiome.}, journal = {The Journal of clinical investigation}, volume = {132}, number = {7}, pages = {}, pmid = {35362479}, issn = {1558-8238}, support = {R01 CA196845/CA/NCI NIH HHS/United States ; R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; R56 DK107726/DK/NIDDK NIH HHS/United States ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, abstract = {Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for the discovery and characterization of unculturable microbes with prediction of their function. Key NGS methods include 16S rRNA gene sequencing, shotgun metagenomic sequencing, and RNA sequencing. The choice of which NGS methodology to pursue for a given purpose is often unclear for clinicians and researchers. In this Review, we describe the fundamentals of NGS, with a focus on 16S rRNA and shotgun metagenomic sequencing. We also discuss pros and cons of each methodology as well as important concepts in data variability, study design, and clinical metadata collection. We further present examples of how NGS studies of the human microbiome have advanced our understanding of human disease pathophysiology across diverse clinical contexts, including the development of diagnostics and therapeutics. Finally, we share insights as to how NGS might further be integrated into and advance microbiome research and clinical care in the coming years.}, }
@article {pmid35361114, year = {2022}, author = {Rudar, J and Porter, TM and Wright, M and Golding, GB and Hajibabaei, M}, title = {LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {110}, pmid = {35361114}, issn = {1471-2105}, support = {RGPIN-2020-05733//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Algorithms ; Biomarkers ; *High-Throughput Nucleotide Sequencing ; Machine Learning ; Support Vector Machine ; }, abstract = {BACKGROUND: Identification of biomarkers, which are measurable characteristics of biological datasets, can be challenging. Although amplicon sequence variants (ASVs) can be considered potential biomarkers, identifying important ASVs in high-throughput sequencing datasets is challenging. Noise, algorithmic failures to account for specific distributional properties, and feature interactions can complicate the discovery of ASV biomarkers. In addition, these issues can impact the replicability of various models and elevate false-discovery rates. Contemporary machine learning approaches can be leveraged to address these issues. Ensembles of decision trees are particularly effective at classifying the types of data commonly generated in high-throughput sequencing (HTS) studies due to their robustness when the number of features in the training data is orders of magnitude larger than the number of samples. In addition, when combined with appropriate model introspection algorithms, machine learning algorithms can also be used to discover and select potential biomarkers. However, the construction of these models could introduce various biases which potentially obfuscate feature discovery.<br><br>RESULTS: We developed a decision tree ensemble, LANDMark, which uses oblique and non-linear cuts at each node. In synthetic and toy tests LANDMark consistently ranked as the best classifier and often outperformed the Random Forest classifier. When trained on the full metabarcoding dataset obtained from Canada's Wood Buffalo National Park, LANDMark was able to create highly predictive models and achieved an overall balanced accuracy score of 0.96 ± 0.06. The use of recursive feature elimination did not impact LANDMark's generalization performance and, when trained on data from the BE amplicon, it was able to outperform the Linear Support Vector Machine, Logistic Regression models, and Stochastic Gradient Descent models (p ≤ 0.05). Finally, LANDMark distinguishes itself due to its ability to learn smoother non-linear decision boundaries.<br><br>CONCLUSIONS: Our work introduces LANDMark, a meta-classifier which blends the characteristics of several machine learning models into a decision tree and ensemble learning framework. To our knowledge, this is the first study to apply this type of ensemble approach to amplicon sequencing data and we have shown that analyzing these datasets using LANDMark can produce highly predictive and consistent models.}, }
@article {pmid35360922, year = {2022}, author = {Kaiser, T and Jahansouz, C and Staley, C}, title = {Network-based approaches for the investigation of microbial community structure and function using metagenomics-based data.}, journal = {Future microbiology}, volume = {17}, number = {}, pages = {621-631}, doi = {10.2217/fmb-2021-0219}, pmid = {35360922}, issn = {1746-0921}, mesh = {Host Microbial Interactions ; *Metagenomics/methods ; *Microbiota ; }, abstract = {Network-based approaches offer a powerful framework to evaluate microbial community organization and function as it relates to a variety of environmental processes. Emerging studies are exploring network theory as a method for data integration that is likely to be critical for the integration of 'omics' data using systems biology approaches. Intricacies of network theory and methodological and computational complexities in network construction, however, impede the use of these tools for translational science. We provide a perspective on the methods of network construction, interpretation and emerging uses for these techniques in understanding host-microbiota interactions.}, }
@article {pmid35355372, year = {2022}, author = {Lugli, GA and Longhi, G and Mancabelli, L and Alessandri, G and Tarracchini, C and Fontana, F and Turroni, F and Milani, C and van Sinderen, D and Ventura, M}, title = {Tap water as a natural vehicle for microorganisms shaping the human gut microbiome.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15988}, pmid = {35355372}, issn = {1462-2920}, support = {GR-2018-12365988//Ministero della Salute/ ; SFI/12/RC/2273a/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273b/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {Fresh potable water is an indispensable drink which humans consume daily in substantial amounts. Nonetheless, very little is known about the composition of the microbial community inhabiting drinking water or its impact on our gut microbiota. In the current study, an exhaustive shotgun metagenomics analysis of the tap water microbiome highlighted the occurrence of a highly genetic biodiversity of the microbial communities residing in fresh water and the existence of a conserved core tap water microbiota largely represented by novel microbial species, representing microbial dark matter. Furthermore, genome reconstruction of this microbial dark matter from water samples unveiled homologous sequences present in the faecal microbiome of humans from various geographical locations. Accordingly, investigation of the faecal microbiota content of a subject that daily consumed tap water for 3 years provides proof for horizontal transmission and colonization of water bacteria in the human gut.}, }
@article {pmid35354069, year = {2022}, author = {Liu, Y and Méric, G and Havulinna, AS and Teo, SM and Åberg, F and Ruuskanen, M and Sanders, J and Zhu, Q and Tripathi, A and Verspoor, K and Cheng, S and Jain, M and Jousilahti, P and Vázquez-Baeza, Y and Loomba, R and Lahti, L and Niiranen, T and Salomaa, V and Knight, R and Inouye, M}, title = {Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting.}, journal = {Cell metabolism}, volume = {34}, number = {5}, pages = {719-730.e4}, doi = {10.1016/j.cmet.2022.03.002}, pmid = {35354069}, issn = {1932-7420}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Liver Diseases ; Metagenomics ; *Microbiota ; Prospective Studies ; Risk Factors ; }, abstract = {The gut microbiome has shown promise as a predictive biomarker for various diseases. However, the potential of gut microbiota for prospective risk prediction of liver disease has not been assessed. Here, we utilized shallow shotgun metagenomic sequencing of a large population-based cohort (N > 7,000) with ∼15 years of follow-up in combination with machine learning to investigate the predictive capacity of gut microbial predictors individually and in conjunction with conventional risk factors for incident liver disease. Separately, conventional and microbial factors showed comparable predictive capacity. However, microbiome augmentation of conventional risk factors using machine learning significantly improved the performance. Similarly, disease-free survival analysis showed significantly improved stratification using microbiome-augmented models. Investigation of predictive microbial signatures revealed previously unknown taxa for liver disease, as well as those previously associated with hepatic function and disease. This study supports the potential clinical validity of gut metagenomic sequencing to complement conventional risk factors for prediction of liver diseases.}, }
@article {pmid35344714, year = {2022}, author = {Li, MX and Li, MY and Lei, JX and Wu, YZ and Li, ZH and Chen, LM and Zhou, CL and Su, JY and Huang, GX and Huang, XQ and Zheng, XB}, title = {Huangqin decoction ameliorates DSS-induced ulcerative colitis: Role of gut microbiota and amino acid metabolism, mTOR pathway and intestinal epithelial barrier.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {100}, number = {}, pages = {154052}, doi = {10.1016/j.phymed.2022.154052}, pmid = {35344714}, issn = {1618-095X}, mesh = {Amino Acids/metabolism ; Animals ; *Colitis/chemically induced/drug therapy/metabolism ; *Colitis, Ulcerative/chemically induced/drug therapy/metabolism ; Colon/pathology ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; *Drugs, Chinese Herbal/therapeutic use ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Scutellaria baicalensis/chemistry ; TOR Serine-Threonine Kinases/metabolism ; }, abstract = {BACKGROUND: The clinical treatment of ulcerative colitis (UC) is limited. A traditional Chinese medicinal formula, Huangqin decoction (HQD), is chronicled in Shang Han Lun and is widely used to ameliorate gastrointestinal disorders, such as UC; however, its mechanism is yet to be clarified.<br><br>PURPOSE: The present study aimed to investigate the effect of HQD on 7-day colitis induced by 3% dextran sulfate sodium (DSS) in mice and further explore the inhibitory effect of metabolites on DSS-damaged FHC cells.<br><br>METHODS: The therapeutic efficacy of HQD was evaluated in a well-established DSS-induced colitis mice model. The clinical symptoms were analyzed, and biological samples were collected for microscopic examination, metabolomics, metagenomics, and the evaluation of the epithelial barrier function. The mechanism of metabolites regulated by HQD was evaluated in the DSS-induced FHC cell damage model. The samples were collected to detect the physiological functions of the cells.<br><br>RESULTS: HQD suppressed the inflammation of DSS-induced colitis in vivo, attenuated DSS-induced clinical manifestations, reversed colon length reduction, and reduced histological injury. After HQD treatment, the DSS-induced gut dysbiosis was modulated, and the gut microbiota achieved a new equilibrium state. In addition, HQD activated the mTOR signaling pathway by upregulating amino acid metabolism. Significant phosphorylation of S6 and 4E-BP1 ameliorated intestinal epithelial barrier dysfunction. Moreover, HQD-regulated metabolites protected the epithelial barrier integrity by inhibiting DSS-induced apoptosis of FHC cells and regulating the proteins affecting apoptosis and cell-cell junction.<br><br>CONCLUSIONS: These findings indicated that the mechanism of HQD was related to regulating the gut microbiota and amino acid metabolism, activating the mTOR signaling pathway, and protecting the intestinal mucosal barrier integrity.}, }
@article {pmid35343768, year = {2022}, author = {Lotankar, M and Mokkala, K and Houttu, N and Koivuniemi, E and Sørensen, N and Nielsen, HB and Munukka, E and Lahti, L and Laitinen, K}, title = {Distinct Diet-Microbiota-Metabolism Interactions in Overweight and Obese Pregnant Women: a Metagenomics Approach.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0089321}, pmid = {35343768}, issn = {2165-0497}, support = {//Academy of Finland (AKA)/ ; //Diabetestutkimussäätiö (The Diabetes Research Foundation)/ ; //Juho Vainion Säätiö (Reppy Institute)/ ; //Janssen Research and Development, LLC/ ; //The Biocodex foundation/ ; //Academy of Finland (AKA)/ ; //Sydäntutkimussäätiö (Finnish Foundation for Cardiovascular Research)/ ; }, mesh = {Cross-Sectional Studies ; Diet ; Feces ; Female ; Humans ; Inflammation/metabolism ; Metagenomics ; *Microbiota ; Obesity ; *Overweight/complications/metabolism ; Pregnancy ; Pregnant Women ; }, abstract = {Diet and gut microbiota are known to modulate metabolic health. Our aim was to apply a metagenomics approach to investigate whether the diet-gut microbiota-metabolism and inflammation relationships differ in pregnant overweight and obese women. This cross-sectional study was conducted in overweight (n = 234) and obese (n = 152) women during early pregnancy. Dietary quality was measured by a validated index of diet quality (IDQ). Gut microbiota taxonomic composition and species diversity were assessed by metagenomic profiling (Illumina HiSeq platform). Markers for glucose metabolism (glucose, insulin) and low-grade inflammation (high sensitivity C-reactive protein [hsCRP], glycoprotein acetylation [GlycA]) were analyzed from blood samples. Higher IDQ scores were positively associated with a higher gut microbiota species diversity (r = 0.273, P = 0.007) in obese women, but not in overweight women. Community composition (beta diversity) was associated with the GlycA level in the overweight women (P = 0.04) but not in the obese. Further analysis at the species level revealed a positive association between the abundance of species Alistipes finegoldii and the GlycA level in overweight women (logfold change = 4.74, P = 0.04). This study has been registered at ClinicalTrials.gov under registration no. NCT01922791 (https://clinicaltrials.gov/ct2/show/NCT01922791). IMPORTANCE We observed partially distinct diet-gut microbiota-metabolism and inflammation responses in overweight and obese pregnant women. In overweight women, gut microbiota community composition and the relative abundance of A. finegoldii were associated with an inflammatory status. In obese women, a higher dietary quality was related to a higher gut microbiota diversity and a healthy inflammatory status.}, }
@article {pmid35337386, year = {2022}, author = {Podlesny, D and Arze, C and Dörner, E and Verma, S and Dutta, S and Walter, J and Fricke, WF}, title = {Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {53}, pmid = {35337386}, issn = {2049-2618}, mesh = {Adult ; *Clostridium Infections/therapy ; Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; Treatment Outcome ; }, abstract = {BACKGROUND: The understanding of how microbiomes assemble, function, and evolve requires metagenomic tools that can resolve microbiota compositions at the strain level. However, the identification and tracking of microbial strains in fecal metagenomes is challenging and available tools variably classify subspecies lineages, which affects their applicability to infer microbial persistence and transfer.<br><br>RESULTS: We introduce SameStr, a bioinformatic tool that identifies shared strains in metagenomes by determining single-nucleotide variants (SNV) in species-specific marker genes, which are compared based on a maximum variant profile similarity. We validated SameStr on mock strain populations, available human fecal metagenomes from healthy individuals and newly generated data from recurrent Clostridioides difficile infection (rCDI) patients treated with fecal microbiota transplantation (FMT). SameStr demonstrated enhanced sensitivity to detect shared dominant and subdominant strains in related samples (where strain persistence or transfer would be expected) when compared to other tools, while being robust against false-positive shared strain calls between unrelated samples (where neither strain persistence nor transfer would be expected). We applied SameStr to identify strains that are stably maintained in fecal microbiomes of healthy adults over time (strain persistence) and that successfully engraft in rCDI patients after FMT (strain engraftment). Taxonomy-dependent strain persistence and engraftment frequencies were positively correlated, indicating that a specific core microbiota of intestinal species is adapted to be competitive both in healthy microbiomes and during post-FMT microbiome assembly. We explored other use cases for strain-level microbiota profiling, as a metagenomics quality control measure and to identify individuals based on the persisting core gut microbiota.<br><br>CONCLUSION: SameStr provides for a robust identification of shared strains in metagenomic sequence data with sufficient specificity and sensitivity to examine strain persistence, transfer, and engraftment in human fecal microbiomes. Our findings identify a persisting healthy adult core gut microbiota, which should be further studied to shed light on microbiota contributions to chronic diseases. Video abstract.}, }
@article {pmid35332832, year = {2022}, author = {Crits-Christoph, A and Hallowell, HA and Koutouvalis, K and Suez, J}, title = {Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2055944}, pmid = {35332832}, issn = {1949-0984}, support = {DP5 OD029603/OD/NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota/genetics ; }, abstract = {A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.}, }
@article {pmid35332724, year = {2022}, author = {Wang, Y and Zhang, J and Ling, ZX and Deng, SL}, title = {[Dynamic Microbial Shifts and Functional Analysis of Saliva Microbial Communities with Caries Children].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {53}, number = {2}, pages = {242-249}, doi = {10.12182/20220360103}, pmid = {35332724}, issn = {1672-173X}, mesh = {Child ; *Dental Caries ; Dental Caries Susceptibility ; Humans ; *Microbiota/genetics ; Saliva ; Sequence Analysis, DNA ; }, abstract = {Objective: To observe the dynamic changes in the salivary microbiota of children with dental caries and those who were caries-free and to analyze the functional differences in the oral microecology of the two groups during the course of sugar metabolism and the synthesis and transport of multiple amino acids.<br><br>Methods: Ten children with dental caries and 10 caries-free children were enrolled. We employed Illumina metagenomics technology to analyze the composition and function of salivary microbiome in children with and without caries. Six months later, PacBio single-molecule long-read sequencing technology was used to analyze the changes over time in the oral microbial communities of the two groups. We studied the patterns of change in the oral microbial communities under diseased or healthy conditions and attempted to offer a comprehensive interpretation of children's oral microbiota in terms of its composition and functions.<br><br>Results: The composition of the oral microbiota of children with or without dental caries changed significantly over time. At the phylum level, changing trends in the salivary microbial communities of children with dental caries were in line with those in caries-free children. In these microbial communities, increased proportions of Firmicutes and decreased proportions of Actinobacteria and Bacteroidetes were found in the two groups. At the genus level, however, the two groups showed significantly different changes of the salivary microbial communities. Upward trends in the abundance of Lactobacillus, Methylobacterium, and Megasphaera were found in the caries group, while the abundance of these genera in the caries-free group showed downward trends. At the species level, L. fermentum, L. gasseri, L. oris, S. downei, and some other species belonging to the genus Lactobacillus showed upward trends in the saliva of children with caries, while they consistently stayed at a relative low level of abundance in caries-free children. The abundance of S. gordonii and S. mutans decreased to a certain extent in children with dental caries, but the abundance of S. gordonii and S. mutans in caries-free children were always at a low level. Species such as S. mutans and C. gracilis were positively correlated to the sum of decayed, missing and filled teeth (dmft), while N. flavescens was negatively correlated to dmft. gltA, icd, and mqo, the key genes related to tricarboxylic acid (TCA) cycle, gudB, a glutamate synthesis-related gene, and argAB/C/J, arginine synthesis-related genes, were significantly increased in caries-free children. In addition, the abundance of the NADH dehydrogenase-related gene nuoB/C/D/E/H/I/J/K/L/M in the electron transport chain increased significantly in caries-free children.<br><br>Conclusion: Dynamic changes were found in the oral microbiota of children with or without caries. The trends of microbial shifts over time were associated with the oral health status. Oxidative phosphorylation and the synthesis and transport of amino acids such as glutamate and arginine in the oral microecology were more active in caries-free children.}, }
@article {pmid35327556, year = {2022}, author = {Sanchez-Cid, C and Tignat-Perrier, R and Franqueville, L and Delaurière, L and Schagat, T and Vogel, TM}, title = {Sequencing Depth Has a Stronger Effect than DNA Extraction on Soil Bacterial Richness Discovery.}, journal = {Biomolecules}, volume = {12}, number = {3}, pages = {}, pmid = {35327556}, issn = {2218-273X}, mesh = {Bacteria/genetics ; DNA ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Soil ; }, abstract = {Although Next-Generation Sequencing techniques have increased our access to the soil microbiome, each step of soil metagenomics presents inherent biases that prevent the accurate definition of the soil microbiome and its ecosystem function. In this study, we compared the effects of DNA extraction and sequencing depth on bacterial richness discovery from two soil samples. Four DNA extraction methods were used, and sequencing duplicates were generated for each DNA sample. The V3-V4 region of the 16S rRNA gene was sequenced to determine the taxonomical richness measured by each method at the amplicon sequence variant (ASV) level. Both the overall functional richness and antibiotic resistance gene (ARG) richness were evaluated by metagenomics sequencing. Despite variable DNA extraction methods, sequencing depth had a greater influence on bacterial richness discovery at both the taxonomical and functional levels. Sequencing duplicates from the same sample provided access to different portions of bacterial richness, and this was related to differences in the sequencing depth. Thus, the sequencing depth introduced biases in the comparison of DNA extraction methods. An optimisation of the soil metagenomics workflow is needed in order to sequence at a sufficient and equal depth. This would improve the accuracy of metagenomic comparisons and soil microbiome profiles.}, }
@article {pmid35325312, year = {2022}, author = {Borjigin, Q and Zhang, B and Yu, X and Gao, J and Zhang, X and Qu, J and Ma, D and Hu, S and Han, S}, title = {Metagenomics study to compare the taxonomic composition and metabolism of a lignocellulolytic microbial consortium cultured in different carbon conditions.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {38}, number = {5}, pages = {78}, pmid = {35325312}, issn = {1573-0972}, support = {31760353//National Natural Science Foundation of China/ ; 32060434//National Natural Science Foundation of China/ ; 2020MS03086//Natural Science Foundation of Inner Mongolia/ ; 2018ZD02//Natural Science Foundation of Inner Mongolia/ ; CARS-02-63//Earmarked Fund for China Agriculture Research System/ ; 25204120//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {Bacteria/metabolism ; Carbon/metabolism ; Metagenomics ; *Microbial Consortia/genetics ; *Sphingobacterium ; }, abstract = {A lignocellulolytic microbial consortium holds promise for the in situ biodegradation of crop straw and the comprehensive and effective utilization of agricultural waste. In this study, we applied metagenomics technology to comprehensively explore the metabolic functional potential and taxonomic diversity of the microbial consortia CS (cultured on corn stover) and FP (cultured on filter paper). Analyses of the data on metagenomics taxonomic affiliations revealed considerable differences in the taxonomic composition and carbohydrate-active enzymes profile of the microbial consortia CS and FP. Pseudomonas, Dysgonomonas and Sphingobacterium in CS and Cellvibrio and Pseudomonas in FP had a much wider distribution of lignocellulose degradative ability. The genes for more lignocellulose degradative enzymes were detected when the relatively simple substrate filter paper was used as the carbon source. Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses revealed considerable levels of similarity, and carbohydrate metabolic and amino acid metabolic pathways were the most enriched in CS and FP, respectively. The mechanism used by the two microbial consortia to degrade lignocellulose was similar, but the annotation of quantity of genes indicated that they are diverse and vary greatly. These data underlie the interactions between microorganisms and the synergism of enzymes during the degradative process of lignocellulose under different substrates and suggest the development of potential microbial resources.}, }
@article {pmid35324742, year = {2022}, author = {Kim, H and Park, YH and Yang, JE and Kim, HS and Kim, SC and Oh, EJ and Moon, J and Cho, W and Shin, W and Yu, C}, title = {Analysis of Major Bacteria and Diversity of Surface Soil to Discover Biomarkers Related to Soil Health.}, journal = {Toxics}, volume = {10}, number = {3}, pages = {}, pmid = {35324742}, issn = {2305-6304}, support = {2019R1I1A2A01057002//National Research Foundation of Korea (NRF)/ ; 2019R1A61A03033167//National Research Foundation of Korea (NRF)/ ; 2020002480005//Korean Ministry of Environment as" Development of soil Health Assessment System for Con-taminated and Remediated Soil' project/ ; 2019002820004//Korea Ministry of Environment through the strategic EcoSSSoil Project, KEITI (Korea Environ-mental Industry and Technology Institute)/ ; }, abstract = {The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-generation sequencing (NGS)-based molecular-biological methods have revealed information on soil biodiversity; however, whether this biodiversity is related to soil health remains unclear. In this study, we performed NGS on grassland surface soil to compare the prokaryotic and eukaryotic genetic diversity to determine the chemical soil quality and examined markers associated with soil health. Microorganisms associated with the nitrogen cycle, bioremediation, plant pathogenicity, antibiotic production, and material degradation showed potential for use as markers. To propose a framework for soil health assessment, we not only used traditional indicators, such as chemical and physical measures, but also assessed metagenomics data of soil by land use to identify the major factors influencing the microbial structure in soil. Moreover, major keystone species were identified. Furthermore, the microbial genetic diversity of generally healthy surface soil, such as forests, farmland, and parks, was determined. These findings provide basic data for exploring soil health-related biomarkers.}, }
@article {pmid35323827, year = {2022}, author = {Boeckman, JX and Sprayberry, S and Korn, AM and Suchodolski, JS and Paulk, C and Genovese, K and Rech, RR and Giaretta, PR and Blick, AK and Callaway, T and Gill, JJ}, title = {Effect of chronic and acute enterotoxigenic E. coli challenge on growth performance, intestinal inflammation, microbiome, and metabolome of weaned piglets.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5024}, pmid = {35323827}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Diarrhea/prevention &amp; control/veterinary ; *Enterotoxigenic Escherichia coli ; *Escherichia coli Infections/prevention &amp; control ; Inflammation ; Leukocyte L1 Antigen Complex ; Metabolome ; *Microbiota ; Swine ; *Swine Diseases/prevention &amp; control ; Weaning ; }, abstract = {Post-weaning enteropathies in swine caused by pathogenic E. coli, such as post-weaning diarrhea (PWD) or edema disease (ED), remain a significant problem for the swine industry. Reduction in the use of antibiotics over concerns of antibiotic resistance and public health concerns, necessitate the evaluation of effective antibiotic alternatives to prevent significant loss of livestock and/or reductions in swine growth performance. For this purpose, an appropriate piglet model of pathogenic E. coli enteropathy is required. In this study, we attempted to induce clinical signs of post-weaning disease in a piglet model using a one-time acute or lower daily chronic dose of a pathogenic E. coli strain containing genes for both heat stable and labile toxins, as well as Shiga toxin. The induced disease state was monitored by determining fecal shedding and colonization of the challenge strain, animal growth performance, cytokine levels, fecal calprotectin, histology, fecal metabolomics, and fecal microbiome shifts. The most informative analyses were colonization and shedding of the pathogen, serum cytokines, metabolomics, and targeted metagenomics to determine dysbiosis. Histopathological changes of the gastrointestinal (GI) tract and tight junction leakage as measured by fecal calprotectin concentrations were not observed. Chronic dosing was similar to the acute regimen suggesting that a high dose of pathogen, as used in many studies, may not be necessary. The piglet disease model presented here can be used to evaluate alternative PWD treatment options.}, }
@article {pmid35320603, year = {2022}, author = {Kohler, TJ and Fodelianakis, S and Michoud, G and Ezzat, L and Bourquin, M and Peter, H and Busi, SB and Pramateftaki, P and Deluigi, N and Styllas, M and Tolosano, M and de Staercke, V and Schön, M and Brandani, J and Marasco, R and Daffonchio, D and Wilmes, P and Battin, TJ}, title = {Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.}, journal = {Global change biology}, volume = {28}, number = {12}, pages = {3846-3859}, doi = {10.1111/gcb.16169}, pmid = {35320603}, issn = {1365-2486}, support = {CRSII5_180241//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; PRIDE17/11823097//Luxembourg National Research Fund/ ; //The NOMIS Foundation/ ; }, mesh = {Bacteria/genetics ; Climate Change ; Ecosystem ; *Ice Cover/microbiology ; *Microbiota ; Phylogeny ; Water ; }, abstract = {The shrinking of glaciers is among the most iconic consequences of climate change. Despite this, the downstream consequences for ecosystem processes and related microbiome structure and function remain poorly understood. Here, using a space-for-time substitution approach across 101 glacier-fed streams (GFSs) from six major regions worldwide, we investigated how glacier shrinkage is likely to impact the organic matter (OM) decomposition rates of benthic biofilms. To do this, we measured the activities of five common extracellular enzymes and estimated decomposition rates by using enzyme allocation equations based on stoichiometry. We found decomposition rates to average 0.0129 (% d-1), and that decreases in glacier influence (estimated by percent glacier catchment coverage, turbidity, and a glacier index) accelerates decomposition rates. To explore mechanisms behind these relationships, we further compared decomposition rates with biofilm and stream water characteristics. We found that chlorophyll-a, temperature, and stream water N:P together explained 61% of the variability in decomposition. Algal biomass, which is also increasing with glacier shrinkage, showed a particularly strong relationship with decomposition, likely indicating their importance in contributing labile organic compounds to these carbon-poor habitats. We also found high relative abundances of chytrid fungi in GFS sediments, which putatively parasitize these algae, promoting decomposition through a fungal shunt. Exploring the biofilm microbiome, we then sought to identify bacterial phylogenetic clades significantly associated with decomposition, and found numerous positively (e.g., Saprospiraceae) and negatively (e.g., Nitrospira) related clades. Lastly, using metagenomics, we found evidence of different bacterial classes possessing different proportions of EEA-encoding genes, potentially informing some of the microbial associations with decomposition rates. Our results, therefore, present new mechanistic insights into OM decomposition in GFSs by demonstrating that an algal-based "green food web" is likely to increase in importance in the future and will promote important biogeochemical shifts in these streams as glaciers vanish.}, }
@article {pmid35320047, year = {2022}, author = {Beller, L and Deboutte, W and Vieira-Silva, S and Falony, G and Tito, RY and Rymenans, L and Yinda, CK and Vanmechelen, B and Van Espen, L and Jansen, D and Shi, C and Zeller, M and Maes, P and Faust, K and Van Ranst, M and Raes, J and Matthijnssens, J}, title = {The virota and its transkingdom interactions in the healthy infant gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {13}, pages = {e2114619119}, pmid = {35320047}, issn = {1091-6490}, mesh = {Bacteria ; *Bacteriophages ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Microbiota ; *Viruses ; }, abstract = {SignificanceMicrobes colonizing the infant gut during the first year(s) of life play an important role in immune system development. We show that after birth the (nearly) sterile gut is rapidly colonized by bacteria and their viruses (phages), which often show a strong cooccurrence. Most viruses infecting the infant do not cause clinical signs and their numbers strongly increase after day-care entrance. The infant diet is clearly reflected by identification of plant-infecting viruses, whereas fungi and parasites are not part of a stable gut microbiota. These temporal high-resolution baseline data about the gut colonization process will be valuable for further investigations of pathogenic viruses, dynamics between phages and their bacterial host, as well as studies investigating infants with a disturbed microbiota.}, }
@article {pmid35319433, year = {2022}, author = {Gardner, CM and Gerhard, WA and Redfern, LK and Gunsch, CK}, title = {Evaluation of developing maize microbiomes and associations among nitrogen cyclers and key fungal taxa.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {3}, pages = {}, doi = {10.1099/mic.0.001155}, pmid = {35319433}, issn = {1465-2080}, mesh = {Humans ; *Microbiota/genetics ; *Mycorrhizae ; Nitrogen ; Soil Microbiology ; Zea mays ; }, abstract = {More sustainable approaches to agriculture are urgently needed to protect existing resources and optimize crop yields and to provide food for a growing global human population. More sustainable agricultural practices that utilize plant-microbe relationships across cultivation are urgently needed. The main objectives of this study were to track the prokaryotic and fungal microbiomes associated with key growth stages of developing maize to evaluate the relationships among nitrogen cycling bacteria and major fungal genera including those known to contain arbuscular mycorrhizal fungi and other important taxa. Prokaryotic and fungal microbiomes associated with bulk soils, rhizosphere soils and tissues of developing maize were characterized using Illumina MiSeq sequencing. Similarities in microbiome diversity and abundance were compared to sample metadata to explore the influence of external factors on microbiome development. Correlations among target fungal taxa, bulk bacteria and nitrogen cycling bacteria were determined using non-parametric Spearman correlations. Important maize-associated fungal taxa were detected in all samples across growth stages, with Fusarium, Penicillium and Aspergillus fungi comprising up to 4.21, 4.26 and 0.28% of all fungal genera, respectively. Thirteen statistically significant correlations between nitrogen cycling genera and targeted fungal genera were also identified (r S≥0.70 or r S≤-0.70; P<0.05). This study is the first to note a strong positive association among several nitrifying bacteria and Fusarium (R=0.71; P=0.0046), Aspergillus (R=0.71; P=0.0055) and Cladosporium spcies (R=0.74; P=0.0038), suggesting the levels of soil nitrate, nitrite or nitrification intermediates may have large roles in the proliferation of important maize-associated fungi.}, }
@article {pmid35318388, year = {2022}, author = {Skipper, PJA and Skipper, LK and Dixon, RA}, title = {A metagenomic analysis of the bacterial microbiome of limestone, and the role of associated biofilms in the biodeterioration of heritage stone surfaces.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4877}, pmid = {35318388}, issn = {2045-2322}, mesh = {Bacteria/genetics ; Biofilms ; Calcium Carbonate ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {There is growing concern surrounding the aesthetic and physical effects of microbial biofilms on heritage buildings and monuments. Carboniferous stones, such as limestone and marble, are soluble in weak acid solutions and therefore particularly vulnerable to biocorrosion. This paper aims to determine the differences and commonalities between the microbiome of physically damaged and undamaged Lincolnshire limestone, an area of research which has not been previously studied. A lack of information about the core microbiome has resulted in conflicting claims in the literature regarding the biodeteriorative potential of many microorganisms. To address this, we used metagenomics alongside traditional microbiological techniques to produce an in-depth analysis of differences between the bacterial microbiomes found on deteriorated and undamaged external limestone surfaces. We demonstrate there is a core microbiome on Lincolnshire limestone present on both damaged and undamaged surfaces. In addition to the core microbiome, significant differences were found between species isolated from undamaged compared to damaged surfaces. Isolated species were characterised for biofilm formation and biodeteriorative processes, resulting in the association of species with biodeterioration that had not been previously described. Additionally, we have identified a previously undescribed method of biofilm-associated biomechanical damage. This research adds significant new understanding to the field, aiding decision making in conservation of stone surfaces.}, }
@article {pmid35317857, year = {2022}, author = {Murakami, T and Takeuchi, N and Mori, H and Hirose, Y and Edwards, A and Irvine-Fynn, T and Li, Z and Ishii, S and Segawa, T}, title = {Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {50}, pmid = {35317857}, issn = {2049-2618}, mesh = {*Cyanobacteria/genetics ; Ecosystem ; *Ice Cover/microbiology ; Metagenomics ; Nitrogen/metabolism ; Phycoerythrin/metabolism ; }, abstract = {BACKGROUND: Cryoconite granules are mineral-microbial aggregates found on glacier surfaces worldwide and are hotspots of biogeochemical reactions in glacier ecosystems. However, despite their importance within glacier ecosystems, the geographical diversity of taxonomic assemblages and metabolic potential of cryoconite communities around the globe remain unclear. In particular, the genomic content of cryoconite communities on Asia's high mountain glaciers, which represent a substantial portion of Earth's ice masses, has rarely been reported. Therefore, in this study, to elucidate the taxonomic and ecological diversities of cryoconite bacterial consortia on a global scale, we conducted shotgun metagenomic sequencing of cryoconite acquired from a range of geographical areas comprising Polar (Arctic and Antarctic) and Asian alpine regions.<br><br>RESULTS: Our metagenomic data indicate that compositions of both bacterial taxa and functional genes are particularly distinctive for Asian cryoconite. Read abundance of the genes responsible for denitrification was significantly more abundant in Asian cryoconite than the Polar cryoconite, implying that denitrification is more enhanced in Asian glaciers. The taxonomic composition of Cyanobacteria, the key primary producers in cryoconite communities, also differs between the Polar and Asian samples. Analyses on the metagenome-assembled genomes and fluorescence emission spectra reveal that Asian cryoconite is dominated by multiple cyanobacterial lineages possessing phycoerythrin, a green light-harvesting component for photosynthesis. In contrast, Polar cryoconite is dominated by a single cyanobacterial species Phormidesmis priestleyi that does not possess phycoerythrin. These findings suggest that the assemblage of cryoconite bacterial communities respond to regional- or glacier-specific physicochemical conditions, such as the availability of nutrients (e.g., nitrate and dissolved organic carbon) and light (i.e., incident shortwave radiation).<br><br>CONCLUSIONS: Our genome-resolved metagenomics provides the first characterization of the taxonomic and metabolic diversities of cryoconite from contrasting geographical areas, highlighted by the distinct light-harvesting approaches of Cyanobacteria and nitrogen utilization between Polar and Asian cryoconite, and implies the existence of environmental controls on the assemblage of cryoconite communities. These findings deepen our understanding of the biodiversity and biogeochemical cycles of glacier ecosystems, which are susceptible to ongoing climate change and glacier decline, on a global scale. Video abstract.}, }
@article {pmid35316680, year = {2022}, author = {He, C and Liu, J and Wang, R and Li, Y and Zheng, Q and Jiao, F and He, C and Shi, Q and Xu, Y and Zhang, R and Thomas, H and Batt, J and Hill, P and Lewis, M and Maclntyre, H and Lu, L and Zhang, Q and Tu, Q and Shi, T and Chen, F and Jiao, N}, title = {Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment.}, journal = {Water research}, volume = {216}, number = {}, pages = {118281}, doi = {10.1016/j.watres.2022.118281}, pmid = {35316680}, issn = {1879-2448}, mesh = {2,5-Dimethoxy-4-Methylamphetamine/metabolism ; Bacteria/genetics/metabolism ; *Diatoms/genetics ; Dissolved Organic Matter ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Phytoplankton/genetics/metabolism ; }, abstract = {Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source. The DOM composition, community structure, and metabolic pathways were characterised using multi-omics approaches. The addition of diatom lysate introduced a mass of labile DOM into the incubation seawater, which led to a low degradation index (IDEG) and refractory molecular lability boundary (RMLB) on days 1 and 18. The molecular compositions of the DOM molecules in the later incubation period (from day 120 to day 220) were more similar in composition to those on day 0, suggesting a rapid turnover of phytoplankton debris by microbial communities. Taxonomically, while Alpha proteobacteria dominated during the entire incubation period, Gamma proteobacteria became more sensitive and abundant than the other bacterial groups on days 1 and 18. Recalcitrant measurements such as IDEG and RMLB were closely related to the DOM molecules, bacterial community, and Kyoto encyclopaedia of Genes and Genomes (KEGG) modules, suggesting close associations between RDOM accumulation and microbial metabolism. KEGG modules that showed strong positive correlation with CRAMs were identified using a microbial ecological network approach. The identified KEGG modules produced the substrates, such as the acetyl-CoA or 3‑hydroxy-3-methylglutaryl-CoA, which could participate in the mevalonate pathway to generate the precursor of CRAM analogues, isopentenyl-PP, suggesting a potential generation pathway of CRAM analogues in bacteria and archaea. This study revealed the potential genetic and molecular processes involved in the microbial origin of CRAM analogues, and thus indicated a vital ecological role of bacteria and archaea in RDOM production. This study also offered new perspectives on the carbon sequestration in the ocean.}, }
@article {pmid35315560, year = {2022}, author = {Adler, A and Poirier, S and Pagni, M and Maillard, J and Holliger, C}, title = {Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter.}, journal = {Environmental microbiology}, volume = {24}, number = {4}, pages = {2136-2156}, doi = {10.1111/1462-2920.15947}, pmid = {35315560}, issn = {1462-2920}, support = {200020_182016//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Bacteria/genetics ; *Betaproteobacteria/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sewage/microbiology ; }, abstract = {Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulibacter, a phosphate-accumulating organism of interest for wastewater treatment, were sequenced with both PacBio and Illumina. Different strategies of genome assembly and binning were investigated, including published protocols and a binning procedure adapted to the binning of long contigs (MuLoBiSC). Multiple criteria were considered to select the best strategy for Ca. Accumulibacter, whose multiple strains in every sample represent a challenging microdiversity. In this case, the best strategy relies on long-read only assembly and a custom binning procedure including MuLoBiSC in metaWRAP. Several high-quality Ca. Accumulibacter MAGs, including a novel species, were obtained independently from different samples. Comparative genomic analysis showed that MAGs retrieved in different samples harbour genomic rearrangements in addition to accumulation of point mutations. The microdiversity of Ca. Accumulibacter, likely driven by mobile genetic elements, causes major difficulties in recovering MAGs, but it is also a hallmark of the panmictic lifestyle of these bacteria.}, }
@article {pmid35311904, year = {2022}, author = {Wang, Y and Guan, LL}, title = {Translational multi-omics microbiome research for strategies to improve cattle production and health.}, journal = {Emerging topics in life sciences}, volume = {6}, number = {2}, pages = {201-213}, doi = {10.1042/ETLS20210257}, pmid = {35311904}, issn = {2397-8554}, mesh = {Animals ; Cattle ; Metagenomics ; Methane ; *Microbiota ; Milk ; *Rumen ; }, abstract = {Cattle microbiome plays a vital role in cattle growth and performance and affects many economically important traits such as feed efficiency, milk/meat yield and quality, methane emission, immunity and health. To date, most cattle microbiome research has focused on metataxonomic and metagenomic characterization to reveal who are there and what they may do, preventing the determination of the active functional dynamics in vivo and their causal relationships with the traits. Therefore, there is an urgent need to combine other advanced omics approaches to improve microbiome analysis to determine their mode of actions and host-microbiome interactions in vivo. This review will critically discuss the current multi-omics microbiome research in beef and dairy cattle, aiming to provide insights on how the information generated can be applied to future strategies to improve production efficiency, health and welfare, and environment-friendliness in cattle production through microbiome manipulations.}, }
@article {pmid35311446, year = {2022}, author = {Ranaivo, H and Thirion, F and Béra-Maillet, C and Guilly, S and Simon, C and Sothier, M and Van Den Berghe, L and Feugier-Favier, N and Lambert-Porcheron, S and Dussous, I and Roger, L and Roume, H and Galleron, N and Pons, N and Le Chatelier, E and Ehrlich, SD and Laville, M and Doré, J and Nazare, JA}, title = {Increasing the diversity of dietary fibers in a daily-consumed bread modifies gut microbiota and metabolic profile in subjects at cardiometabolic risk.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2044722}, pmid = {35311446}, issn = {1949-0984}, mesh = {Bread/analysis ; *Cardiovascular Diseases ; Dietary Fiber/analysis ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; }, abstract = {Some cardiometabolic risk factors such as dyslipidemia and insulin resistance are known to be associated with low gut microbiota richness. A link between gut microbiota richness and the diversity of consumed dietary fibers (DF) has also been reported. We introduced a larger diversity of consumed DF by using a daily consumed bread in subjects at cardiometabolic risk and assessed the impacts on the composition and functions of gut microbiota as well as on cardiometabolic profile. Thirty-nine subjects at cardiometabolic risk were included in a double-blind, randomized, cross-over, twice 8-week study, and consumed daily 150 g of standard bread or enriched with a 7-dietary fiber mixture (5.55 g and 16.05 g of fibers, respectively). Before and after intervention, stool samples were collected for gut microbiota analysis from species determination down to gene-level abundance using shotgun metagenomics, and cardiometabolic profile was assessed. Multi-fiber bread consumption significantly decreased Bacteroides vulgatus, whereas it increased Parabacteroides distasonis, Fusicatenibacter saccharivorans, an unclassified Acutalibacteraceae and an unclassified Eisenbergiella (q < 0.1). The fraction of gut microbiota carrying the gene coding for five families/subfamilies of glycoside hydrolases (CAZymes) were also increased and negatively correlated with peaks and total/incremental area under curve (tAUC/iAUC) of postprandial glycemia and insulinemia. Compared to control bread, multi-fiber bread decreased total cholesterol (-0.42 mM; q < 0.01), LDL cholesterol (-0.36 mM; q < 0.01), insulin (-2.77 mIU/l; q < 0.05), and HOMA (-0.78; q < 0.05). In conclusion, increasing the diversity of DF in a daily consumed product modifies gut microbiota composition and function and could be a relevant nutritional tool to improve cardiometabolic profile.}, }
@article {pmid35310842, year = {2022}, author = {Di Guglielmo, MD and Franke, KR and Robbins, A and Crowgey, EL}, title = {Impact of Early Feeding: Metagenomics Analysis of the Infant Gut Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {816601}, pmid = {35310842}, issn = {2235-2988}, support = {P30 GM114736/GM/NIGMS NIH HHS/United States ; U54 GM104941/GM/NIGMS NIH HHS/United States ; }, mesh = {Breast Feeding ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant Formula ; Metagenomics ; *Microbiota ; }, abstract = {Background: Different feeding regimens in infancy alter the gastrointestinal (gut) microbial environment. The fecal microbiota in turn influences gastrointestinal homeostasis including metabolism, immune function, and extra-/intra-intestinal signaling. Advances in next generation sequencing (NGS) have enhanced our ability to study the gut microbiome of breast-fed (BF) and formula-fed (FF) infants with a data-driven hypothesis approach.<br><br>Methods: Next generation sequencing libraries were constructed from fecal samples of BF (n=24) and FF (n=10) infants and sequenced on an Illumina HiSeq 2500. Taxonomic classification of the NGS data was performed using the Sunbeam/Kraken pipeline and a functional analysis at the gene level was performed using publicly available algorithms, including BLAST, and custom scripts. Differentially represented genera, genes, and NCBI Clusters of Orthologous Genes (COG) were determined between cohorts using count data and R (statistical packages edgeR and DESeq2).<br><br>Results: Thirty-nine genera were found to be differentially represented between the BF and FF cohorts (FDR ≤ 0.01) including Parabacteroides, Enterococcus, Haemophilus, Gardnerella, and Staphylococcus. A Welch t-test of the Shannon diversity index for BF and FF samples approached significance (p=0.061). Bray-Curtis and Jaccard distance analyses demonstrated clustering and overlap in each analysis. Sixty COGs were significantly overrepresented and those most significantly represented in BF vs. FF samples showed dichotomy of categories representing gene functions. Over 1,700 genes were found to be differentially represented (abundance) between the BF and FF cohorts.<br><br>Conclusions: Fecal samples analyzed from BF and FF infants demonstrated differences in microbiota genera. The BF cohort includes greater presence of beneficial genus Bifidobacterium. Several genes were identified as present at different abundances between cohorts indicating differences in functional pathways such as cellular defense mechanisms and carbohydrate metabolism influenced by feeding. Confirmation of gene level NGS data via PCR and electrophoresis analysis revealed distinct differences in gene abundances associated with important biologic pathways.}, }
@article {pmid35309369, year = {2022}, author = {Fan, Y and Gao, Y and Ma, Q and Yang, Z and Zhao, B and He, X and Yang, J and Yan, B and Gao, F and Qian, L and Wang, W and Zhu, F and Ma, X}, title = {Multi-Omics Analysis Reveals Aberrant Gut-Metabolome-Immune Network in Schizophrenia.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {812293}, pmid = {35309369}, issn = {1664-3224}, mesh = {Bacteria ; Cytokines ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; *Schizophrenia ; }, abstract = {Schizophrenia (SCZ) is associated with several immune dysfunctions, including elevated levels of pro-inflammatory cytokines. Microorganisms and their metabolites have been found to regulate the immune system, and that intestinal microbiota is significantly disturbed in schizophrenic patients. To systematically investigate aberrant gut-metabolome-immune network in schizophrenia, we performed an integrative analysis of intestinal microbiota, serum metabolome, and serum inflammatory cytokines in 63 SCZ patients and 57 healthy controls using a multi-omics strategy. Eighteen differentially abundant metabolite clusters were altered in patients displayed higher cytokine levels, with a significant increase in pro-inflammatory metabolites and a significant decrease in anti-inflammatory metabolites (such as oleic acid and linolenic acid). The bacterial co-abundance groups in the gut displayed more numerous and stronger correlations with circulating metabolites than with cytokines. By integrating these data, we identified that certain bacteria might affect inflammatory cytokines by modulating host metabolites, such as amino acids and fatty acids. A random forest model was constructed based on omics data, and seven serum metabolites significantly associated with cytokines and α-diversity of intestinal microbiota were able to accurately distinguish the cases from the controls with an area under the receiver operating characteristic curve of 0.99. Our results indicated aberrant gut-metabolome-immune network in SCZ and gut microbiota may influence immune responses by regulating host metabolic processes. These findings suggest a mechanism by which microbial-derived metabolites regulated inflammatory cytokines and insights into the diagnosis and treatment of mental disorders from the microbial-immune system in the future.}, }
@article {pmid35302439, year = {2022}, author = {Gehrig, JL and Portik, DM and Driscoll, MD and Jackson, E and Chakraborty, S and Gratalo, D and Ashby, M and Valladares, R}, title = {Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data.}, journal = {Microbial genomics}, volume = {8}, number = {3}, pages = {}, doi = {10.1099/mgen.0.000794}, pmid = {35302439}, issn = {2057-5858}, mesh = {Humans ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {A long-standing challenge in human microbiome research is achieving the taxonomic and functional resolution needed to generate testable hypotheses about the gut microbiota's impact on health and disease. With a growing number of live microbial interventions in clinical development, this challenge is renewed by a need to understand the pharmacokinetics and pharmacodynamics of therapeutic candidates. While short-read sequencing of the bacterial 16S rRNA gene has been the standard for microbiota profiling, recent improvements in the fidelity of long-read sequencing underscores the need for a re-evaluation of the value of distinct microbiome-sequencing approaches. We leveraged samples from participants enrolled in a phase 1b clinical trial of a novel live biotherapeutic product to perform a comparative analysis of short-read and long-read amplicon and metagenomic sequencing approaches to assess their utility for generating clinical microbiome data. Across all methods, overall community taxonomic profiles were comparable and relationships between samples were conserved. Comparison of ubiquitous short-read 16S rRNA amplicon profiling to long-read profiling of the 16S-ITS-23S rRNA amplicon showed that only the latter provided strain-level community resolution and insight into novel taxa. All methods identified an active ingredient strain in treated study participants, though detection confidence was higher for long-read methods. Read coverage from both metagenomic methods provided evidence of active-ingredient strain replication in some treated participants. Compared to short-read metagenomics, approximately twice the proportion of long reads were assigned functional annotations. Finally, compositionally similar bacterial metagenome-assembled genomes (MAGs) were recovered from short-read and long-read metagenomic methods, although a greater number and more complete MAGs were recovered from long reads. Despite higher costs, both amplicon and metagenomic long-read approaches yielded added microbiome data value in the form of higher confidence taxonomic and functional resolution and improved recovery of microbial genomes compared to traditional short-read methodologies.}, }
@article {pmid35298370, year = {2022}, author = {Cuscó, A and Pérez, D and Viñes, J and Fàbregas, N and Francino, O}, title = {Novel canine high-quality metagenome-assembled genomes, prophages and host-associated plasmids provided by long-read metagenomics together with Hi-C proximity ligation.}, journal = {Microbial genomics}, volume = {8}, number = {3}, pages = {}, doi = {10.1099/mgen.0.000802}, pmid = {35298370}, issn = {2057-5858}, mesh = {Animals ; Bacteria/genetics ; Dogs ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Plasmids/genetics ; Prophages/genetics ; }, abstract = {The human gut microbiome has been extensively studied, yet the canine gut microbiome is still largely unknown. The availability of high-quality genomes is essential in the fields of veterinary medicine and nutrition to unravel the biological role of key microbial members in the canine gut environment. Our aim was to evaluate nanopore long-read metagenomics and Hi-C (high-throughput chromosome conformation capture) proximity ligation to provide high-quality metagenome-assembled genomes (HQ MAGs) of the canine gut environment. By combining nanopore long-read metagenomics and Hi-C proximity ligation, we retrieved 27 HQ MAGs and 7 medium-quality MAGs of a faecal sample of a healthy dog. Canine MAGs (CanMAGs) improved genome contiguity of representatives from the animal and human MAG catalogues - short-read MAGs from public datasets - for the species they represented: they were more contiguous with complete ribosomal operons and at least 18 canonical tRNAs. Both canine-specific bacterial species and gut generalists inhabit the dog's gastrointestinal environment. Most of them belonged to Firmicutes, followed by Bacteroidota and Proteobacteria. We also assembled one Actinobacteriota and one Fusobacteriota MAG. CanMAGs harboured antimicrobial-resistance genes (ARGs) and prophages and were linked to plasmids. ARGs conferring resistance to tetracycline were most predominant within CanMAGs, followed by lincosamide and macrolide ones. At the functional level, carbohydrate transport and metabolism was the most variable within the CanMAGs, and mobilome function was abundant in some MAGs. Specifically, we assigned the mobilome functions and the associated mobile genetic elements to the bacterial host. The CanMAGs harboured 50 bacteriophages, providing novel bacterial-host information for eight viral clusters, and Hi-C proximity ligation data linked the six potential plasmids to their bacterial host. Long-read metagenomics and Hi-C proximity ligation are likely to become a comprehensive approach to HQ MAG discovery and assignment of extra-chromosomal elements to their bacterial host. This will provide essential information for studying the canine gut microbiome in veterinary medicine and animal nutrition.}, }
@article {pmid35296830, year = {2022}, author = {Walsh, CAJ and Momigliano, P and Boussarie, G and Robbins, WD and Bonnin, L and Fauvelot, C and Kiszka, JJ and Mouillot, D and Vigliola, L and Manel, S}, title = {Genomic insights into the historical and contemporary demographics of the grey reef shark.}, journal = {Heredity}, volume = {128}, number = {4}, pages = {225-235}, pmid = {35296830}, issn = {1365-2540}, mesh = {Animals ; Coral Reefs ; Gene Flow ; Metagenomics ; Population Density ; *Sharks/genetics ; }, abstract = {Analyses of genetic diversity can shed light on both the origins of biodiversity hotspots, as well as the conservation status of species that are impacted by human activities. With these objectives, we assembled a genomic dataset of 14,935 single nucleotide polymorphisms from 513 grey reef sharks (Carcharhinus amblyrhynchos) sampled across 17 locations in the tropical Indo-Pacific. We analysed geographic variation in genetic diversity, estimated ancient and contemporary effective population size (Ne) across sampling locations (using coalescent and linkage disequilibrium methods) and modelled the history of gene flow between the Coral Triangle and the Coral Sea. Genetic diversity decreased with distance away from the Coral Triangle and north-western Australia, implying that C. amblyrhynchos may have originated in this region. Increases in Ne were detected across almost all sampling locations 40,000-90,000 generations ago (approximately 0.6-1.5 mya, given an estimated generation time of 16.4 years), suggesting a range expansion around this time. More recent, secondary increases in Ne were inferred for the Misool and North Great Barrier Reef sampling locations, but joint modelling did not clarify whether these were due to population growth, migration, or both. Despite the greater genetic diversity and ancient Ne observed at sites around Australia and the Coral Triangle, remote reefs around north-western New Caledonia had the highest contemporary Ne, demonstrating the importance of using multiple population size assessment methods. This study provides insight into both the past and present demographics of C. amblyrhynchos and contributes to our understanding of evolution in marine biodiversity hotspots.}, }
@article {pmid35296712, year = {2022}, author = {Schaefer, L and Hernandez, H and Coats, RA and Yu, Z and Pflugfelder, SC and Britton, RA and de Paiva, CS}, title = {Gut-derived butyrate suppresses ocular surface inflammation.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4512}, pmid = {35296712}, issn = {2045-2322}, support = {EY026893/NH/NIH HHS/United States ; F32 EY007001/EY/NEI NIH HHS/United States ; T32 EY007001/EY/NEI NIH HHS/United States ; EY007001/EY/NEI NIH HHS/United States ; R01 EY026893/EY/NEI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Butyrates/metabolism/pharmacology ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Inflammation/drug therapy/metabolism ; Mice ; Monocarboxylic Acid Transporters/metabolism ; Tears/metabolism ; }, abstract = {Dry eye is a common ocular inflammatory disorder characterized by tear film instability and reduced tear production. There is increasing evidence that homeostasis of the ocular surface is impacted by the intestinal microbiome. We are interested in investigating the potential role of microbially produced small molecules in mediating the interaction between the intestinal microbiota and the ocular surface. One such molecule is butyrate, a short-chain fatty acid (SCFA) produced by certain members of the gut microbiota through fermentation of dietary fiber. Here we show that SCFA transporter SLC5A8 is expressed in vivo in murine conjunctival and corneal epithelium. Pre-treatment of in vitro corneal epithelial cultures or bone marrow-derived dendritic cells (BMDCs) with phenylbutyrate (PBA) reduces lipopolysaccharide-induced pro-inflammatory Tnf expression. Corneal epithelial cultures and BMDCs isolated from Slc5a8 knockout mice are unable to respond to PBA pre-treatment, suggesting that SLC5A8 is required for the protective effect of PBA. The treatment of mice undergoing desiccating stress (DS) with oral tributyrin, a prodrug form of butyrate, reduces inflammation at the ocular surface in vivo, and this effect partially requires SLC5A8. Finally, expression analysis on conjunctival tissue isolated from mice subjected to DS with and without tributyrin treatment revealed that treatment downregulated genes involved in Type I interferon signaling. Together these data support our hypothesis that SCFAs produced in the gut participate in the maintenance of ocular surface homeostasis.}, }
@article {pmid35293806, year = {2022}, author = {Wang, L and Cheng, X and Bai, L and Gao, M and Kang, G and Cao, X and Huang, H}, title = {Positive Interventional Effect of Engineered Butyrate-Producing Bacteria on Metabolic Disorders and Intestinal Flora Disruption in Obese Mice.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0114721}, pmid = {35293806}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics/metabolism ; Butyrates/adverse effects/metabolism ; *Gastrointestinal Microbiome/physiology ; Glucose/adverse effects ; *Metabolic Diseases ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Obesity/therapy ; }, abstract = {The substantially increased prevalence of obesity and obesity-related diseases has generated considerable concern. Currently, synthetic biological strategies have played an essential role in preventing and treating chronic diseases such as obesity. A growing number of symbiotic bacteria used as vectors for genetic engineering have been applied to create living therapeutics. In this study, using Bacillus subtilis as a cellular chassis, we constructed the engineered butyrate-producing strain BsS-RS06551 with a butyrate yield of 1.5 g/liter. A mouse model of obesity induced by a high-fat diet (HFD) was established to study the long-term intervention effects of this butyrate-producing bacteria on obesity. Combined with phenotypic assay results, we found that BsS-RS06551 could effectively retard body weight gain induced by a high-fat diet and visceral fat accumulation of mice, whereas it could improve glucose tolerance and insulin tolerance, reducing liver damage. We explored the BsS-RS06551 mechanism of action on host function and changes in intestinal flora by integrating multiple omics profiling, including untargeted metabolomics and metagenomics. The results showed that 24 major differential metabolites were involved in the metabolic regulation of BsS-RS06551 to prevent obesity in mice, including bile acid metabolism, branch chain amino acids, aromatic amino acids, and other metabolic pathways. Continuous ingestion of BsS-RS06551 could regulate gut microbiota composition and structure and enhance intestinal flora metabolic function abundance, which was closely related to host interactions. Our results demonstrated that engineered butyrate-producing bacteria had potential as an effective strategy to prevent obesity. IMPORTANCE Obesity is a chronic metabolic disease with an imbalance between energy intake and energy expenditure, and obesity-related metabolic diseases have become increasingly common. There is an urgent need to develop effective interventions for the prevention and treatment of obesity. This study showed that long-term consumption of BsS-RS06551 had a significant inhibitory effect on obesity induced by a high-fat diet and was more potent in inhibiting obesity than prebiotic inulin. In addition, this study showed a beneficial effect on host glucose, lipid metabolism, and gut microbe composition. Considering its colonization potential, this engineered bacteria provided a new strategy for the effective and convenient treatment of obesity in the long term.}, }
@article {pmid35293551, year = {2022}, author = {Berbert, L and Santos, A and Magro, DO and Guadagnini, D and Assalin, HB and Lourenço, LH and Martinez, CAR and Saad, MJA and Coy, CSR}, title = {Metagenomics analysis reveals universal signatures of the intestinal microbiota in colorectal cancer, regardless of regional differences.}, journal = {Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas}, volume = {55}, number = {}, pages = {e11832}, pmid = {35293551}, issn = {1414-431X}, mesh = {*Colorectal Neoplasms/pathology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut microbiota is a complex and dynamic community of microorganisms living in our intestines and has emerged as an important factor for colorectal adenocarcinoma (CRC). The purpose of our study was to investigate the microbiota composition in Brazilian CRC patients compared with a local control population (CTL) to find out which changes could be considered universal or regional features in CRC microbiota. Fecal samples were obtained from 28 CRC and 23 CTL individuals. The 16S rRNA gene was used for metagenomic analysis. In addition to the anthropometric variables, the clinical stage (TNM 2018) was considered. Patients with CRC had a significant increase in alpha diversity and a higher percentage of genus Prevotella and a decreased proportion of Megamonas and Ruminococcus. Additionally, the proportion of Faecalibacterium prausnitzii was associated with a better prognosis in the first stages of CRC, and Fusobacterium nucleatum proved to be an important marker of colorectal carcinogenesis and tumor aggressiveness. Although regional differences influence the composition of the microbiota, in the case of CRC, the microhabitat created by the tumor seems to be a major factor. Our results contribute to a better understanding of the carcinogenic process, and even in different environments, some factors appear to be characteristic of the microbiota of patients with CRC.}, }
@article {pmid35292384, year = {2022}, author = {Tang, L and Su, C and Fan, C and Li, R and Wang, Y and Gao, S and Chen, M}, title = {Long-term effect of perfluorooctanoic acid on the anammox system based on metagenomics: Performance, sludge characteristic and microbial community dynamic.}, journal = {Bioresource technology}, volume = {351}, number = {}, pages = {127002}, doi = {10.1016/j.biortech.2022.127002}, pmid = {35292384}, issn = {1873-2976}, mesh = {*Ammonium Compounds ; Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bioreactors ; Caprylates ; Denitrification ; Fluorocarbons ; Metagenomics ; *Microbiota ; Nitrogen/metabolism ; Oxidation-Reduction ; Sewage ; }, abstract = {The effects of PFOA on the nitrogen removal performance, microbial community and functional genes of anaerobic ammonium oxidation (anammox) sludge in an anaerobic baffled reactor (ABR) were investigated. The removal efficiencies of ammonia nitrogen (NH4+-N) and nitrite (NO2--N) decreased from 93.90 ± 3.64% and 98.6 ± 1.84% to 77.81 ± 6.86% and 77.96 ± 1.88% when PFOA increased from 5 mg/L to 50 mg/L, respectively. X-ray photoelectron spectra analysis of the anammox sludge showed the presence of both C-F and CaF2 forms of F. Metagenomics analysis of the anammox sludge in the first compartment illustrated that the relative abundance of Ca.Brocadia and Ca.Kuenenia decreased from 22.21% and 5.61% to 2.11% and 2.84% at 50 mg/L PFOA compared with that without PFOA. In addition, the nitrogen metabolism pathway showed that adding 50 mg/L PFOA decreased the expression of HzsB, HzsC, and Hdh (anammox genes) by 0.096%, 0.05% and 0.062%, respectively.}, }
@article {pmid35289669, year = {2022}, author = {Poulsen, CS and Ekstrøm, CT and Aarestrup, FM and Pamp, SJ}, title = {Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0009022}, pmid = {35289669}, issn = {2165-0497}, support = {643476//Horizon2020/ ; NNF16OC0021856//Novo Nordisk Foundation/ ; }, mesh = {Animals ; Bacteria/genetics ; Bias ; DNA ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; Swine ; }, abstract = {Metagenomics is increasingly used to describe microbial communities in biological specimens. Ideally, the steps involved in the processing of the biological specimens should not change the microbiome composition in a way that it could lead to false interpretations of inferred microbial community composition. Common steps in sample preparation include sample collection, storage, DNA isolation, library preparation, and DNA sequencing. Here, we assess the effect of three library preparation kits and two DNA sequencing platforms. Of the library preparation kits, one involved a PCR step (Nextera), and two were PCR free (NEXTflex and KAPA). We sequenced the libraries on Illumina HiSeq and NextSeq platforms. As example microbiomes, two pig fecal samples and two sewage samples of which aliquots were stored at different storage conditions (immediate processing and storage at -80°C) were assessed. All DNA isolations were performed in duplicate, totaling 80 samples, excluding controls. We found that both library preparation and sequencing platform had systematic effects on the inferred microbial community composition. The different sequencing platforms introduced more variation than library preparation and freezing the samples. The results highlight that all sample processing steps need to be considered when comparing studies. Standardization of sample processing is key to generating comparable data within a study, and comparisons of differently generated data, such as in a meta-analysis, should be performed cautiously. IMPORTANCE Previous research has reported effects of sample storage conditions and DNA isolation procedures on metagenomics-based microbiome composition; however, the effect of library preparation and DNA sequencing in metagenomics has not been thoroughly assessed. Here, we provide evidence that library preparation and sequencing platform introduce systematic biases in the metagenomic-based characterization of microbial communities. These findings suggest that library preparation and sequencing are important parameters to keep consistent when aiming to detect small changes in microbiome community structure. Overall, we recommend that all samples in a microbiome study are processed in the same way to limit unwanted variations that could lead to false conclusions. Furthermore, if we are to obtain a more holistic insight from microbiome data generated around the world, we will need to provide more detailed sample metadata, including information about the different sample processing procedures, together with the DNA sequencing data at the public repositories.}, }
@article {pmid35288138, year = {2022}, author = {Shen, J and Luo, Y and Tao, Q and White, PJ and Sun, G and Li, M and Luo, J and He, Y and Li, B and Li, Q and Xu, Q and Cai, Y and Li, H and Wang, C}, title = {The exacerbation of soil acidification correlates with structural and functional succession of the soil microbiome upon agricultural intensification.}, journal = {The Science of the total environment}, volume = {828}, number = {}, pages = {154524}, doi = {10.1016/j.scitotenv.2022.154524}, pmid = {35288138}, issn = {1879-1026}, mesh = {Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Oryza ; Protons ; Soil/chemistry ; Soil Microbiology ; *Streptomyces ; Triticum ; }, abstract = {Agricultural intensification driven by land-use changes has caused continuous and cumulative soil acidification (SA) throughout the global agroecosystem. Microorganisms mediate acid-generating reactions; however, the microbial mechanisms responsible for exacerbating SA feedback remain largely unknown. To determine the microbial community composition and putative function associated with SA, we conducted a metagenomic analysis of soils across a chronosequence that has elapsed since the conversion of rice-wheat (RW) to rice-vegetable (RV) rotations. Compared to RW rotations, soil pH decreased by 0.50 and 1.56 units (p < 0.05) in response to 10-year and 20-year RV rotations, respectively. Additionally, acid saturation ratios were increased by 7.3% and 36.2% (p < 0.05), respectively. The loss of microbial beta-diversity was a key element that contributed to the exacerbation of SA in the RV. Notably, the 20-year RV-enriched microbial taxa were more hydrogen (H+)-, aluminium (Al3+)-, and nitrate nitrogen (NO3--N) -dependent and contained more genera exhibiting dehydrogenation functions than did RW-enriched taxa. "M00115, M00151, M00417, and M00004" and "M00531 and M00135" that are the "proton-pumping" and "proton-consuming" gene modules, respectively, were linked to the massive recruitment of acid-dependent biomarkers in 20-year RV soils, particularly Rhodanobacter, Gemmatirosa, Sphingomonas, and Streptomyces. Collectively, soils in long-term RV rotations were highly acidified and acid-sensitive, as the enrichment of microbial dehydrogenation genes allowing for soil buffering capacity is more vulnerable to H+ loading and consequently promotes the colonization of more acid-tolerant and acidogenic microbes, and ultimately provide new clues for researchers to elucidate the interaction between SA and the soil microbiome.}, }
@article {pmid35286304, year = {2022}, author = {Kalmar, L and Gupta, S and Kean, IRL and Ba, X and Hadjirin, N and Lay, EM and de Vries, SPW and Bateman, M and Bartlet, H and Hernandez-Garcia, J and Tucker, AW and Restif, O and Stevens, MP and Wood, JLN and Maskell, DJ and Grant, AJ and Holmes, MA}, title = {HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.}, journal = {PLoS genetics}, volume = {18}, number = {3}, pages = {e1009776}, pmid = {35286304}, issn = {1553-7404}, support = {MR/N002660/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents ; *Anti-Infective Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Metagenomics ; *Microbiota ; Swine ; }, abstract = {Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.}, }
@article {pmid35281043, year = {2022}, author = {Cheng, M and Liu, H and Han, M and Li, SC and Bu, D and Sun, S and Hu, Z and Yang, P and Wang, R and Liu, Y and Chen, F and Peng, J and Peng, H and Song, H and Xia, Y and Chu, L and Zhou, Q and Guan, F and Wu, J and Tan, G and Ning, K}, title = {Microbiome Resilience and Health Implications for People in Half-Year Travel.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {848994}, pmid = {35281043}, issn = {1664-3224}, mesh = {Carbohydrates ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Travel entail change in geography and diet, both of which are known as determinant factors in shaping the human gut microbiome. Additionally, altered gut microbiome modulates immunity, bringing about health implications in humans. To explore the effects of the mid-term travel on the gut microbiome, we generated 16S rRNA gene and metagenomic sequencing data from longitudinal samples collected over six months. We monitored dynamic trajectories of the gut microbiome variation of a Chinese volunteer team (VT) in their whole journey to Trinidad and Tobago (TAT). We found gut microbiome resilience that VT's gut microbial compositions gradually transformed to the local TAT's enterotypes during their six-month stay in TAT, and then reverted to their original enterotypes after VT's return to Beijing in one month. Moreover, we identified driven species in this bi-directional plasticity that could play a role in immunity modulation, as exemplified by Bacteroides dorei that attenuated atherosclerotic lesion formation and effectively suppressed proinflammatory immune response. Another driven species P. copri could play a crucial role in rheumatoid arthritis pathogenesis, a chronic autoimmune disease. Carbohydrate-active enzymes are often implicated in immune and host-pathogen interactions, of which glycoside hydrolases were found decreased but glycosyltransferases and carbohydrate esterases increased during the travel; these functions were then restored after VT' returning to Beijing. Furthermore, we discovered these microbial changes and restoration were mediated by VT people's dietary changes. These findings indicate that half-year travel leads to change in enterotype and functional patterns, exerting effects on human health. Microbial intervention by dietary guidance in half-year travel would be conducive to immunity modulation for maintaining health.}, }
@article {pmid35279076, year = {2022}, author = {Garber, AI and Armbruster, CR and Lee, SE and Cooper, VS and Bomberger, JM and McAllister, SM}, title = {SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {202}, pmid = {35279076}, issn = {1471-2164}, support = {ARMBRU19F0//Cystic Fibrosis Foundation/ ; T32HL129949/NH/NIH HHS/United States ; R33HL137077/NH/NIH HHS/United States ; R33HL137077/NH/NIH HHS/United States ; R33HL137077/NH/NIH HHS/United States ; U01AI124302/NH/NIH HHS/United States ; R01HL12377/NH/NIH HHS/United States ; CFF BOMBER18G0/NH/NIH HHS/United States ; CFF RDP BOMBER19R0/NH/NIH HHS/United States ; UL1 TR0000005//University of Pittsburgh CTSI Pilot Program/NIH NCATS/ ; UL1 TR0000005//University of Pittsburgh CTSI Pilot Program/NIH NCATS/ ; Investigator Sponsored Research Award//Gilead Sciences/ ; Investigator Sponsored Research Award//Gilead Sciences/ ; Investigator Sponsored Research Award//Gilead Sciences/ ; NA15OAR4320063//Joint Institute for the Study of the Atmosphere and Ocean/ ; }, mesh = {Bacteria/genetics ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Software ; }, abstract = {BACKGROUND: Shotgun sequencing of cultured microbial isolates/individual eukaryotes (whole-genome sequencing) and microbial communities (metagenomics) has become commonplace in biology. Very often, sequenced samples encompass organisms spanning multiple domains of life, necessitating increasingly elaborate software for accurate taxonomic classification of assembled sequences.<br><br>RESULTS: While many software tools for taxonomic classification exist, SprayNPray offers a quick and user-friendly, semi-automated approach, allowing users to separate contigs by taxonomy (and other metrics) of interest. Easy installation, usage, and intuitive output, which is amenable to visual inspection and/or further computational parsing, will reduce barriers for biologists beginning to analyze genomes and metagenomes. This approach can be used for broad-level overviews, preliminary analyses, or as a supplement to other taxonomic classification or binning software. SprayNPray profiles contigs using multiple metrics, including closest homologs from a user-specified reference database, gene density, read coverage, GC content, tetranucleotide frequency, and codon-usage bias.<br><br>CONCLUSIONS: The output from this software is designed to allow users to spot-check metagenome-assembled genomes, identify, and remove contigs from putative contaminants in isolate assemblies, identify bacteria in eukaryotic assemblies (and vice-versa), and identify possible horizontal gene transfer events.}, }
@article {pmid35278679, year = {2022}, author = {Wani, AK and Roy, P and Kumar, V and Mir, TUG}, title = {Metagenomics and artificial intelligence in the context of human health.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {100}, number = {}, pages = {105267}, doi = {10.1016/j.meegid.2022.105267}, pmid = {35278679}, issn = {1567-7257}, mesh = {Artificial Intelligence ; DNA ; Humans ; *Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Human microbiome is ubiquitous, dynamic, and site-specific consortia of microbial communities. The pathogenic nature of microorganisms within human tissues has led to an increase in microbial studies. Characterization of genera, like Streptococcus, Cutibacterium, Staphylococcus, Bifidobacterium, Lactococcus and Lactobacillus through culture-dependent and culture-independent techniques has been reported. However, due to the unique environment within human tissues, it is difficult to culture these microorganisms making their molecular studies strenuous. MGs offer a gateway to explore and characterize hidden microbial communities through a culture-independent mode by direct DNA isolation. By function and sequence-based MGs, Scientists can explore the mechanistic details of numerous microbes and their interaction with the niche. Since the data generated from MGs studies is highly complex and multi-dimensional, it requires accurate analytical tools to evaluate and interpret the data. Artificial intelligence (AI) provides the luxury to automatically learn the data dimensionality and ease its complexity that makes the disease diagnosis and disease response easy, accurate and timely. This review provides insight into the human microbiota and its exploration and expansion through MG studies. The review elucidates the significance of MGs in studying the changing microbiota during disease conditions besides highlighting the role of AI in computational analysis of MG data.}, }
@article {pmid35273319, year = {2022}, author = {Burgess, BT and Irvine, RL and Russello, MA}, title = {Population genomics of Sitka black-tailed deer supports invasive species management and ecological restoration on islands.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {223}, pmid = {35273319}, issn = {2399-3642}, mesh = {Animals ; Biodiversity ; *Deer/genetics ; *Introduced Species ; Islands ; Metagenomics ; }, abstract = {Invasive mammals represent a critical threat to island biodiversity; eradications can result in ecological restoration yet may fail in the absence of key population parameters. Over-browsing by invasive Sitka black-tailed deer (Odocoileus hemionus sitkensis) is causing severe ecological and cultural impacts across the Haida Gwaii archipelago (Canada). Previous eradication attempts demonstrate forest regeneration upon deer removal, but reinvasion reverses conservation gains. Here we use restriction-site associated DNA sequencing (12,947 SNPs) to investigate connectivity and gene flow of invasive deer (n = 181) across 15 islands, revealing little structure throughout Haida Gwaii and identifying the large, central island of Moresby (>2600 km2) as the greatest source of migrants. As a result, the archipelago itself should be considered the primary eradication unit, with the exception of geographically isolated islands like SGang Gwaay. Thus, limiting eradications to isolated islands combined with controlled culling and enhanced biosecurity may be the most effective strategies for achieving ecological restoration goals.}, }
@article {pmid35273169, year = {2022}, author = {Cai, YY and Huang, FQ and Lao, X and Lu, Y and Gao, X and Alolga, RN and Yin, K and Zhou, X and Wang, Y and Liu, B and Shang, J and Qi, LW and Li, J}, title = {Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {11}, pmid = {35273169}, issn = {2055-5008}, mesh = {Animals ; *Atherosclerosis ; Choline ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Methylamines ; Mice ; }, abstract = {Microbial trimethylamine (TMA)-lyase activity promotes the development of atherosclerosis by generating of TMA, the precursor of TMA N-oxide (TMAO). TMAO is well documented, but same can not be said of TMA-producing bacteria. This work aimed to identify TMA-producing genera in human intestinal microbiota. We retrieved the genomes of human-associated microorganisms from the Human Microbiome Project database comprising 1751 genomes, Unified Human Gastrointestinal Genome collection consisting 4644 gut prokaryotes, recapitulated 4930 species-level genome bins and public gut metagenomic data of 2134 individuals from 11 populations. By sequence searching, 216 TMA-lyase-containing species from 102 genera were found to contain the homologous sequences of cntA/B, yeaW/X, and/or cutC/D. We identified 13 strains from 5 genera with cntA sequences, and 30 strains from 14 genera with cutC showing detectable relative abundance in healthy individuals. Lachnoclostridium (p = 2.9e-05) and Clostridium (p = 5.8e-04), the two most abundant cutC-containing genera, were found to be much higher in atherosclerotic patients compared with healthy persons. Upon incubation with choline (substrate), L. saccharolyticum effectively transformed it to TMA at a rate higher than 98.7% while that for C. sporogenes was 63.8-67.5% as detected by liquid chromatography-triple quadrupole mass spectrometry. In vivo studies further showed that treatment of L. saccharolyticum and choline promoted a significant increase in TMAO level in the serum of ApoE-/- mice with obvious accumulation of aortic plaque in same. This study discloses the significance and efficiency of the gut bacterium L. saccharolyticum in transforming choline to TMA and consequently promoting the development of atherosclerosis.}, }
@article {pmid35272699, year = {2022}, author = {Bates, KA and Sommer, U and Hopkins, KP and Shelton, JMG and Wierzbicki, C and Sergeant, C and Tapley, B and Michaels, CJ and Schmeller, DS and Loyau, A and Bosch, J and Viant, MR and Harrison, XA and Garner, TWJ and Fisher, MC}, title = {Microbiome function predicts amphibian chytridiomycosis disease dynamics.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {44}, pmid = {35272699}, issn = {2049-2618}, mesh = {Animals ; Anura/genetics/microbiology ; *Chytridiomycota/genetics ; *Microbiota/genetics ; *Mycoses/microbiology/veterinary ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood.<br><br>METHODS: Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection.<br><br>RESULTS: Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes.<br><br>CONCLUSIONS: Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection. Video Abstract.}, }
@article {pmid35271887, year = {2022}, author = {Balinandi, S and Hayer, J and Cholleti, H and Wille, M and Lutwama, JJ and Malmberg, M and Mugisha, L}, title = {Identification and molecular characterization of highly divergent RNA viruses in cattle, Uganda.}, journal = {Virus research}, volume = {313}, number = {}, pages = {198739}, doi = {10.1016/j.virusres.2022.198739}, pmid = {35271887}, issn = {1872-7492}, mesh = {Animals ; Cattle ; *Cattle Diseases/epidemiology ; *Coltivirus ; *Flaviviridae ; Humans ; Phylogeny ; *RNA Viruses/genetics ; *Reoviridae/genetics ; Uganda/epidemiology ; }, abstract = {The risk for the emergence of novel viral zoonotic diseases in animals and humans in Uganda is high given its geographical location with high biodiversity. We aimed to identify and characterize viruses in 175 blood samples from cattle selected in Uganda using molecular approaches. We identified 8 viral species belonging to 4 families (Flaviviridae, Peribunyaviridae, Reoviridae and Rhabdoviridae) and 6 genera (Hepacivirus, Pestivirus, Orthobunyavirus, Coltivirus, Dinovernavirus and Ephemerovirus). Four viruses were highly divergent and tetantively named Zikole virus (Family: Flaviviridae), Zeboroti virus (Family: Reoviridae), Zebtine virus (Family: Rhabdoviridae) and Kokolu virus (Family: Rhabdoviridae). In addition, Bovine Hepacivirus, Obodhiang virus, Aedes pseudoscutellaris reovirus and Schmallenberg virus were identified for the first time in Ugandan cattle. We report 8 viral species belonging to 4 viral families including divergent ones in the blood of cattle in Uganda. Hence, cattle may be reservoir hosts for likely emergence of novel viruses with pathogenic potential to cause zoonotic diseases in different species with serious public health implications.}, }
@article {pmid35266795, year = {2022}, author = {Barbosa da Costa, N and Hébert, MP and Fugère, V and Terrat, Y and Fussmann, GF and Gonzalez, A and Shapiro, BJ}, title = {A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0148221}, pmid = {35266795}, issn = {2379-5077}, support = {//Canada Research Chairs (Chaires de recherche du Canada)/ ; //Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, abstract = {Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, the herbicide glyphosate has the potential to indirectly select for antibiotic-resistant bacteria. Such cross-selection could occur if the same genes (encoding efflux pumps, for example) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added a glyphosate-based herbicide (GBH) to 1,000-liter mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS. Together, these results indicate that GBHs can cross-select for antibiotic resistance in natural freshwater bacteria. IMPORTANCE Glyphosate-based herbicides (GBHs) such as Roundup formulations may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remain unknown in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff. Moreover, the resistance provided by ARGs compared to canonical mutations in the glyphosate target enzyme, EPSPS, remains unclear. Here, we performed a freshwater mesocosm experiment showing that a GBH strongly selects for ARGs, particularly multidrug efflux pumps. These selective effects were evident after just a few days, and the ability of bacteria to survive and thrive after GBH stress was predictable by the number of ARGs in their genomes and, to a lesser extent, by mutations in EPSPS. Intensive GBH application may therefore have the unintended consequence of selecting for ARGs in natural freshwater communities.}, }
@article {pmid35265196, year = {2022}, author = {Hu, W and Chen, ZM and Li, XX and Lu, L and Yang, GH and Lei, ZX and You, LJ and Cui, XB and Lu, SC and Zhai, ZY and Zeng, ZY and Chen, Y and Huang, SL and Gong, W}, title = {Faecal microbiome and metabolic signatures in rectal neuroendocrine tumors.}, journal = {Theranostics}, volume = {12}, number = {5}, pages = {2015-2027}, pmid = {35265196}, issn = {1838-7640}, mesh = {*Gastrointestinal Microbiome ; Humans ; Metabolome ; Metabolomics/methods ; Metagenome ; Metagenomics ; *Microbiota ; *Neuroendocrine Tumors ; Tumor Microenvironment ; }, abstract = {Background: The prevalence of rectal neuroendocrine tumors (RNET) has increased substantially over the past decades. Little is known on mechanistic alteration in the pathogenesis of such disease. We postulate that perturbations of human gut microbiome-metabolome interface influentially affect the development of RNET. The study aims to characterize the composition and function of faecal microbiome and metabolites in RNET individuals. Methods: We performed deep shotgun metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling of faecal samples from the discovery cohort (18 RNET patients, 40 controls), and validated the microbiome and metabolite-based classifiers in an independent cohort (15 RNET participants, 19 controls). Results: We uncovered a dysbiotic gut ecological microenvironment in RNET patients, characterized by aberrant depletion and attenuated connection of microbial species, and abnormally aggregated lipids and lipid-like molecules. Functional characterization based on our in-house and Human Project Unified Metabolic Analysis Network 2 (HUMAnN2) pipelines further indicated a nutrient deficient gut microenvironment in RNET individuals, evidenced by diminished activities such as energy metabolism, vitamin biosynthesis and transportation. By integrating these data, we revealed 291 robust associations between representative differentially abundant taxonomic species and metabolites, indicating a tight interaction of gut microbiome with metabolites in RNET pathogenesis. Finally, we identified a cluster of gut microbiome and metabolite-based signatures, and replicated them in an independent cohort, showing accurate prediction of such neoplasm from healthy people. Conclusions: Our current study is the first to comprehensively characterize the perturbed interface of gut microbiome and metabolites in RNET patients, which may provide promising targets for microbiome-based diagnostics and therapies for this disorder.}, }
@article {pmid35262396, year = {2022}, author = {Kong, G and Lê Cao, KA and Hannan, AJ}, title = {Alterations in the Gut Fungal Community in a Mouse Model of Huntington's Disease.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0219221}, pmid = {35262396}, issn = {2165-0497}, support = {//Department of Health | National Health and Medical Research Council (NHMRC)/ ; //UNIMELB | Faculty of Science, University of Melbourne/ ; }, mesh = {Animals ; Bacteria/genetics ; Disease Models, Animal ; *Gastrointestinal Microbiome/genetics ; *Huntington Disease/genetics/microbiology ; Metagenomics ; Mice ; Mice, Transgenic ; *Mycobiome/genetics ; }, abstract = {Huntington's disease (HD) is a neurodegenerative disorder caused by a trinucleotide expansion in the HTT gene, which is expressed throughout the brain and body, including the gut epithelium and enteric nervous system. Afflicted individuals suffer from progressive impairments in motor, psychiatric, and cognitive faculties, as well as peripheral deficits, including the alteration of the gut microbiome. However, studies characterizing the gut microbiome in HD have focused entirely on the bacterial component, while the fungal community (mycobiome) has been overlooked. The gut mycobiome has gained recognition for its role in host homeostasis and maintenance of the gut epithelial barrier. We aimed to characterize the gut mycobiome profile in HD using fecal samples collected from the R6/1 transgenic mouse model (and wild-type littermate controls) from 4 to 12 weeks of age, corresponding to presymptomatic through to early disease stages. Shotgun sequencing was performed on fecal DNA samples, followed by metagenomic analyses. The HD gut mycobiome beta diversity was significantly different from that of wild-type littermates at 12 weeks of age, while no genotype differences were observed at the earlier time points. Similarly, greater alpha diversity was observed in the HD mice by 12 weeks of age. Key taxa, including Malassezia restricta, Yarrowia lipolytica, and Aspergillus species, were identified as having a negative association with HD. Furthermore, integration of the bacterial and fungal data sets at 12 weeks of age identified negative correlations between the HD-associated fungal species and Lactobacillus reuteri. These findings provide new insights into gut microbiome alterations in HD and may help identify novel therapeutic targets. IMPORTANCE Huntington's disease (HD) is a fatal neurodegenerative disorder affecting both the mind and body. We have recently discovered that gut bacteria are disrupted in HD. The present study provides the first evidence of an altered gut fungal community (mycobiome) in HD. The genomes of many thousands of gut microbes were sequenced and used to assess "metagenomics" in particular the different types of fungal species in the HD versus control gut, in a mouse model. At an early disease stage, before the onset of symptoms, the overall gut mycobiome structure (array of fungi) in HD mice was distinct from that of their wild-type littermates. Alterations of multiple key fungi species were identified as being associated with the onset of disease symptoms, some of which showed strong correlations with the gut bacterial community. This study highlights the potential role of gut fungi in HD and may facilitate the development of novel therapeutic approaches.}, }
@article {pmid35259160, year = {2022}, author = {Kieser, S and Zdobnov, EM and Trajkovski, M}, title = {Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart.}, journal = {PLoS computational biology}, volume = {18}, number = {3}, pages = {e1009947}, pmid = {35259160}, issn = {1553-7358}, mesh = {Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; Mice ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Mouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Accordingly, the similarity between human and mouse microbiomes at a low taxonomic level is not clear. We construct a comprehensive mouse microbiota genome (CMMG) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 41'798 genomes cluster into 1'573 species, of which 78.1% are uncultured, and we discovered 226 new genera, seven new families, and one new order. CMMG enables an unprecedented coverage of the mouse gut microbiome exceeding 86%, increases the mapping rate over four-fold, and allows functional microbiota analyses of human and mouse linking them to the driver species. Comparing CMMG to microbiota from the unified human gastrointestinal genomes shows an overlap of 62% at the genus but only 10% at the species level, demonstrating that human and mouse gut microbiota are largely distinct. CMMG contains the most comprehensive collection of consistently functionally annotated species of the mouse and human microbiome to date, setting the ground for analysis of new and reanalysis of existing datasets at an unprecedented depth.}, }
@article {pmid35255937, year = {2022}, author = {van Dijk, LR and Walker, BJ and Straub, TJ and Worby, CJ and Grote, A and Schreiber, HL and Anyansi, C and Pickering, AJ and Hultgren, SJ and Manson, AL and Abeel, T and Earl, AM}, title = {StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {74}, pmid = {35255937}, issn = {1474-760X}, support = {R01 DK121822/DK/NIDDK NIH HHS/United States ; U01 AI095776/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x.}, }
@article {pmid35253207, year = {2022}, author = {Pfenninger, M and Bálint, M}, title = {On the use of population genomic time series for environmental monitoring.}, journal = {American journal of botany}, volume = {109}, number = {4}, pages = {497-499}, doi = {10.1002/ajb2.1836}, pmid = {35253207}, issn = {1537-2197}, mesh = {*Environmental Monitoring ; *Metagenomics ; Time Factors ; }, }
@article {pmid35250904, year = {2021}, author = {Song, Y and Hou, J and Kwok, JSL and Weng, H and Tang, MF and Wang, MH and Leung, ASY and Tao, KP and Wong, GWK and Chan, RWY and Tsui, SKW and Leung, TF}, title = {Whole-Genome Shotgun Sequencing for Nasopharyngeal Microbiome in Pre-school Children With Recurrent Wheezing.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {792556}, pmid = {35250904}, issn = {1664-302X}, abstract = {Microbiome mediates early life immune deviation in asthma development. Recurrent wheeze (RW) in pre-school years is a risk factor for asthma diagnosis in school-age children. Dysbiosis exists in asthmatic airways, while its origin in pre-school years and relationship to RW is not clearly defined. This study investigated metagenomics of nasopharyngeal microbiome in pre-school children with RW. We applied whole-genome shotgun sequencing and human rhinovirus (HRV) detection on nasopharyngeal samples collected from three groups of pre-school children: (i) RW group: 16 children at-risk for asthma who were hospitalized for RW, (ii) inpatient control (IC): 18 subjects admitted for upper respiratory infection, and (iii) community control (CC): 36 children without respiratory syndromes. Sequence reads were analyzed by MetaPhlAn2 and HUMAnN2 algorithm for taxonomic and functional identification. Linear discriminant analysis effect size (LEfSe) analysis was used to identify discriminative features. We identified that Moraxella catarrhalis and Dolosigranulum pigrum were predominant species in nasopharynx. RW had lower alpha diversity (Shannon diversity index) than CC (0.48 vs. 1.07; P adj = 0.039), characterized by predominant Proteobacteria. LEfSe analysis revealed D. pigrum was the only discriminative species across groups (LDA = 5.57, P = 0.002), with its relative abundance in RW, IC, and CC being 9.6, 14.2, and 37.3%, respectively (P < 0.05). LEfSe identified five (ribo)nucleotides biosynthesis pathways to be group discriminating. Adjusting for HRV status, pre-school children with RW have lower nasopharyngeal biodiversity, which is associated with Proteobacteria predominance and lower abundance of D. pigrum. Along with discriminative pathways found in RW and CC, these microbial biomarkers help to understand RW pathogenesis.}, }
@article {pmid35247565, year = {2022}, author = {Gupta, J and Rathour, R and Dupont, C and Mishra, A and Shekhar Thakur, I}, title = {Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing.}, journal = {Bioresource technology}, volume = {351}, number = {}, pages = {126936}, doi = {10.1016/j.biortech.2022.126936}, pmid = {35247565}, issn = {1873-2976}, mesh = {Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; Waste Disposal Facilities ; }, abstract = {Most of the discarded waste material paves their way to the utmost common dumping grounds, Landfills. Despite their widespread use, the landfill microbiomes are still not well characterized. Metagenomics approach provides insight into the identification of operational parameters influencing the microbiome composition and their biodegradation competencies. The metagenomic DNA was prepared to explore taxonomical community structure, phylogenetic relationships, and functional profile at the same time. A total of 100,021,052 high-quality filtered reads were acquired with a GC abundance of 62.59%. Taxonomical abundance revealed the dominance of phylum Proteobacteria and genes involved in biomolecules metabolism, aromatic compound degradation, stress tolerance, xenobiotic biodegradation etc. were revealed functionally. The intricate heterogeneous environment of landfill revealed well flourished biogeochemical metabolic profiles including nitrogen metabolism. This is the first study for the generated metagenome of Ghazipur landfill and the obtained results propose that microbial communities in landfill settings are far more intricate than expected. It remain mostly unexplored which demands the usage of multiple platforms for a better understanding.}, }
@article {pmid35247173, year = {2022}, author = {Jimoh, AA and Ikhimiukor, OO and Adeleke, R}, title = {Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {24}, pages = {35615-35642}, pmid = {35247173}, issn = {1614-7499}, mesh = {Biodegradation, Environmental ; Hydrocarbons ; *Microbiota ; *Petroleum ; *Petroleum Pollution/analysis ; Soil Microbiology ; *Soil Pollutants ; }, abstract = {Hypersaline environments are underappreciated and are frequently exposed to pollution from petroleum hydrocarbons. Unlike other environs, the high salinity conditions present are a deterrent to various remediation techniques. There is also production of hypersaline waters from oil-polluted ecosystems which contain toxic hydrophobic pollutants that are threat to public health, environmental protection, and sustainability. Currently, innovative advances are being proposed for the remediation of oil-contaminated hypersaline regions. Such advancements include the exploration and stimulation of native microbial communities capable of utilizing and degrading petroleum hydrocarbons. However, prevailing salinity in these environments is unfavourable for the growth of non-halophylic microorganisms, thus limiting effective bioremediation options. An in-depth understanding of the potentials of various remediation technologies of hydrocarbon-polluted hypersaline environments is lacking. Thus, we present an overview of petroleum hydrocarbon pollution in hypersaline ecosystems and discuss the challenges and prospects associated with several technologies that may be employed in remediation of hydrocarbon pollution in the presence of delimiting high salinities. The application of biological remediation technologies including the utilization of halophilic and halotolerant microorganisms is also discussed.}, }
@article {pmid35246229, year = {2022}, author = {Zhou, H and Beltrán, JF and Brito, IL}, title = {Host-microbiome protein-protein interactions capture disease-relevant pathways.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {72}, pmid = {35246229}, issn = {1474-760X}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; }, mesh = {*Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/genetics ; Metagenomics ; *Microbiota ; Obesity ; }, abstract = {BACKGROUND: Host-microbe interactions are crucial for normal physiological and immune system development and are implicated in a variety of diseases, including inflammatory bowel disease (IBD), colorectal cancer (CRC), obesity, and type 2 diabetes (T2D). Despite large-scale case-control studies aimed at identifying microbial taxa or genes involved in pathogeneses, the mechanisms linking them to disease have thus far remained elusive.<br><br>RESULTS: To identify potential pathways through which human-associated bacteria impact host health, we leverage publicly-available interspecies protein-protein interaction (PPI) data to find clusters of microbiome-derived proteins with high sequence identity to known human-protein interactors. We observe differential targeting of putative human-interacting bacterial genes in nine independent metagenomic studies, finding evidence that the microbiome broadly targets human proteins involved in immune, oncogenic, apoptotic, and endocrine signaling pathways in relation to IBD, CRC, obesity, and T2D diagnoses.<br><br>CONCLUSIONS: This host-centric analysis provides a mechanistic hypothesis-generating platform and extensively adds human functional annotation to commensal bacterial proteins.}, }
@article {pmid35240353, year = {2022}, author = {Yang, WY and Chou, CH and Wang, C}, title = {The effects of feed supplementing Akkemansia muciniphila on incidence, severity, and gut microbiota of necrotic enteritis in chickens.}, journal = {Poultry science}, volume = {101}, number = {4}, pages = {101751}, doi = {10.1016/j.psj.2022.101751}, pmid = {35240353}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Chickens ; *Clostridium Infections/pathology/prevention &amp; control/veterinary ; Clostridium perfringens ; *Coccidiosis/parasitology/prevention &amp; control/veterinary ; *Eimeria ; *Enteritis/pathology/prevention &amp; control/veterinary ; *Gastrointestinal Microbiome ; Incidence ; Mucins ; *Poultry Diseases/parasitology/prevention &amp; control ; }, abstract = {Akkermansia muciniphila (AM) is a mucin-degrading anaerobe, exerting beneficial effects on gut integrity improvement, inflammatory alleviation, and metabolic regulations in humans. Excess amounts of mucin and mucogenesis in the gut facilitate the development of necrotic enteritis (NE) in chickens. The study aimed to evaluate the effects of oral inoculation of AM on NE prevention and gut modulation in a NE-reproduced model coinfecting with Clostridium perfringens (CP) and Eimeria parasites. A total of 105 commercial 1-day-old broilers were randomly allocated into 5 groups, respectively challenged with Eimeria (Eimeria group), Eimeria and CP (Eimeria+CP group), Eimeria and CP with AM (Eimeria+CP+AM group), Eimeria and AM (Eimeria+AM group), and a placebo (Noninfected group). The treatment of AM exhibited a low degree of amelioration on NE severity. The application neither protected broilers from NE by decreasing NE-positive numbers nor reached a significant reduction in lesion scores in the small intestines. The development of NE reduced species diversity in jejunal microbiota; the pretreatments of AM exacerbated the consequence by losing species richness and promoted the similarity of the jejunal microbial community presented in the Eimeria+CP group. The participation of AM enhanced the increments of genera Clostridium sensu stricto 1 and Escherichia_Shigella and decreased the number of Lactobacillus. The significant variations of genera Clostridium sensu stricto 1 and Lactobacillus in jejunal microbiota were associated with NE development and promotion. In conclusion, oral inoculation of AM promoted the development of NE and modulated the jejunal microbiota favorable for CP overgrowth in broilers. The application of AM as a probiotic in broilers should be cautious on account of the effects to predispose NE.}, }
@article {pmid35238677, year = {2022}, author = {Bohl, JA and Lay, S and Chea, S and Ahyong, V and Parker, DM and Gallagher, S and Fintzi, J and Man, S and Ponce, A and Sreng, S and Kong, D and Oliveira, F and Kalantar, K and Tan, M and Fahsbender, L and Sheu, J and Neff, N and Detweiler, AM and Yek, C and Ly, S and Sath, R and Huch, C and Kry, H and Leang, R and Huy, R and Lon, C and Tato, CM and DeRisi, JL and Manning, JE}, title = {Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {11}, pages = {e2115285119}, pmid = {35238677}, issn = {1091-6490}, mesh = {Asia, Southeastern/epidemiology ; Cambodia/epidemiology ; *Disease Susceptibility ; Female ; Fever/epidemiology/etiology ; *Health Resources ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenome ; Metagenomics/*methods ; *Public Health Surveillance ; Seroepidemiologic Studies ; }, abstract = {SignificanceMetagenomic pathogen sequencing offers an unbiased approach to characterizing febrile illness. In resource-scarce settings with high biodiversity, it is critical to identify disease-causing pathogens in order to understand burden and to prioritize efforts for control. Here, metagenomic next-generation sequencing (mNGS) characterization of the pathogen landscape in Cambodia revealed diverse vector-borne and zoonotic pathogens irrespective of age and gender as risk factors. Identification of key pathogens led to changes in national program surveillance. This study is a "real world" example of the use of mNGS surveillance of febrile individuals, executed in-country, to identify outbreaks of vector-borne, zoonotic, and other emerging pathogens in a resource-scarce setting.}, }
@article {pmid35235560, year = {2022}, author = {Tierney, BT and Tan, Y and Yang, Z and Shui, B and Walker, MJ and Kent, BM and Kostic, AD and Patel, CJ}, title = {Systematically assessing microbiome-disease associations identifies drivers of inconsistency in metagenomic research.}, journal = {PLoS biology}, volume = {20}, number = {3}, pages = {e3001556}, pmid = {35235560}, issn = {1545-7885}, support = {R01 AI127250/AI/NIAID NIH HHS/United States ; R01 ES032470/ES/NIEHS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteria/classification/*genetics ; Biomedical Research/*methods ; Cardiovascular Diseases/metabolism/microbiology ; Colorectal Neoplasms/metabolism/microbiology ; Diabetes Mellitus, Type 1/metabolism/microbiology ; Diabetes Mellitus, Type 2/metabolism/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/metabolism/microbiology ; Liver Cirrhosis/metabolism/microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Models, Theoretical ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Evaluating the relationship between the human gut microbiome and disease requires computing reliable statistical associations. Here, using millions of different association modeling strategies, we evaluated the consistency-or robustness-of microbiome-based disease indicators for 6 prevalent and well-studied phenotypes (across 15 public cohorts and 2,343 individuals). We were able to discriminate between analytically robust versus nonrobust results. In many cases, different models yielded contradictory associations for the same taxon-disease pairing, some showing positive correlations and others negative. When querying a subset of 581 microbe-disease associations that have been previously reported in the literature, 1 out of 3 taxa demonstrated substantial inconsistency in association sign. Notably, >90% of published findings for type 1 diabetes (T1D) and type 2 diabetes (T2D) were particularly nonrobust in this regard. We additionally quantified how potential confounders-sequencing depth, glucose levels, cholesterol, and body mass index, for example-influenced associations, analyzing how these variables affect the ostensible correlation between Faecalibacterium prausnitzii abundance and a healthy gut. Overall, we propose our approach as a method to maximize confidence when prioritizing findings that emerge from microbiome association studies.}, }
@article {pmid35234986, year = {2022}, author = {Kachroo, N and Monga, M and Miller, AW}, title = {Comparative functional analysis of the urinary tract microbiome for individuals with or without calcium oxalate calculi.}, journal = {Urolithiasis}, volume = {50}, number = {3}, pages = {303-317}, pmid = {35234986}, issn = {2194-7236}, support = {1R01DK121689-01A1/DK/NIDDK NIH HHS/United States ; 1R01DK121689-01A1/DK/NIDDK NIH HHS/United States ; }, mesh = {Calcium/urine ; Calcium Oxalate/metabolism ; Female ; Humans ; *Kidney Calculi ; Male ; *Microbiota ; *Urinary Calculi/urine ; *Urinary Tract/chemistry/metabolism ; *Urolithiasis/urine ; }, abstract = {Individuals with urinary stone disease (USD) exhibit dysbiosis in the urinary tract and the loss of Lactobacillus that promote urinary tract health. However, the microbial metabolic functions that differentiate individuals with USD from healthy individuals are unknown. The objective of the current study was to determine the microbial functions across prokaryotic, viral, fungal, and protozoan domains that are associated with calcium oxalate (CaOx) stone formers through comparative shotgun metagenomics of midstream, voided urine samples for a small number of patients (n = 5 CaOx stone formers, n = 5 healthy controls). Results revealed that CaOx stone formers had reduced levels of genes associated with oxalate metabolism, as well as transmembrane transport, proteolysis, and oxidation-reduction processes. From 17 draft genomes extracted from the data and > 42,000 full length reference genomes, genes enriched in the Control group mapped overwhelming to Lactobacillus crispatus and those associated with CaOx mapped to Pseudomonas aeruginosa and Burkholderia sp. The microbial functions that differentiated the clinical cohorts are associated with known mechanisms of stone formation. While the prokaryotes most differentiated the CaOx and Control groups, a diverse, trans-domain microbiome was apparent. While our sample numbers were small, results corroborate previous studies and suggest specific microbial metabolic pathways in the urinary tract that modulate stone formation. Future studies that target these metabolic pathways as well as the influence of viruses, fungi, and protozoa on urinary tract physiology is warranted.}, }
@article {pmid35234490, year = {2022}, author = {Tourlousse, DM and Narita, K and Miura, T and Ohashi, A and Matsuda, M and Ohyama, Y and Shimamura, M and Furukawa, M and Kasahara, K and Kameyama, K and Saito, S and Goto, M and Shimizu, R and Mishima, R and Nakayama, J and Hosomi, K and Kunisawa, J and Terauchi, J and Sekiguchi, Y and Kawasaki, H}, title = {Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0191521}, pmid = {35234490}, issn = {2165-0497}, mesh = {DNA ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Indicators and Reagents ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; }, abstract = {Standardization and quality assurance of microbiome community analysis by high-throughput DNA sequencing require widely accessible and well-characterized reference materials. Here, we report on newly developed DNA and whole-cell mock communities to serve as control reagents for human gut microbiota measurements by shotgun metagenomics and 16S rRNA gene amplicon sequencing. The mock communities were formulated as near-even blends of up to 20 bacterial species prevalent in the human gut, span a wide range of genomic guanine-cytosine (GC) contents, and include multiple strains with Gram-positive type cell walls. Through a collaborative study, we carefully characterized the mock communities by shotgun metagenomics, using previously developed standardized protocols for DNA extraction and sequencing library construction. Further, we validated fitness of the mock communities for revealing technically meaningful differences among protocols for DNA extraction and metagenome/16S rRNA gene amplicon library construction. Finally, we used the mock communities to reveal varying performance of metagenome-based taxonomic profilers and the impact of trimming and filtering of sequencing reads on observed species profiles. The latter showed that aggressive preprocessing of reads may result in substantial GC-dependent bias and should thus be carefully evaluated to minimize unintended effects on species abundances. Taken together, the mock communities are expected to support a myriad of applications that rely on well-characterized control reagents, ranging from evaluation and optimization of methods to assessment of reproducibility in interlaboratory studies and routine quality control. IMPORTANCE Application of high-throughput DNA sequencing has greatly accelerated human microbiome research and its translation into new therapeutic and diagnostic capabilities. Microbiome community analyses results can, however, vary considerably across studies or laboratories, and establishment of measurement standards to improve accuracy and reproducibility has become a priority. The here-developed mock communities, which are available from the NITE Biological Resource Center (NBRC) at the National Institute of Technology and Evaluation (NITE, Japan), provide well-characterized control reagents that allow users to judge the accuracy of their measurement results. Widespread and consistent adoption of the mock communities will improve reproducibility and comparability of microbiome community analyses, thereby supporting and accelerating human microbiome research and development.}, }
@article {pmid35230155, year = {2022}, author = {Yang, J and Tong, C and Xiao, D and Xie, L and Zhao, R and Huo, Z and Tang, Z and Hao, J and Zeng, Z and Xiong, W}, title = {Metagenomic Insights into Chicken Gut Antibiotic Resistomes and Microbiomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0190721}, pmid = {35230155}, issn = {2165-0497}, support = {2019BT02N054//the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; NT2021006//Lingnan Modern Agricultural Science and Technology Guangdong Laboratory Independent Scientific Research/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Chickens ; Genes, Bacterial ; Lactobacillus ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {The chicken gut microbiota, as a reservoir of antibiotic resistance genes (ARGs), poses a high risk to humans and animals worldwide. Yet a comprehensive exploration of the chicken gut antibiotic resistomes remains incomplete. In this study, we established the largest chicken gut resistance gene catalogue to date through metagenomic analysis of 629 chicken gut samples. We found significantly higher abundance of ARGs in the Chinese chicken gut than that in the Europe. tetX, mcr, and blaNDM, the genes resistant to antibiotics of last resort for human and animal health, were detected in the Chinese chicken gut. The abundance of ARGs was linearly correlated with that of mobile genetic elements (MGEs). The host-tracking analysis identified Escherichia, Enterococcus, Staphylococcus, Klebsiella, and Lactobacillus as the major ARG hosts. Especially, Lactobacillus, an intestinal probiotic, carried multiple drug resistance genes, and was proportional to ISLhe63, highlighting its potential risk in agricultural production processes. We first established a reference gene catalogue of chicken gut antibiotic resistomes. Our study helps to improve the knowledge and understanding of chicken antibiotic resistomes for knowledge-based sustainable chicken meat production. IMPORTANCE The prevalence of antibiotic resistance genes in the chicken gut environment poses a serious threat to human health; however, we lack a comprehensive exploration of antibiotic resistomes and microbiomes in the chicken gut environment. The results of this study demonstrate the diversity and abundance of antibiotic resistance genes and flora in the chicken gut environment and identify a variety of potential hosts carrying antibiotic resistance genes. Further analysis showed that mobile genetic elements were linearly correlated with antibiotic resistance genes abundance, implying that we should pay attention to the role played by mobile genetic elements in antibiotic resistance genes transmission. We established a reference genome of gut antibiotic resistance genes in chickens, which will help to rationalize the use of drugs in poultry farming.}, }
@article {pmid35229726, year = {2022}, author = {Underhill, DM and Braun, J}, title = {Fungal microbiome in inflammatory bowel disease: a critical assessment.}, journal = {The Journal of clinical investigation}, volume = {132}, number = {5}, pages = {}, pmid = {35229726}, issn = {1558-8238}, mesh = {Animals ; Bacteria ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/genetics/microbiology ; Metagenomics ; Mice ; *Microbiota ; *Mycobiome/genetics ; }, abstract = {The gut microbiome is at the center of inflammatory bowel disease (IBD) pathogenesis and disease activity. While this has mainly been studied in the context of the bacterial microbiome, recent advances have provided tools for the study of host genetics and metagenomics of host-fungal interaction. Through these tools, strong evidence has emerged linking certain fungal taxa, such as Candida and Malassezia, with cellular and molecular pathways of IBD disease biology. Mouse models and human fecal microbial transplant also suggest that some disease-participatory bacteria and fungi may act not via the host directly, but via their fungal-bacterial ecologic interactions. We hope that these insights, and the study design and multi-omics strategies used to develop them, will facilitate the inclusion of the fungal community in basic and translational IBD research.}, }
@article {pmid35229641, year = {2022}, author = {Lv, Y and Yang, S and Xiao, X and Zhang, Y}, title = {Stimulated Organic Carbon Cycling and Microbial Community Shift Driven by a Simulated Cold-Seep Eruption.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0008722}, pmid = {35229641}, issn = {2150-7511}, support = {2016YFC0300709//National Key R&amp;D Program of China/ ; 41776173//NNSF of China/ ; 41921006//NNSF of China/ ; 42122043//NNSF of China/ ; 41476123//NNSF of China/ ; }, mesh = {Carbon Cycle ; Metagenomics ; Methane ; *Methylococcaceae ; *Microbiota ; }, abstract = {Cold seeps are a major methane source in marine systems, and microbe-mediated anaerobic oxidation of methane (AOM) serves as an effective barrier for preventing methane emissions from sediment to water. However, how the periodic eruption of cold seeps drives the microbial community shift and further affects carbon cycling has been largely neglected, mainly due to the technical challenge of analyzing the in situ communities undergoing such geological events. Using a continuously running high-pressure bioreactor to simulate these events, we found that under the condition of simulated eruptions, the abundance of AOM-related species decreased, and some methane was oxidized to methyl compounds to feed heterotrophs. The methanogenic archaeon Methanolobus replaced ANME-2a as the dominant archaeal group; moreover, the levels of methylotrophic bacteria, such as Pseudomonas, Halomonas, and Methylobacter, quickly increased, while those of sulfate-reducing bacteria decreased. According to the genomic analysis, Methylobacter played an important role in incomplete methane oxidation during eruptions; this process was catalyzed by the genes pmoABC under anaerobic conditions when the methane pressure was high, possibly generating organic carbon. Additionally, the findings showed that methyl compounds can also be released to the environment during methanogenesis and AOM under eruption conditions when the methane pressure is high. IMPORTANCE In the ocean, almost all of the emission and consumption of deeply buried methane occurs in cold seeps; therefore, understanding the methane cycling in cold seeps is crucial to estimating the oceanic methane budget. Cold-seep eruptions often lead to the dramatic destruction of microbial ecosystems that drive methane cycling. Because of technical challenges, the direct monitoring of these communities as well as the activity shifts during eruptions has never been achieved. In this study, we took an alternative approach by simulating cold-seep eruptions and using genome-resolved metagenomics to interpret the dynamic changes in the microbial community. The results show that the periodical cold-seep eruptions intensify organic carbon cycling, undermine the direct oxidation of methane to carbon dioxide, and drive microbial community shifts. These results further suggest that a more sophisticated calculation of the methane budget in cold seeps that considers their eruption status is needed.}, }
@article {pmid35227842, year = {2022}, author = {Du, C and Yang, F and Li, X and Liao, H and Li, Z and Gao, J and Zhang, L}, title = {Metagenomic analysis of microbial community structure and distribution of resistance genes in Daihai Lake, China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {302}, number = {}, pages = {119065}, doi = {10.1016/j.envpol.2022.119065}, pmid = {35227842}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents ; China ; Genes, Bacterial ; *Lakes/microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {The emergence of resistance genes is a global phenomenon that poses a significant threat to both animals and humans. Lakes are important reservoirs of genes that confer resistant to antibiotics and metals. In this study, we investigated the distribution and diversity of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the sediment of Daihai Lake using high-throughput sequencing and metagenomic analysis. The results indicated that all sampling sites had similar bacterial community structures, with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes being the most abundant. A total of 16 ARG types containing 111 ARG subtypes were deposited in the sediment. Among the resistance genes to bacitracin, multidrug, macrolide-lincosamide-streptogramin (MLS), tetracycline, beta-lactam, and sulfonamide were the dominant ARG types, accounting for 89.9-94.3% of the total ARGs. Additionally, 15 MRG types consisting of 146 MRG subtypes were identified. In all samples, MRGs of the same type presented resistance to Pb, Ni, Hg, W, Zn, Ag, Cr, Fe, As, Cu, and multimetals. Overall, the distribution and diversity of antibiotic and metal resistance genes showed no significant differences in the samples. Plasmids (91.03-91.82%) were the most dominant mobile genetic elements in the sediments of Daihai Lake. Network analysis indicated that the target ARGs and MRGs were significantly positively correlated with the microorganisms. Potential hosts for various ARGs and MRGs include Proteobacteria, Euryarchaeota, Actinobacteria, Chloroflexi, and Bacteroidetes.}, }
@article {pmid35227283, year = {2022}, author = {Du, Y and Sun, F}, title = {HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {63}, pmid = {35227283}, issn = {1474-760X}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Cluster Analysis ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the HiCzin normalization method and the Leiden clustering algorithm and includes the spurious contact detection into binning pipelines for the first time. HiCBin is validated on one synthetic and two real metagenomic samples and is shown to outperform the existing Hi-C-based binning methods. HiCBin is available at https://github.com/dyxstat/HiCBin .}, }
@article {pmid35222325, year = {2022}, author = {Ataeian, M and Liu, Y and Kouris, A and Hawley, AK and Strous, M}, title = {Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {780346}, pmid = {35222325}, issn = {1664-302X}, abstract = {Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.}, }
@article {pmid35215951, year = {2022}, author = {Du, H and Zhang, L and Zhang, X and Yun, F and Chang, Y and Tuersun, A and Aisaiti, K and Ma, Z}, title = {Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species.}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215951}, issn = {1999-4915}, mesh = {Animals ; Animals, Wild/virology ; China ; Genetic Variation ; Genome, Viral/*genetics ; Genotype ; Gerbillinae/classification/*virology ; Humans ; Metagenomics ; Phylogeny ; RNA Viruses/classification/*genetics/isolation &amp; purification/pathogenicity ; RNA, Viral/genetics ; Rodent Diseases/virology ; Viral Proteins/genetics ; Viral Zoonoses/virology ; Virome/*genetics ; }, abstract = {Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used for zoonotic virus detection and virome characterization on 32 Great gerbils of Rhombomys opimus, Meriones meridianus, and Meiiones Unguiculataus species in Xinjiang, Northwest China. In total, 1848 viral genomes that are potentially pathogenic to rodents and humans, as well as to other wildlife, were identified namely Retro-, Flavi-, Pneumo-, Picobirna-, Nairo-, Arena-, Hepe-, Phenui-, Rhabdo-, Calici-, Reo-, Corona-, Orthomyxo-, Peribunya-, and Picornaviridae families. In addition, a new genotype of rodent Hepacivirus was identified in heart and lung homogenates of seven viscera pools and phylogenetic analysis revealed the closest relationship to rodent Hepacivirus isolate RtMm-HCV/IM2014 that was previously reported to infect rodents from Inner Mongolia, China. Moreover, nine new genotype viral sequences that corresponded to Picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae, comprising of three segment I and six segment II sequences, were identified in intestines and liver of seven viscera pools. In the two phylogenetic trees that were constructed using ORF1 and ORF2 of segment I, the three segment I sequences were clustered into distinct clades. Additionally, phylogenetic analysis showed that PBV sequences were distributed in the whole tree that was constructed using the RNA-dependent RNA polymerase (RdRp) gene of segment II with high diversity, sharing 68.42-82.67% nucleotide identities with other genogroup I and genogroup II PBV strains based on the partial RdRp gene. By RNA sequencing, we found a high degree of biodiversity of Retro-, Flavi-, Pneumo-, and Picobirnaridae families and other zoonotic viruses in gerbils, indicating that zoonotic viruses are a common presence in gerbils from Xinjiang, China. Therefore, further research is needed to determine the zoonotic potential of these viruses that are carried by other rodent species from different ecosystems and wildlife in general.}, }
@article {pmid35215871, year = {2022}, author = {Bai, GH and Lin, SC and Hsu, YH and Chen, SY}, title = {The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications.}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215871}, issn = {1999-4915}, mesh = {Animals ; COVID-19/therapy ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; Metagenomics/*methods ; Mice ; Obesity/complications ; SARS-CoV-2/genetics ; Virome/*genetics ; Virus Diseases/*drug therapy/therapy ; Viruses/classification/genetics ; }, abstract = {The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships. Viral metagenomic analyses often lack standard references and are potentially subject to bias. Moreover, most virome-related review articles have focused on the gut virome and did not investigate the roles of the virome in other sites of the body in human disease. This review presents an overview of viral metagenomics, with updates regarding the relations between alterations in the human virome and the pathogenesis of human diseases, recent findings related to COVID-19, and therapeutic applications related to the human virome.}, }
@article {pmid35215838, year = {2022}, author = {Forero-Junco, LM and Alanin, KWS and Djurhuus, AM and Kot, W and Gobbi, A and Hansen, LH}, title = {Bacteriophages Roam the Wheat Phyllosphere.}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215838}, issn = {1999-4915}, mesh = {Bacteriophages/classification/genetics/*isolation &amp; purification ; Genome, Viral/genetics ; Metagenome/genetics ; Microbiota ; Plant Leaves/microbiology ; Pseudomonadaceae/classification/genetics/isolation &amp; purification/virology ; Toxins, Biological/genetics ; Triticum/*microbiology ; }, abstract = {The phyllosphere microbiome plays an important role in plant fitness. Recently, bacteriophages have been shown to play a role in shaping the bacterial community composition of the phyllosphere. However, no studies on the diversity and abundance of phyllosphere bacteriophage communities have been carried out until now. In this study, we extracted, sequenced, and characterized the dsDNA and ssDNA viral community from a phyllosphere for the first time. We sampled leaves from winter wheat (Triticum aestivum), where we identified a total of 876 virus operational taxonomic units (vOTUs), mostly predicted to be bacteriophages with a lytic lifestyle. Remarkably, 848 of these vOTUs corresponded to new viral species, and we estimated a minimum of 2.0 × 106 viral particles per leaf. These results suggest that the wheat phyllosphere harbors a large and active community of novel bacterial viruses. Phylloviruses have potential applications as biocontrol agents against phytopathogenic bacteria or as microbiome modulators to increase plant growth-promoting bacteria.}, }
@article {pmid35213794, year = {2022}, author = {Meng, J and Németh, Z and Peng, M and Fekete, E and Garrigues, S and Lipzen, A and Ng, V and Savage, E and Zhang, Y and Grigoriev, IV and Mäkelä, MR and Karaffa, L and de Vries, RP}, title = {GalR, GalX and AraR co-regulate d-galactose and l-arabinose utilization in Aspergillus nidulans.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14025}, pmid = {35213794}, issn = {1751-7915}, support = {308284//Academy of Finland/ ; 15807//Stichting voor de Technische Wetenschappen/ ; CSC201907720027//China Scholarship Council/ ; NN128867//Hungarian National Research, Development and Innovation Fund/ ; K138489//Hungarian National Research, Development and Innovation Fund/ ; }, abstract = {Filamentous fungi produce a wide variety of enzymes in order to efficiently degrade plant cell wall polysaccharides. The production of these enzymes is controlled by transcriptional regulators, which also control the catabolic pathways that convert the released monosaccharides. Two transcriptional regulators, GalX and GalR, control d-galactose utilization in the model filamentous fungus Aspergillus nidulans, while the arabinanolytic regulator AraR regulates l-arabinose catabolism. d-Galactose and l-arabinose are commonly found together in polysaccharides, such as arabinogalactan, xylan and rhamnogalacturonan I. Therefore, the catabolic pathways that convert d-galactose and l-arabinose are often also likely to be active simultaneously. In this study, we investigated the interaction between GalX, GalR and AraR in d-galactose and l-arabinose catabolism. For this, we generated single, double and triple mutants of the three regulators, and analysed their growth and enzyme and gene expression profiles. Our results clearly demonstrated that GalX, GalR and AraR co-regulate d-galactose catabolism in A. nidulans. GalX has a prominent role on the regulation of genes of d-galactose oxido-reductive pathway, while AraR can compensate for the absence of GalR and/or GalX.}, }
@article {pmid35212476, year = {2022}, author = {Belouhova, M and Daskalova, E and Yotinov, I and Topalova, Y and Velkova, L and Dolashki, A and Dolashka, P}, title = {Microbial diversity of garden snail mucus.}, journal = {MicrobiologyOpen}, volume = {11}, number = {1}, pages = {e1263}, pmid = {35212476}, issn = {2045-8827}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Computational Biology ; In Situ Hybridization, Fluorescence ; Isoelectric Point ; Metagenomics ; Microbiota ; Mucus/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; Snails/chemistry/*microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tandem Mass Spectrometry ; }, abstract = {The search for new natural compounds for application in medicine and cosmetics is a trend in biotechnology. One of the sources of such active compounds is the snail mucus. Snail physiology and the biological activity of their fluids (especially the mucus) are still poorly studied. Only a few previous studies explored the relationship between snails and their microbiome. The present study was focused on the biodiversity of the snail mucus used in the creation of cosmetic products, therapeutics, and nutraceuticals. The commonly used cultivation techniques were applied for the determination of the number of major bacterial groups. Fluorescence in situ hybridization for key taxa was performed. The obtained images were subjected to digital image analysis. Sequencing of the 16S rRNA gene was also done. The results showed that the mucus harbors a rich bacterial community (10.78 × 1010 CFU/ml). Among the dominant bacteria, some are known for their ability to metabolize complex polysaccharides or are usually found in soil and plants (Rhizobiaceae, Shewanella, Pedobacter, Acinetobacter, Alcaligenes). The obtained data demonstrated that the snail mucus creates a unique environment for the development of the microbial community that differs from other parts of the animal and which resulted from the combined contribution of the microbiomes derived from the soil, plants, and the snails.}, }
@article {pmid35211421, year = {2022}, author = {Plauzolles, A and Toumi, E and Bonnet, M and Pénaranda, G and Bidaut, G and Chiche, L and Allardet-Servent, J and Retornaz, F and Goutorbe, B and Halfon, P}, title = {Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {722886}, pmid = {35211421}, issn = {2235-2988}, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/methods ; }, abstract = {Microbiotas play critical roles in human health, yet in most cases scientists lack standardized and reproducible methods from collection and preservation of samples, as well as the choice of omic analysis, up to the data processing. To date, stool sample preservation remains a source of technological bias in metagenomic sequencing, despite newly developed storage solutions. Here, we conducted a comparative study of 10 storage methods for human stool over a 14-day period of storage at fluctuating temperatures. We first compared the performance of each stabilizer with observed bacterial composition variation within the same specimen. Then, we identified the nature of the observed variations to determine which bacterial populations were more impacted by the stabilizer. We found that DNA stabilizers display various stabilizing efficacies and affect the recovered bacterial profiles thus highlighting that some solutions are more performant in preserving the true gut microbial community. Furthermore, our results showed that the bias associated with the stabilizers can be linked to the phenotypical traits of the bacterial populations present in the studied samples. Although newly developed storage solutions have improved our capacity to stabilize stool microbial content over time, they are nevertheless not devoid of biases hence requiring the implantation of standard operating procedures. Acknowledging the biases and limitations of the implemented method is key to better interpret and support true associated microbiome patterns that will then lead us towards personalized medicine, in which the microbiota profile could constitute a reliable tool for clinical practice.}, }
@article {pmid35209070, year = {2022}, author = {Liu, W and He, K and Wu, D and Zhou, L and Li, G and Lin, Z and Yang, X and Liu, J and Pui Man Hoi, M}, title = {Natural Dietary Compound Xanthohumol Regulates the Gut Microbiota and Its Metabolic Profile in a Mouse Model of Alzheimer's Disease.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {4}, pages = {}, pmid = {35209070}, issn = {1420-3049}, support = {SZXK069//Shenzhen Key Medical Discipline Construction Fund/ ; SZSM201611090//Sanming Project of Medicine in Shenzhen/ ; File no. 127/2014/A3, 0015/2019/ASC, 0023/2020/AFJ, 0035/2020/AGJ//The Science and Technology Development Fund, Macau SAR/ ; Project no. MYRG2015-0061-ICMS-QRCM, MYRG2017-00150-ICMS//The University of Macau Research Grant/ ; }, mesh = {Alzheimer Disease/drug therapy/etiology/metabolism/pathology ; Amyloid beta-Peptides/metabolism ; Animals ; Biodiversity ; Biological Products/chemistry/*pharmacology ; Cognition/drug effects ; Disease Models, Animal ; Flavonoids/chemistry/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Metabolome/*drug effects ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Transgenic ; Propiophenones/chemistry/*pharmacology ; }, abstract = {Discovering new and effective drugs for the treatment of Alzheimer's disease (AD) is a major clinical challenge. This study focuses on chemical modulation of the gut microbiome in an established murine AD model. We used the 16S rDNA sequencing technique to investigate the effect of xanthohumol (Xn) on the diversity of intestinal microflora in 2-month- and 6-month-old APP/PS1 mice, respectively. APP/PS1 and wild-type mice were treated by gavage with corn oil with or without Xn every other day for 90 days. Prior to and following treatment, animals were tested for spatial learning, cognitive and memory function. We found Xn reduced cognitive dysfunction in APP/PS1 mice and significantly regulated the composition and abundance of gut microbiota both in prevention experiments (with younger mice) and therapeutic experiments (with older mice). Differential microflora Gammaproteobacteria were significantly enriched in APP/PS1 mice treated with Xn. Nodosilineaceae and Rikenellaceae may be the specific microflora modulated by Xn. The penicillin and cephalosporin biosynthesis pathway and the atrazine degradation pathway may be the principal modulation pathways. Taken together, oral treatment with Xn may have a neuroprotective role by regulating the composition of intestinal microflora, a result that contributes to the scientific basis for a novel prophylactic and therapeutic approach to AD.}, }
@article {pmid35196818, year = {2022}, author = {Lu, J and Yang, S and Wang, C and Wang, H and Gong, G and Xi, Y and Pan, J and Wang, X and Zeng, J and Zhang, J and Li, P and Shen, Q and Shan, T and Zhang, W}, title = {Gut Virome of the World's Highest-Elevation Lizard Species (Phrynocephalus erythrurus and Phrynocephalus theobaldi) Reveals Versatile Commensal Viruses.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0187221}, pmid = {35196818}, issn = {2165-0497}, mesh = {Animals ; Bacteriophages/genetics ; *Gastrointestinal Microbiome ; Lizards/metabolism/*virology ; Metagenome ; Metagenomics ; Phylogeny ; Symbiosis/*physiology ; Tibet ; *Virome/physiology ; Viruses/classification/genetics ; }, abstract = {The gut virome is a reservoir of diverse symbiotic and pathogenic viruses coevolving with their hosts, and yet limited research has explored the gut viromes of highland-dwelling rare species. Using viral metagenomic analysis, the viral communities of the Phrynocephalus lizards living in the Qinghai-Tibet Plateau were investigated. Phage-encoded functional genes and antibiotic resistance genes (ARGs) were analyzed. The viral communities of different lizard species were all predominated by bacteriophages, especially the Caudovirales order. The virome of Phrynocephalus erythrurus living around the Namtso Lake possessed a unique structure, with the greatest abundance of the Parvoviridae family and the highest number of exclusive viral species. Several vertebrate-infecting viruses were discovered, including caliciviruses, astroviruses, and parvoviruses. Phylogenetic analyses demonstrated that the virus hallmark genes of bacteriophages possessed high genetic diversity. After functional annotation, the majority of phage-associated functional genes were classified in the energy metabolism category. In addition, plenty of ARGs belonging to the multidrug category were discovered, and five ARGs were exclusive to the virome from Phrynocephalus theobaldi. This study provided the first insight into the structure and function of the virome in highland lizards, contributing to the protection of threatened lizard species. Also, our research is of exemplary significance for the gut virome research of lizard species and other cold-blooded and highland-dwelling animals, prompting a better understanding of the interspecific differences and transmission of commensal viruses. IMPORTANCE The Phrynocephalus lizards inhabiting the Qinghai-Tibet Plateau (QTP) are considered to be the highest-altitude lizard species in the world, and they have been added to the IUCN list of threatened species. Living in the QTP with hypoxic, arid, natural conditions, the lizards presented a unique pattern of gut virome, which could provide both positive and negative effects, such as the enrichment of functional genes and the dissemination of antibiotic resistance genes (ARGs). This work provides the foundation for further research on the gut virome in these endangered lizard species and other cold-blooded and highland-dwelling animals, contributing to the maintenance of ecological balance on the plateau.}, }
@article {pmid35196800, year = {2022}, author = {Xiao, G and Cai, Z and Guo, Q and Ye, T and Tang, Y and Guan, P and Zhang, J and Ou, M and Fu, X and Ren, L and Yu, M and Wang, Z and Liu, L and Yang, L and Zhang, G}, title = {Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0190121}, pmid = {35196800}, issn = {2165-0497}, mesh = {Adult ; Bronchoalveolar Lavage Fluid ; Drug Resistance, Bacterial ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Lung/*microbiology ; Male ; *Metagenome ; Metagenomics/*methods ; Microbiota/drug effects/*physiology ; Mycobacterium tuberculosis ; RNA, Ribosomal, 16S/genetics ; Sputum ; Tuberculosis, Pulmonary/drug therapy/*metabolism ; }, abstract = {The microbiota plays an important role in human health and disease development. The lung microbiota profile in pulmonary tuberculosis (TB) patients and the effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively. This study primarily aimed to determine the lung microbiota profile associated with pulmonary TB and characterize the longitudinal changes during anti-TB treatment. A total of 53 participants, comprising 8 healthy individuals, 12 untreated pulmonary TB patients, 15 treated pulmonary TB patients, 11 cured pulmonary TB patients, and 7 lung cancer patients, were recruited in the present study. Bronchioalveolar lavage fluid (BALF) samples were collected from the above participants, and throat swabs were taken from healthy individuals. Microbiomes in the samples were examined using metagenomic next-generation sequencing (mNGS). Differences in microbiota profiles were determined through a comparison of the indicated groups. Our findings indicated that the BALF samples displayed decreased richness and diversity of the microbiota compared to those of the throat swab samples, and these two kinds of samples exhibited obvious separation on principal-coordinate analysis (PCoA) plots. Untreated pulmonary TB patients displayed a unique lung microbiota signature distinct from that of healthy individuals and lung cancer patients. Our data first demonstrated that anti-TB treatment with first-line drugs increases alpha diversity and significantly affects the beta diversity of the lung microbiota, while it also induces antibiotic resistance genes (ARGs). IMPORTANCE Characterization of the lung microbiota could lead to a better understanding of the pathogenesis of pulmonary TB. Here, we applied the metagenomic shotgun sequencing instead of 16S rRNA sequencing method to characterize the lung microbiota using the BALF samples instead of sputum. We found that alterations in the lung microbiota are associated with TB infection and that anti-TB treatment significantly affects the alpha and beta diversity of the lung microbiota in pulmonary TB patients. These findings could help us better understand TB pathogenesis.}, }
@article {pmid35195242, year = {2022}, author = {Díaz-Cruz, GA and Cassone, BJ}, title = {Changes in the phyllosphere and rhizosphere microbial communities of soybean in the presence of pathogens.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {3}, pages = {}, doi = {10.1093/femsec/fiac022}, pmid = {35195242}, issn = {1574-6941}, mesh = {*Microbiota ; *Mycobiome ; Rhizosphere ; Soil Microbiology ; Soybeans ; }, abstract = {Soybean (Glycine max L.) is host to an array of foliar- and root-infecting pathogens that can cause significant yield losses. To provide insights into the roles of microorganisms in disease development, we evaluated the bacterial and fungal communities associated with the soybean rhizosphere and phyllosphere. For this, leaf and soil samples of healthy, Phytophthora sojae-infected and Septoria glycines-infected plants were sampled at three stages during the production cycle, and then subjected to 16S and Internal Transcribed Spacer (ITS) amplicon sequencing. The results indicated that biotic stresses did not have a significant impact on species richness and evenness regardless of growth stage. However, the structure and composition of soybean microbial communities were dramatically altered by biotic stresses, particularly for the fungal phyllosphere. Additionally, we cataloged a variety of microbial genera that were altered by biotic stresses and their associations with other genera, which could serve as biological indicators for disease development. In terms of soybean development, the rhizosphere and phyllosphere had distinct microbial communities, with the fungal phyllosphere most influenced by growth stage. Overall, this study characterized the phyllosphere and rhizosphere microbial communities of soybean, and described the impact of pathogen infection and plant development in shaping these bacterial and fungal communities.}, }
@article {pmid35194028, year = {2022}, author = {Tamburini, FB and Maghini, D and Oduaran, OH and Brewster, R and Hulley, MR and Sahibdeen, V and Norris, SA and Tollman, S and Kahn, K and Wagner, RG and Wade, AN and Wafawanaka, F and Gómez-Olivé, FX and Twine, R and Lombard, Z and ,  and Hazelhurst, S and Bhatt, AS}, title = {Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {926}, pmid = {35194028}, issn = {2041-1723}, support = {K43 TW010698/TW/FIC NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; 085477/Z/08/Z/WT_/Wellcome Trust/United Kingdom ; R25 TW009338/TW/FIC NIH HHS/United States ; U54 HG006938/HG/NHGRI NIH HHS/United States ; 058893/Z/99/A/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 085477/B/08/Z/WT_/Wellcome Trust/United Kingdom ; 069683/Z/02/Z/WT_/Wellcome Trust/United Kingdom ; P30 CA124435/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; *Microbiota ; Rural Population ; South Africa ; }, abstract = {Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.}, }
@article {pmid35189961, year = {2022}, author = {Coker, OO and Liu, C and Wu, WKK and Wong, SH and Jia, W and Sung, JJY and Yu, J}, title = {Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {35}, pmid = {35189961}, issn = {2049-2618}, mesh = {*Adenoma/diagnosis ; Carcinogenesis ; *Colorectal Neoplasms/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Gut microbiota contributes to colorectal cancer (CRC) pathogenesis through microbes and their metabolites. The importance of microbiota-associated metabolites in colorectal carcinogenesis highlights the need to investigate the gut metabolome along the adenoma-carcinoma sequence to determine their mechanistic implications in the pathogenesis of CRC. To date, how and which microbes and metabolites interactively promote early events of CRC development are still largely unclear. We aim to determine gut microbiota-associated metabolites and their linkage to colorectal carcinogenesis.<br><br>RESULTS: We performed metabolomics and metagenomics profiling on fecal samples from 386 subjects including 118 CRC patients, 140 colorectal adenomas (CRA) patients and 128 healthy subjects as normal controls (NC). We identified differences in the gut metabolite profiles among NC, CRA and CRC groups by partial least squares-discriminant and principal component analyses. Among the altered metabolites, norvaline and myristic acid showed increasing trends from NC, through CRA, to CRC. CRC-associated metabolites were enriched in branched-chain amino acids, aromatic amino acids and aminoacyl-tRNA biosynthesis pathways. Moreover, metabolites marker signature (twenty metabolites) classified CRC from NC subjects with an area under the curve (AUC) of 0.80, and CRC from CRA with an AUC of 0.79. Integrative analyses of metabolomics and metagenomics profiles demonstrated that the relationships among CRC-associated metabolites and bacteria were altered across CRC stages; certain associations exhibited increasing or decreasing strengths while some were reversed from negative to positive or vice versa. Combinations of gut bacteria with the metabolite markers improved their diagnostic performances; CRC vs NC, AUC: 0.94; CRC vs CRA, AUC 0.92; and CRA vs NC, AUC: 0.86, indicating a potential for early diagnosis of colorectal neoplasia.<br><br>CONCLUSIONS: This study underscores potential early-driver metabolites in stages of colorectal tumorigenesis. The Integrated metabolite and microbiome analysis demonstrates that gut metabolites and their association with gut microbiota are perturbed along colorectal carcinogenesis. Fecal metabolites can be utilized, in addition to bacteria, for non-invasive diagnosis of colorectal neoplasia. Video Abstract.}, }
@article {pmid35188453, year = {2022}, author = {Forde, TL and Dennis, TPW and Aminu, OR and Harvey, WT and Hassim, A and Kiwelu, I and Medvecky, M and Mshanga, D and Van Heerden, H and Vogel, A and Zadoks, RN and Mmbaga, BT and Lembo, T and Biek, R}, title = {Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity.}, journal = {Microbial genomics}, volume = {8}, number = {2}, pages = {}, pmid = {35188453}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Anthrax/epidemiology/microbiology/veterinary ; *Bacillus anthracis/genetics ; Genomics ; Metagenomics ; Phylogeography ; }, abstract = {Genomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogen's evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide SNPs among 73 B. anthracis isolates derived from 33 livestock carcasses sampled over 1 year throughout the Ngorongoro Conservation Area, Tanzania, a region hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique B. anthracis genotypes (i.e. SNP profiles) within the study area. However, phylogeographical structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for B. anthracis, with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence, as well as co-infection.}, }
@article {pmid35187178, year = {2022}, author = {Sun, RX and Huang, WJ and Xiao, Y and Wang, DD and Mu, GH and Nan, H and Ni, BR and Huang, XQ and Wang, HC and Liu, YF and Fu, Q and Zhao, JX}, title = {Shenlian (SL) Decoction, a Traditional Chinese Medicine Compound, May Ameliorate Blood Glucose via Mediating the Gut Microbiota in db/db Mice.}, journal = {Journal of diabetes research}, volume = {2022}, number = {}, pages = {7802107}, pmid = {35187178}, issn = {2314-6753}, mesh = {Animals ; Blood Glucose/*drug effects/metabolism ; China ; Coptis/*metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects/physiology ; Medicine, Chinese Traditional/methods/*standards ; Mice ; Mice, Inbred C57BL/metabolism ; Panax/*metabolism ; }, abstract = {Shenlian (SL) decoction is a herbal formula composed of Coptis and ginseng, of which berberine and ginsenoside are the main constituents. Even though SL decoction is widely used in treating diabetes in China, the mechanism of its antidiabetes function still needs further study. Gut microbiota disorder is one of the important factors that cause diabetes. To explore the effect of SL decoction on intestinal microbiota, gut microbiota of mice was analyzed by sequencing the gut bacterial 16S rRNA V3+V4 region and metagenomics. In this study, results demonstrated that SL decoction had a better hypoglycemic effect and β cell protection effect than either ginseng or Coptis chinensis. Alpha diversity analysis showed that all interventions with ginseng, Coptis, and SL decoction could reverse the increased diversity and richness of gut microbiota in db/db mice. PCoA analysis showed oral SL decoction significantly alters gut microbiota composition in db/db mice. 395 OTUs showed significant differences after SL treatment, of which 37 OTUs enriched by SL decoction showed a significant negative correlation with FBG, and 204 OTUs decreased by SL decoction showed a significant positive correlation with FBG. Results of KEGG analysis and metagenomic sequencing showed that SL decoction could reduce the Prevotellaceae, Rikenellaceae, and Helicobacteraceae, which were related to lipopolysaccharide biosynthesis, riboflavin metabolism, and peroxisome, respectively. It could also upregulate the abundance of Bacteroidaceae, which contributed to the metabolism of starch and sucrose as well as pentose-glucuronate interconversions. In the species level, SL decoction significantly upregulates the relative abundance of Bacteroides_acidifaciens which showed a significant negative correlation with FBG and was reported to be a potential agent for modulating metabolic disorders such as diabetes and obesity. In conclusion, SL decoction was effective in hypoglycemia and its mechanism may be related to regulating gut microbiota via upregulating Bacteroides_acidifaciens.}, }
@article {pmid35183223, year = {2022}, author = {Yang, M and Liu, Q and Dai, M and Peng, R and Li, X and Zuo, W and Gou, J and Zhou, F and Yu, S and Liu, H and Huang, M}, title = {FOXQ1-mediated SIRT1 upregulation enhances stemness and radio-resistance of colorectal cancer cells and restores intestinal microbiota function by promoting β-catenin nuclear translocation.}, journal = {Journal of experimental &amp; clinical cancer research : CR}, volume = {41}, number = {1}, pages = {70}, pmid = {35183223}, issn = {1756-9966}, mesh = {Animals ; Cell Line, Tumor ; Colorectal Neoplasms/*genetics/pathology ; Female ; Forkhead Transcription Factors/*metabolism ; Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Mice, Nude ; Neoplastic Stem Cells/*metabolism ; Sirtuin 1/*metabolism ; Up-Regulation ; beta Catenin/*metabolism ; }, abstract = {BACKGROUND: Resistance of colorectal cancer (CRC) cells to radiotherapy considerably contributes to poor clinical outcomes of CRC patients. Microarray profiling in this study revealed the differentially expressed forkhead box Q1 (FOXQ1) in CRC, and thus we aimed to illustrate the role of FOXQ1 in CRC by modulating stemness and radio-resistance of CRC cells.<br><br>METHODS: CRC and adjacent normal tissues were collected from CRC patients, and the correlation between FOXQ1 expression and CRC prognosis was analyzed. Subsequently, we determined the expression of FOXQ1, sirtuin 1 (SIRT1) and β-catenin in CRC tissues and cell lines. The binding affinity between FOXQ1 and SIRT1 and that between SIRT1 and β-catenin were validated with luciferase reporter gene, Co-IP and ChIP assays. Following a metagenomics analysis of CRC intestinal microbiota, the effects of the FOXQ1/SIRT1/β-catenin axis on CRC stem cell phenotypes and radio-resistance was evaluated in vitro and in vivo through manipulation of gene expression. Besides, mouse feces were collected to examine changes in intestinal microbiota.<br><br>RESULTS: FOXQ1 was highly expressed in CRC tissues and cells and positively correlated with poor prognosis of CRC patients. FOXQ1 overexpression contributed to resistance of CRC cells to radiation. Knockdown of FOXQ1 inhibited the stemness of CRC cells and reversed their radio-resistance. FOXQ1 enhanced the transcriptional expression of SIRT1, and SIRT1 enhanced the expression and nuclear translocation of β-catenin. Knockdown of FOXQ1 repressed SIRT1 expression, thus reducing the stemness and radio-resistance of CRC cells. Moreover, FOXQ1 knockdown suppressed CRC xenograft formation in xenograft-bearing nude mice through inhibiting SIRT1 and β-catenin to reduce the content of pathological bacteria that were up-regulated in CRC.<br><br>CONCLUSION: FOXQ1-mediated SIRT1 upregulation augments expression and nuclear translocation of β-catenin and benefits CRC-related intestinal pathological bacterial, thereby enhancing the stemness and radio-resistance of CRC cells.}, }
@article {pmid35181661, year = {2022}, author = {Johansen, J and Plichta, DR and Nissen, JN and Jespersen, ML and Shah, SA and Deng, L and Stokholm, J and Bisgaard, H and Nielsen, DS and Sørensen, SJ and Rasmussen, S}, title = {Genome binning of viral entities from bulk metagenomics data.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {965}, pmid = {35181661}, issn = {2041-1723}, mesh = {Bacteriophages/*classification/genetics ; Gastrointestinal Microbiome/*genetics/physiology ; Gastrointestinal Tract/*virology ; Genome, Viral/genetics ; Humans ; Metagenome/*genetics ; Metagenomics ; Virome/*genetics/physiology ; }, abstract = {Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.}, }
@article {pmid35181108, year = {2022}, author = {Zhang, J and Liu, S and Sun, H and Jiang, Z and Xu, Y and Mao, J and Qian, B and Wang, L and Mao, J}, title = {Metagenomics-based insights into the microbial community profiling and flavor development potentiality of baijiu Daqu and huangjiu wheat Qu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {152}, number = {}, pages = {110707}, doi = {10.1016/j.foodres.2021.110707}, pmid = {35181108}, issn = {1873-7145}, mesh = {Amylases ; Fermentation ; Metabolic Networks and Pathways ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Daqu and wheat Qu are saccharification and fermenting agents in Chinese huangjiu and baijiu production. This study aimed to investigate the difference between Daqu and wheat Qu in physicochemical indices, microbial communities, functional genes, and the metabolic network of key microbes responsible for flavor synthesis by whole-metagenome sequencing and metabolite analysis. Herein, physicochemical indices indicated that compared with wheat Qu, Daqu exhibited higher protease and cellulase activity and acidity, and lower glucoamylase and amylase enzyme activity. Metagenomic sequencing reveals that although Daqu and wheat Qu community composition have significant differences at species level, they have similar functional genes. Daqu were enriched in Pediococcus pentosaceus, Weissella paramesenteroides, Rasamsonia emersonii and Byssochlamys spectabilis (22.48% of the total abundance), while wheat Qu harbored greater abundances of Saccharopolyspora (54.78%, Saccharopolyspora rectivirgula, Saccharopolyspora shandongensis, Saccharopolyspora hirsuta, Saccharopolyspora spinose, and Saccharopolyspora erythraea). From a functional perspective, the important functions of Daqu and wheat Qu are both amino acid metabolism and carbohydrate metabolism. Meanwhile, a combined analysis among microbiota, functional genes, and dominant flavors indicated S. shandongensis, S. rectivirgula, and S. spinose might be the main contributor to the synthesis of flavor compounds in wheat Qu, while R. emersonii, W. paramesenteroides, Leuconostoc citreum, Leuconostoc mesenteroides, Weissella cibaria and P. pentosaceus may make the greatest contribution to flavor compounds synthesis in Daqu. This study reveals the microbial and functional dissimilarities of Daqu and wheat Qu, and helps elucidating different metabolic roles of microbes during flavor formation.}, }
@article {pmid35177633, year = {2022}, author = {Schweitzer, HD and Smith, HJ and Barnhart, EP and McKay, LJ and Gerlach, R and Cunningham, AB and Malmstrom, RR and Goudeau, D and Fields, MW}, title = {Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {7}, pmid = {35177633}, issn = {2055-5008}, mesh = {*Coal ; Metagenomics ; Methane ; *Microbiota ; Sulfates ; }, abstract = {Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways was observed but with a predominance of aerobic dioxygenases. The putative low-molecular-weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study-subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes-offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.}, }
@article {pmid35172890, year = {2022}, author = {Zhou, Z and Tran, PQ and Breister, AM and Liu, Y and Kieft, K and Cowley, ES and Karaoz, U and Anantharaman, K}, title = {METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {33}, pmid = {35172890}, issn = {2049-2618}, support = {T15 LM007359/LM/NLM NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genome, Microbial ; Humans ; Lakes ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling.<br><br>RESULTS: We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric "MW-score" (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut.<br><br>CONCLUSION: METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC . Video abstract.}, }
@article {pmid35171009, year = {2022}, author = {Dong, B and Lin, X and Jing, X and Hu, T and Zhou, J and Chen, J and Xiao, L and Wang, B and Chen, Z and Liu, J and Hu, Y and Liu, G and Liu, S and Liu, J and Wei, W and Zou, Y}, title = {A Bacterial Genome and Culture Collection of Gut Microbial in Weanling Piglet.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0241721}, pmid = {35171009}, issn = {2165-0497}, support = {201918/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Male ; Metagenomics ; Phylogeny ; Swine/growth &amp; development/*microbiology ; }, abstract = {The microbiota hosted in the pig gastrointestinal tract are important to health of this biomedical model. However, the individual species and functional repertoires that make up the pig gut microbiome remain largely undefined. Here we comprehensively investigated the genomes and functions of the piglet gut microbiome using culture-based and metagenomics approaches. A collection included 266 cultured genomes and 482 metagenome-assembled genomes (MAGs) that were clustered to 428 species across 10 phyla was established. Among these clustered species, 333 genomes represent potential new species. Less matches between cultured genomes and MAGs revealed a substantial bias for the acquisition of reference genomes by the two strategies. Glycoside hydrolases was the dominant category of carbohydrate-active enzymes. Four-hundred forty-five secondary metabolite biosynthetic genes were predicted from 292 genomes with bacteriocin being the most. Pan genome analysis of Limosilactobacillus reuteri uncover the biosynthesis of reuterin was strain-specific and the production was experimentally determined. This study provides a comprehensive view of the microbiome composition and the function landscape of the gut of weanling piglets and a valuable bacterial resource for further experimentations. IMPORTANCE The microorganism communities resided in mammalian gastrointestinal tract impacted the health and disease of the host. Our study complements metagenomic analysis with culture-based approach to establish a bacteria and genome collection and comprehensively investigate the microbiome composition and function of the gut of weanling piglets. We provide a valuable resource for further study of gut microbiota of weanling piglet and development of probiotics for prevention of disease.}, }
@article {pmid35167588, year = {2022}, author = {Abdill, RJ and Adamowicz, EM and Blekhman, R}, title = {Public human microbiome data are dominated by highly developed countries.}, journal = {PLoS biology}, volume = {20}, number = {2}, pages = {e3001536}, pmid = {35167588}, issn = {1545-7885}, support = {R35 GM128716/GM/NIGMS NIH HHS/United States ; }, mesh = {Asia ; Bangladesh ; Canada ; Developed Countries ; Europe ; Gastrointestinal Microbiome/*genetics ; Genomics/*methods/statistics &amp; numerical data ; Geography ; Humans ; India ; Metagenome/*genetics ; Metagenomics/*methods/statistics &amp; numerical data ; Microbiota/*genetics ; Pakistan ; United States ; }, abstract = {The importance of sampling from globally representative populations has been well established in human genomics. In human microbiome research, however, we lack a full understanding of the global distribution of sampling in research studies. This information is crucial to better understand global patterns of microbiome-associated diseases and to extend the health benefits of this research to all populations. Here, we analyze the country of origin of all 444,829 human microbiome samples that are available from the world's 3 largest genomic data repositories, including the Sequence Read Archive (SRA). The samples are from 2,592 studies of 19 body sites, including 220,017 samples of the gut microbiome. We show that more than 71% of samples with a known origin come from Europe, the United States, and Canada, including 46.8% from the US alone, despite the country representing only 4.3% of the global population. We also find that central and southern Asia is the most underrepresented region: Countries such as India, Pakistan, and Bangladesh account for more than a quarter of the world population but make up only 1.8% of human microbiome samples. These results demonstrate a critical need to ensure more global representation of participants in microbiome studies.}, }
@article {pmid35162506, year = {2022}, author = {Zambrano-Romero, A and Ramirez-Villacis, DX and Trueba, G and Sierra-Alvarez, R and Leon-Reyes, A and Cardenas, P and Ochoa-Herrera, V}, title = {Dynamics of Microbial Communities during the Removal of Copper and Zinc in a Sulfate-Reducing Bioreactor with a Limestone Pre-Column System.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {3}, pages = {}, pmid = {35162506}, issn = {1660-4601}, mesh = {Bioreactors/microbiology ; Calcium Carbonate ; Copper ; *Microbiota ; *Sulfates/chemistry ; Zinc ; }, abstract = {Biological treatment using sulfate-reducing bacteria (SRB) is a promising approach to remediate acid rock drainage (ARD). Our purpose was to assess the performance of a sequential system consisting of a limestone bed filter followed by a sulfate-reducing bioreactor treating synthetic ARD for 375 days and to evaluate changes in microbial composition. The treatment system was effective in increasing the pH of the ARD from 2.7 to 7.5 and removed total Cu(II) and Zn(II) concentrations by up to 99.8% and 99.9%, respectively. The presence of sulfate in ARD promoted sulfidogenesis and changed the diversity and structure of the microbial communities. Methansarcina spp. was the most abundant amplicon sequence variant (ASV); however, methane production was not detected. Biodiversity indexes decreased over time with the bioreactor operation, whereas SRB abundance remained stable. Desulfobacteraceae, Desulfocurvus, Desulfobulbaceae and Desulfovibrio became more abundant, while Desulfuromonadales, Desulfotomaculum and Desulfobacca decreased. Geobacter and Syntrophobacter were enriched with bioreactor operation time. At the beginning, ASVs with relative abundance <2% represented 65% of the microbial community and 21% at the end of the study period. Thus, the results show that the microbial community gradually lost diversity while the treatment system was highly efficient in remediating ARD.}, }
@article {pmid35156268, year = {2022}, author = {Wang, H and Li, J and Liang, X and Tao, S and Wu, Z and Wei, G}, title = {Taxonomic and functional diversity of Dendrobium officinale microbiome in Danxia habitat.}, journal = {Journal of applied microbiology}, volume = {132}, number = {5}, pages = {3758-3770}, doi = {10.1111/jam.15488}, pmid = {35156268}, issn = {1365-2672}, mesh = {*Basidiomycota/genetics ; *Dendrobium/genetics/microbiology ; Humans ; Metagenomics ; *Microbiota/genetics ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil Microbiology ; }, abstract = {AIMS: Microbial communities that inhabit plants are crucial for plant survival and well-being including growth in stressful environments. The medicinal plant, Dendrobium officinale grows in the barren soils of the Danxia Habitat. However, the microbiome composition and functional potential for growth of this plant in this environment are still unexplored.<br><br>METHODS AND RESULTS: In this study, we analysed the taxonomic and functional diversity of the D. officinale Microbiome by metagenomic sequencing of both rhizosphere and endosphere samples. A total of 155 phyla, 122 classes, 271 orders, 620 families and 2194 genera were identified from all samples. The rhizospheric microbes (DXRh) were mainly composed of Proteobacteria and Acidobacteria, while Basidiomycota and Ascomycota were the most dominant phyla in root endosphere (DXRo) and stem endosphere (DXS), respectively. Most of the dominant microbial communities had been reported to have diverse functional potentials that can help plant growth and development in stressful and nutrient-deprived ecological environmental. These include plant growth promoting rhizobacteria (PGPR) such as Massilia, Pseudomonas, Bradyrhizobium, Klebsiella, Streptomyces, Leclercia, Paenibacillus, Frankia and Enterobacter in the DXRh, Tulasnella and Serendipita in the DXRo, Colletotrichum and Burkholderia in the DXS and Paraburkholderia, Rhizophagus and Acetobacter in endosphere. Analysis using the KEGG, eggNOG and CAZy databases showed that metabolic pathways such as carbohydrate metabolism, amino acid metabolism, energy metabolism, genetic information processing and environmental information processing are significantly abundant, which may be related to the survival, growth and development of D. officinale in a stressful environment.<br><br>CONCLUSIONS: We speculated that the microbial community with diverse taxonomic structures and metabolic functions inhabiting in different niches of plants supports the survival and growth of D. officinale in the stressful environment of Danxia Habitat.<br><br>This study provided an important data resource for microbes associated with D. officinale and theoretical foundation for further studies.}, }
@article {pmid35154087, year = {2021}, author = {Song, L and Huang, Y and Liu, G and Li, X and Xiao, Y and Liu, C and Zhang, Y and Li, J and Xu, J and Lu, S and Ren, Z}, title = {A Novel Immunobiotics Bacteroides dorei Ameliorates Influenza Virus Infection in Mice.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {828887}, pmid = {35154087}, issn = {1664-3224}, mesh = {Animals ; Bacteroides/*immunology ; Biomarkers ; Brain-Gut Axis/immunology ; Cytokines/blood/metabolism ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/immunology ; Host-Pathogen Interactions/*immunology ; Immunomodulation ; Influenza A virus/*physiology ; Interferons/metabolism ; Metagenome ; Metagenomics/methods ; Mice ; Microbial Interactions/*immunology ; Orthomyxoviridae Infections/*immunology/metabolism/pathology/*virology ; Probiotics ; Quercetin/metabolism ; Viral Load ; }, abstract = {Objective: Probiotics can modulate immune responses to resist influenza infection. This study aims to evaluate the anti-viral efficacy of B. dorei.<br><br>Methods: C57BL/6J mice were infected with influenza virus together with treatment of PBS vehicle, B. dorei, or oseltamivir respectively. Anti-influenza potency of B. dorei and the underlying mechanism were determined by measuring survival rate, lung viral load and pathology, gene expression and production of cytokines and chemokines, and analysis of gut microbiota.<br><br>Results: Administration of B. dorei increased (by 30%) the survival of influenza-infected mice, and improved their weight loss, lung pathology, lung index, and colon length compared to the vehicle control group. B. dorei treatment reduced (by 61%) the viral load of lung tissue and increased expression of type 1 interferon more rapidly at day 3 postinfection. At day 7 postinfection, B. dorei-treated mice showed lower local (lung) and systemic (serum) levels of interferon and several proinflammatory cytokines or chemokines (IL-1β, IL-6, TNF-α, IL-10, MCP-1 and IP-10) with a efficacy comparable to oseltamivi treatment. B. dorei treatment also altered gut microbiota as indicated by increased levels of Bacteroides, Prevotella, and Lactobacillus and decreased levels of Escherichia, Shigella, and Parabacteroides.<br><br>Conclusion: B. dorei has anti-influenza effect. Its working mechanisms involve promoting earlier interferon expression and down-regulating both local and systemic inflammatory response. B. dorei changes the composition of gut microbiota, which may also contribute to its beneficial effects.}, }
@article {pmid35152539, year = {2022}, author = {Klein, F and Wellhöner, F and Plumeier, I and Kahl, S and Chhatwal, P and Vital, M and Voigtländer, T and Pieper, DH and Manns, MP and Lenzen, H and Solbach, P and Heidrich, B}, title = {The biliary microbiome in ischaemic-type biliary lesions can be shaped by stenting but is resilient to antibiotic treatment.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {42}, number = {5}, pages = {1070-1083}, doi = {10.1111/liv.15194}, pmid = {35152539}, issn = {1478-3231}, support = {01EO1302//Bundesministerium für Bildung und Forschung/ ; EXC 2155 "RESIST" - Project ID 390874280//Deutsche Forschungsgemeinschaft/ ; DZIF Academy//Deutsches Zentrum für Infektionsforschung/ ; Initiative on Aging and Metabolic Programming//Helmholtz-Gemeinschaft/ ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; *Biliary Tract ; Humans ; Ischemia ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {This study aims to characterize the biliary microbiome as neglected factor in patients with ischaemic-type biliary lesions (ITBL) after liver transplantation. Therefore, the V1-V2 region of the 16S rRNA gene was sequenced in 175 bile samples. Samples from patients with anastomotic strictures (AS) served as controls. Multivariate analysis and in silico metagenomics were applied cross-sectionally and longitudinally. The microbial community differed significantly between ITBL and AS in terms of alpha and beta diversity. Both, antibiotic treatment and stenting were associated independently with differences in the microbial community structure. In contrast to AS, in ITBL stenting was associated with pronounced differences in the biliary microbiome, whereas no differences associated with antibiotic treatment could be observed in ITBL contrasting the pronounced differences found in AS. Bacterial pathways involved in the production of antibacterial metabolites were increased in ITBL with antibiotic treatment. After liver transplantation, the biliary tract harbours a complex microbial community with significant differences between ITBL and AS. Fundamental changes in the microbial community in ITBL can be achieved with biliary stenting. However, the effect of antibiotic treatment in ITBL was minimal. Therefore, antibiotics should be administered wisely in order to reduce emerging resistance of the biliary microbiome towards external antibiotics.}, }
@article {pmid35151268, year = {2022}, author = {Da Silva, K and Guilly, S and Thirion, F and Le Chatelier, E and Pons, N and Roume, H and Quinquis, B and Ehrlich, SD and Bekkat, N and Mathiex-Fortunet, H and Sokol, H and Doré, J}, title = {Long-term diosmectite use does not alter the gut microbiota in adults with chronic diarrhea.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {54}, pmid = {35151268}, issn = {1471-2180}, mesh = {Adolescent ; Adult ; Bacteria/classification/genetics ; Chronic Disease/therapy ; Diarrhea/*drug therapy ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics ; Humans ; Male ; *Metagenome ; Middle Aged ; Silicates/*therapeutic use ; Young Adult ; }, abstract = {BACKGROUND: Diosmectite, a natural colloidal clay, has been used worldwide for a number of approved indications, including the treatment of chronic functional diarrhea. Here, we used high-resolution whole metagenome shotgun sequencing to assess the impact of a 5 weeks administration of diosmectite (3 g/sachet, 3 sachets/day) on the fecal microbiota of 35 adults with functional chronic diarrhea.<br><br>RESULTS: Gut microbiota was not impacted by diosmectite administration. In particular, richness remained stable and no microbial species displayed a significant evolution. Segregating patients either by diosmectite response (non responder, early responder, late responder) or by nationality (Great-Britain or Netherlands) yielded the same results.<br><br>CONCLUSION: We concluded that no microbiota-related physiological alterations are expected upon long-term treatment with diosmectite.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov NCT03045926.}, }
@article {pmid35151255, year = {2022}, author = {Qi, Q and Liu, YN and Lv, SY and Wu, HG and Zhang, LS and Cao, Z and Liu, HR and Wang, XM and Wu, LY}, title = {Gut microbiome alterations in colitis rats after moxibustion at bilateral Tianshu acupoints.}, journal = {BMC gastroenterology}, volume = {22}, number = {1}, pages = {62}, pmid = {35151255}, issn = {1471-230X}, support = {2015CB554501//National Basic Research Program of China (973 program)/ ; 20ZR1453100//Natural Science Foundation of Shanghai/ ; 81473758//National Natural Science Foundation of China/ ; 81674074//National Natural Science Foundation of China/ ; ZY(2018-2020)-CCCX-2004-01//Three-year Action Plan Project of Shanghai Traditional Chinese Medicine Development/ ; }, mesh = {Acupuncture Points ; Animals ; *Colitis/chemically induced/therapy ; *Colitis, Ulcerative/therapy ; Dextran Sulfate ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Male ; *Moxibustion ; Rats ; }, abstract = {BACKGROUND: The pathogenesis of ulcerative colitis (UC) is closely related to the gut microbiota. Moxibustion has been used to improve the inflammation and gastrointestinal dysfunctions in gastrointestinal disorders such as UC. In this study, we investigated whether moxibustion could improve the gut microbial dysbiosis induced by dextran sulphate sodium.<br><br>METHODS: Twenty-five male rats were randomly assigned into five groups. The UC rat model was established by administering DSS solution. The rats in the moxibustion and normal rats with moxibustion groups were treated with moxibustion at Tianshu (bilateral, ST25) points, and the mesalazine group rats were treated with mesalazine once daily for 7 consecutive days. Disease activity index (DAI) and haematoxylin and eosin staining were used to evaluate the effect of moxibustion. Gut microbiota profiling was conducted by metagenomic high throughput sequencing technology. The gut microbiota composition, diversity and function were analyzed and compared using metagenomics methodologies.<br><br>RESULTS: The DAI scores and histopathology scores in the moxibustion and mesalazine groups were significantly decreased compared with the UC group (P < 0.01). Moxibustion treatment increased abundance levels of Bacteroidetes, Actinobacteria, Ascomycota, Synergistetes and decreased abundance of Firmicutes, Proteobacteria. At the genus level, the abundance of Bacteroides, Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2, were increased and Bacteroides_bacterium_H3, Parabacteroides, Porphyromonas, Alistipes, Parasutterella were decreased in the UC group in comparsion with those in the NG group. Moxibustion increased the abundance of Bacteroides and Bacteroides_bacterium_H3 and decreased Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2. In UC group, the specie Bacteroides_massiliensis was negatively (P < 0.05) correlated with IL-23, Bacteroides_eggerthii_CAG109 and Bacteroides_eggerthii were negatively (P < 0.05) correlated with TGF-β. And the species Prevotella_sp_CAG1031 and Bacteroides_bacterium_H2 were significant positively (P < 0.05) correlated with IL-23. In addition, compare with the normal group, genes involved in certain metabolic pathways, such as energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, were under-represented in the UC group, and these changes in the metabolic pathways could be reversed by moxibustion treatment and mesalazine treatment.<br><br>CONCLUSIONS: Our findings suggest that moxibustion treatment may protect the host from mucosal inflammation by modulating the intestinal microbiota community.}, }
@article {pmid35145519, year = {2022}, author = {Huang, Y and Zhu, N and Zheng, X and Liu, Y and Lu, H and Yin, X and Hao, H and Tan, Y and Wang, D and Hu, H and Liang, Y and Li, X and Hu, Z and Yin, Y}, title = {Intratumor Microbiome Analysis Identifies Positive Association Between Megasphaera and Survival of Chinese Patients With Pancreatic Ductal Adenocarcinomas.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {785422}, pmid = {35145519}, issn = {1664-3224}, mesh = {Aged ; Aged, 80 and over ; Animals ; Biomarkers ; Carcinoma, Pancreatic Ductal/*mortality/*pathology/therapy ; China ; Cytokines/metabolism ; Disease Models, Animal ; Dysbiosis ; Female ; Humans ; Immunohistochemistry ; Male ; *Megasphaera/classification/genetics ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Middle Aged ; Molecular Targeted Therapy ; Neoplasm Staging ; Pancreatic Neoplasms/*mortality/*pathology/therapy ; Prognosis ; Treatment Outcome ; *Tumor Microenvironment ; }, abstract = {Human tumors harbor a plethora of microbiota. It has been shown that the composition and diversity of intratumor microbiome are significantly associated with the survival of patients with pancreatic ductal adenocarcinoma (PDAC). However, the association in Chinese patients as well as the effect of different microorganisms on inhibiting tumor growth are unclear. In this study, we collected tumor samples resected from long-term and short-term PDAC survivors and performed 16S rRNA amplicon sequencing. We found that the microbiome in samples with different survival time were significantly different, and the differential bacterial composition was associated with the metabolic pathways in the tumor microenvironment. Furthermore, administration of Megasphaera, one of the differential bacteria, induced a better tumor growth inhibition effect when combined with the immune checkpoint inhibitor anti-programmed cell death-1 (anti-PD-1) treatment in mice bearing 4T1 tumor. These results indicate that specific intratumor microbiome can enhance the anti-tumor effect in the host, laying a foundation for further clarifying the underlying detailed mechanism.}, }
@article {pmid35145088, year = {2022}, author = {Tong, F and Wang, T and Gao, NL and Liu, Z and Cui, K and Duan, Y and Wu, S and Luo, Y and Li, Z and Yang, C and Xu, Y and Lin, B and Yang, L and Pauciullo, A and Shi, D and Hua, G and Chen, WH and Liu, Q}, title = {The microbiome of the buffalo digestive tract.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {823}, pmid = {35145088}, issn = {2041-1723}, mesh = {Animals ; Bacteria/genetics ; Cattle ; DNA, Bacterial ; Dietary Fiber/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Genome, Microbial ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; }, abstract = {Buffalo is an important livestock species. Here, we present a comprehensive metagenomic survey of the microbial communities along the buffalo digestive tract. We analysed 695 samples covering eight different sites in three compartments (four-chambered stomach, intestine, and rectum). We mapped ~85% of the raw sequence reads to 4,960 strain-level metagenome-assembled genomes (MAGs) and 3,255 species-level MAGs, 90% of which appear to correspond to new species. In addition, we annotated over 5.8 million nonredundant proteins from the MAGs. In comparison with the rumen microbiome of cattle, the buffalo microbiota seems to present greater potential for fibre degradation and less potential for methane production. Our catalogue of microbial genomes and the encoded proteins provides insights into microbial functions and interactions at distinct sites along the buffalo digestive tract.}, }
@article {pmid35136954, year = {2022}, author = {Ventolero, MF and Wang, S and Hu, H and Li, X}, title = {Computational analyses of bacterial strains from shotgun reads.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {2}, pages = {}, doi = {10.1093/bib/bbac013}, pmid = {35136954}, issn = {1477-4054}, mesh = {Bacteria/genetics ; Genome, Bacterial ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; }, abstract = {Shotgun sequencing is routinely employed to study bacteria in microbial communities. With the vast amount of shotgun sequencing reads generated in a metagenomic project, it is crucial to determine the microbial composition at the strain level. This study investigated 20 computational tools that attempt to infer bacterial strain genomes from shotgun reads. For the first time, we discussed the methodology behind these tools. We also systematically evaluated six novel-strain-targeting tools on the same datasets and found that BHap, mixtureS and StrainFinder performed better than other tools. Because the performance of the best tools is still suboptimal, we discussed future directions that may address the limitations.}, }
@article {pmid35136548, year = {2022}, author = {Li, F and Yang, S and Zhang, L and Qiao, L and Wang, L and He, S and Li, J and Yang, N and Yue, B and Zhou, C}, title = {Comparative metagenomics analysis reveals how the diet shapes the gut microbiota in several small mammals.}, journal = {Ecology and evolution}, volume = {12}, number = {1}, pages = {e8470}, pmid = {35136548}, issn = {2045-7758}, abstract = {The gut microbiomes of the host are large and complex communities, which helps to maintain homeostasis, improves digestive efficiency, and promotes the development of the immune system. The small mammals distributed in Sichuan Province are the most popular species for biodiversity research in Southwest China. However, the effects of different diets on the structure and function of the gut microbial community of these small mammals are poorly understood. In this study, whole-metagenome shotgun sequencing has been used to analyze the composition and functional structures of the gut microbiota of seven small mammals in Laojunshan National Nature Reserve, Sichuan Province, China. Taxonomic classification revealed that the most abundant phyla in the gut of seven small mammals were Bacteroides, Proteobacteria, and Firmicutes. Moreover, Hafnia, Lactobacillus, and Yersinia were the most abundant genus in the gut microbiomes of these seven species. At the functional level, we annotated a series of KEGG functional pathways, six Cazy categories, and 46,163 AROs in the gut microbiomes of the seven species. Comparative analysis found that the difference in the gut microbiomes between the Soricidea and Muridae concentrated on the increase in the F/B (Firmicutes/Bacteroides) ratio in the Soricidea group, probably driven by the high-fat and -calorie digestive requirements due to their insectivorous diet. The comparative functional profiling revealed that functions related to metabolism and carbohydrates were significantly more abundant in Muridae group, which may be attributed to their high carbohydrate digestion requirements caused by their herbivorous diet. These data suggested that different diets in the host may play an important role in shaping the gut microbiota, and lay the foundation for teasing apart the influences of heritable and environmental factors on the evolution of gut microbial communities.}, }
@article {pmid35135613, year = {2022}, author = {Zhang, XL and Deng, YP and Yang, T and Li, LY and Cheng, TY and Liu, GH and Duan, DY}, title = {Metagenomics of the midgut microbiome of Rhipicephalus microplus from China.}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {48}, pmid = {35135613}, issn = {1756-3305}, support = {31902294//the National Science Foundation of China/ ; 2018RS3085//the Planned Programme of Hunan Province Science and Technology Innovation/ ; KH2002001//the Training Programme for Excellent Young Innovators of Changsha/ ; 2020JJ5230//the Natural Science Foundation of Hunan Province, China/ ; 19A235//the Research Foundation of Education Bureau of Hunan Province, China/ ; }, mesh = {*Anaplasmosis ; Animals ; Cattle ; *Cattle Diseases ; Female ; Metagenomics ; *Microbiota/genetics ; *Rhipicephalus/genetics ; *Tick Infestations/veterinary ; *Tick-Borne Diseases ; }, abstract = {BACKGROUND: Ticks, which are ectoparasites of animals, may carry multiple pathogens. The cattle tick Rhipicephalus microplus is an important bovine parasite in China. However, the midgut microbiome of R. microplus from China has not been characterized via metagenomic methods.<br><br>METHODS: Rhipicephalus microplus were collected from cattle in the city of Changsha in Hunan province, China. The DNA of the midgut contents was extracted from fully engorged adult female R. microplus. A DNA library was constructed and sequenced using an Illumina HiSeq sequencing platform. SOAPdenovo software was used to assemble and analyze the clean data. The latent class analysis algorithm applied to system classification by MEGAN software was used to annotate the information on the species' sequences. DIAMOND software was used to compare unigenes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and functional annotation was carried out based on the results of the comparison.<br><br>RESULTS: The dominant phyla in the five samples were Firmicutes, Proteobacteria, and Actinobacteria. Streptococcus, Mycobacterium, Anaplasma, Enterococcus, Shigella, Lactobacillus, Brachyspira, Pseudomonas, Enterobacter, Bacillus, and Lactococcus were the dominant genera in the five samples. The endosymbiotic bacterium Wolbachia was also detected in all of the samples. Mycobacterium malmesburyense, Streptococcus pneumoniae, Anaplasma phagocytophilum, Enterococcus faecium, Shigella sonnei, Enterococcus faecalis, Lactobacillus casei, Brachyspira hampsonii, Pseudomonas syringae, Enterobacter cloacae, and Lactococcus garvieae were the dominant species in the five samples. In addition to these bacterial species, we also detected some eukaryotes, such as Rhizophagus irregularis, Enterospora canceri, Smittium culicis, Zancudomyces culisetae, Trachipleistophora hominis, and viruses such as orf virus, human endogenous retrovirus type W, enzootic nasal tumor virus of goats, bovine retrovirus CH15, and galidia endogenous retrovirus in all of the samples at the species level. The results of the annotated KEGG pathway predictions for the gene functions of the midgut microflora of R. microplus indicated genes involved in lipid and amino acid metabolism, infectious diseases (e.g., Streptococcus pneumonia infection, human granulocytic anaplasmosis, Shigella sonnei infection, Salmonella enterica infection, and pathogenic Escherichia coli infection), and cancer.<br><br>CONCLUSIONS: Our study revealed that the midgut microbiome of R. microplus is not only composed of a large number of bacteria, but that a portion also comprises eukaryotes and viruses. The data presented here enhance our understanding of this tick's midgut microbiome and provide fundamental information for the control of ticks and tick-borne diseases.}, }
@article {pmid35130125, year = {2022}, author = {Lawrence, D and Campbell, DE and Schriefer, LA and Rodgers, R and Walker, FC and Turkin, M and Droit, L and Parkes, M and Handley, SA and Baldridge, MT}, title = {Single-cell genomics for resolution of conserved bacterial genes and mobile genetic elements of the human intestinal microbiota using flow cytometry.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2029673}, pmid = {35130125}, issn = {1949-0984}, support = {R01 OD024917/OD/NIH HHS/United States ; RC2 DK116713/DK/NIDDK NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/classification/*cytology/*genetics/isolation &amp; purification ; Feces/microbiology ; Flow Cytometry/*methods ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Interspersed Repetitive Sequences ; Phylogeny ; Single-Cell Analysis ; }, abstract = {As our understanding of the importance of the human microbiota in health and disease grows, so does our need to carefully resolve and delineate its genomic content. 16S rRNA gene-based analyses yield important insights into taxonomic composition, and metagenomics-based approaches reveal the functional potential of microbial communities. However, these methods generally fail to directly link genetic features, including bacterial genes and mobile genetic elements, to each other and to their source bacterial genomes. Further, they are inadequate to capture the microdiversity present within a genus, species, or strain of bacteria within these complex communities. Here, we present a method utilizing fluorescence-activated cell sorting for isolation of single bacterial cells, amplifying their genomes, screening them by 16S rRNA gene analysis, and selecting cells for genomic sequencing. We apply this method to both a cultured laboratory strain of Escherichia coli and human stool samples. Our analyses reveal the capacity of this method to provide nearly complete coverage of bacterial genomes when applied to isolates and partial genomes of bacterial species recovered from complex communities. Additionally, this method permits exploration and comparison of conserved and variable genomic features between individual cells. We generate assemblies of novel genomes within the Ruminococcaceae family and the Holdemanella genus by combining several 16S rRNA gene-matched single cells, and report novel prophages and conjugative transposons for both Bifidobacterium and Ruminococcaceae. Thus, we demonstrate an approach for flow cytometric separation and sequencing of single bacterial cells from the human microbiota, which yields a variety of critical insights into both the functional potential of individual microbes and the variation among those microbes. This method definitively links a variety of conserved and mobile genomic features, and can be extended to further resolve diverse elements present in the human microbiota.}, }
@article {pmid35128832, year = {2022}, author = {Zeybel, M and Arif, M and Li, X and Altay, O and Yang, H and Shi, M and Akyildiz, M and Saglam, B and Gonenli, MG and Yigit, B and Ulukan, B and Ural, D and Shoaie, S and Turkez, H and Nielsen, J and Zhang, C and Uhlén, M and Borén, J and Mardinoglu, A}, title = {Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {9}, number = {11}, pages = {e2104373}, pmid = {35128832}, issn = {2198-3844}, support = {//Knut and Alice Wallenberg Foundation/ ; //ScandiBio Therapeutics AB, Sweden/ ; //PoLiMeR Innovative Training Network/ ; 812616//Marie Skłodowska-Curie/ ; //European Union's Horizon 2020/ ; sens2019031//Uppsala Multidisciplinary Center for Advanced Computational Science/ ; }, mesh = {Dysbiosis/genetics ; *Fatty Liver/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Metabolic dysfunction-associated fatty liver disease (MAFLD) is a complex disease involving alterations in multiple biological processes regulated by the interactions between obesity, genetic background, and environmental factors including the microbiome. To decipher hepatic steatosis (HS) pathogenesis by excluding critical confounding factors including genetic variants and diabetes, 56 heterogenous MAFLD patients are characterized by generating multiomics data including oral and gut metagenomics as well as plasma metabolomics and inflammatory proteomics data. The dysbiosis in the oral and gut microbiome is explored and the host-microbiome interactions based on global metabolic and inflammatory processes are revealed. These multiomics data are integrated using the biological network and HS's key features are identified using multiomics data. HS is finally predicted using these key features and findings are validated in a follow-up cohort, where 22 subjects with varying degree of HS are characterized.}, }
@article {pmid35127566, year = {2021}, author = {Yan, H and Qin, Q and Chen, J and Yan, S and Li, T and Gao, X and Yang, Y and Li, A and Ding, S}, title = {Gut Microbiome Alterations in Patients With Visceral Obesity Based on Quantitative Computed Tomography.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {823262}, pmid = {35127566}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome ; Humans ; Obesity, Abdominal ; Risk Factors ; Tomography, X-Ray Computed ; Uric Acid ; }, abstract = {The gut microbiota is crucial in the pathogenesis of obesity. Abdominal obesity is known to significantly increase the risk of metabolic syndrome and cardiovascular disease, so further study is needed to investigate the changes of intestinal microorganisms in patients with excessive visceral fat. In our study, 41 people (n = 41) with normal body mass index (BMI) (18.5 ≤ BMI < 23.9) were included and divided into the low visceral fat area (L-VFA) group (n = 23, VFA < 100 cm2) and the high visceral fat area (H-VFA) group (n = 18, VFA ≥ 100 cm2). Several clinical indicators of the H-VFA group were significantly higher than those of the L-VFA group, including the waist circumference (WC), the fasting blood glucose (FBG), the triglyceride (TG), the total cholesterol (TC), the low-density lipoprotein cholesterol (LDL), the serum uric acid (SUA), the white blood cell count (WBC), the blood neutrophil count (NEC), and the blood lymphocyte count (LYC). Using whole-genome shotgun sequencing, we found that the types of the intestinal microbiota of H-VFA patients were different from those of the L-VFA patients, with 18 bacteria enriched in the H-VFA group and nine bacteria in the L-VFA group. A total of 16 species of gut microbes showed a strong correlation with VFA, and Escherichia coli has the strongest correlation, followed by Mitsuokella unclassified, Bifidobacterium longum, Escherichia unclassified, Ruminococcus torques, Dialister succinatiphilus, Eubacterium hallii, and Ruminococcus gnavus. Compared to the VFA, only two species show a strong correlation with BMI and WC. Further functional genetic studies suggested that the degradation of short-chain fatty acids (SCFAs) and the generation of lipopolysaccharide (LPS) might be related to visceral fat accumulation. Together, visceral fat was more closely correlated with the gut microbiome compared with BMI and WC. It suggested an intrinsic connection between the gut microbiome and visceral fat and its related metabolic disorders. Specific microbial species and pathways associated with visceral fat accumulation might contribute to new targeted therapies for visceral fat and its metabolic disorders.}, }
@article {pmid35120121, year = {2022}, author = {Hernandez-Castro, LE and Villacís, AG and Jacobs, A and Cheaib, B and Day, CC and Ocaña-Mayorga, S and Yumiseva, CA and Bacigalupo, A and Andersson, B and Matthews, L and Landguth, EL and Costales, JA and Llewellyn, MS and Grijalva, MJ}, title = {Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.}, journal = {PLoS genetics}, volume = {18}, number = {2}, pages = {e1010019}, pmid = {35120121}, issn = {1553-7404}, support = {P20 GM130418/GM/NIGMS NIH HHS/United States ; R15 AI105749/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Animals ; Chagas Disease/*epidemiology/*genetics ; Disease Vectors ; Ecosystem ; Ecuador/epidemiology ; Gene Expression/genetics ; Gene Expression Profiling/methods ; Gene Flow ; Insect Vectors/genetics ; Metagenomics/methods ; Polymorphism, Single Nucleotide/genetics ; Population Density ; Rhodnius/*genetics/pathogenicity ; Transcriptome/genetics ; Trypanosoma cruzi/genetics ; }, abstract = {Accurate prediction of vectors dispersal, as well as identification of adaptations that allow blood-feeding vectors to thrive in built environments, are a basis for effective disease control. Here we adopted a landscape genomics approach to assay gene flow, possible local adaptation, and drivers of population structure in Rhodnius ecuadoriensis, an important vector of Chagas disease. We used a reduced-representation sequencing technique (2b-RADseq) to obtain 2,552 SNP markers across 272 R. ecuadoriensis samples from 25 collection sites in southern Ecuador. Evidence of high and directional gene flow between seven wild and domestic population pairs across our study site indicates insecticide-based control will be hindered by repeated re-infestation of houses from the forest. Preliminary genome scans across multiple population pairs revealed shared outlier loci potentially consistent with local adaptation to the domestic setting, which we mapped to genes involved with embryogenesis and saliva production. Landscape genomic models showed elevation is a key barrier to R. ecuadoriensis dispersal. Together our results shed early light on the genomic adaptation in triatomine vectors and facilitate vector control by predicting that spatially-targeted, proactive interventions would be more efficacious than current, reactive approaches.}, }
@article {pmid35118004, year = {2021}, author = {Yu, X and Jin, Y and Zhou, W and Xiao, T and Wu, Z and Su, J and Gao, H and Shen, P and Zheng, B and Luo, Q and Li, L and Xiao, Y}, title = {Rifaximin Modulates the Gut Microbiota to Prevent Hepatic Encephalopathy in Liver Cirrhosis Without Impacting the Resistome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {761192}, pmid = {35118004}, issn = {2235-2988}, mesh = {Escherichia coli ; *Gastrointestinal Microbiome/physiology ; *Hepatic Encephalopathy/drug therapy/etiology/prevention &amp; control ; Humans ; Liver Cirrhosis/complications/microbiology ; Prospective Studies ; Rifaximin/therapeutic use ; }, abstract = {The gut microbiota has an important role in the pathogenesis of hepatic encephalopathy(HE). Rifaximin, an intestinal non-absorbable antibacterial agent, is effective in the treatment of HE. However, whether long-term prophylactic use induces antibacterial resistance and its mechanism for treating HE remains unclear. This prospective study assessed the impact of 12 weeks rifaximin administration on the gut microbiota and resistome in cirrhotic patients. Fecal sampling was conducted 1 day before the first rifaximin administration and at Weeks 1, 2, 4, 6, 8, 10, 12 of the study. Thirty cirrhotic patients who were in remission from recurrent HE was enrolled to receive rifaximin (400mg TID for 12 weeks). Rifaximin improved hyperammonemia and cognitive function in the 21 patients who completed rifaximin treatment. The dynamic observations showed the gut microbiota diversity, composition and the number of resistance genes, plasmids, insertion sequences did not change significantly during the period(P>0.05). Metabolic pathways such as aromatic amino acids, tryptophan synthesis, urea cycle, and LPS synthesis reduced. No new antimicrobial resistance genes was emergenced. However, the number of aminoglycosides, rifamycin and phenolic resistance genes increased, whereas tetracycline, fosfomycin and cephamycin decreased (P<0.05). Changes in the abundance of E. coli, K. pneumoniae, and B. longum strains correlated with changes of resistance genes. Prophylactic use of rifaximin for 12 weeks improved hyperammonemia and neurophysiological function, maintained gut microbiota diversity, composition and did not change the overall resistome. Rifaximin altered expression of HE-related metabolic pathways. All of these effects could play a key role in preventing HE. Clinical Trial Registration: ChiCTR1900022234 (registered at the Chinese Clinical Trial Registry).}, }
@article {pmid35115615, year = {2022}, author = {Lee, CZ and Zoqratt, MZHM and Phipps, ME and Barr, JJ and Lal, SK and Ayub, Q and Rahman, S}, title = {The gut virome in two indigenous populations from Malaysia.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1824}, pmid = {35115615}, issn = {2045-2322}, mesh = {Feces/virology ; Female ; Gastrointestinal Microbiome/*genetics ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Indigenous Peoples ; Malaysia ; Metagenomics/methods ; Phylogeny ; Virome/genetics ; Viruses/classification/*genetics ; }, abstract = {The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool samples from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these individuals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.}, }
@article {pmid35115599, year = {2022}, author = {Stege, PB and Hordijk, J and Shetty, SA and Visser, M and Viveen, MC and Rogers, MRC and Gijsbers, E and Dierikx, CM and van der Plaats, RQJ and van Duijkeren, E and Franz, E and Willems, RJL and Fuentes, S and Paganelli, FL}, title = {Impact of long-term dietary habits on the human gut resistome in the Dutch population.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1892}, pmid = {35115599}, issn = {2045-2322}, mesh = {Adult ; Bacteria/drug effects/*genetics/growth &amp; development ; *Diet ; Diet, Vegan ; Diet, Vegetarian ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; *Feeding Behavior ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Meat ; Metagenome ; Metagenomics ; Middle Aged ; Netherlands ; Nutritive Value ; Seafood ; Time Factors ; Vegetables ; }, abstract = {The human gut microbiome plays a central role in health and disease. Environmental factors, such as lifestyle and diet, are known to shape the gut microbiome as well as the reservoir of resistance genes that these microbes harbour; the resistome. In this study we assessed whether long-term dietary habits within a single geographical region (the Netherlands) impact the human gut resistome. Faecal samples from Dutch omnivores, pescatarians, vegetarians and vegans were analysed by metagenomic shotgun sequencing (MSS) (n = 149) and resistome capture sequencing approach (ResCap) (n = 64). Among all diet groups, 119 and 145 unique antibiotic resistance genes (ARGs) were detected by MSS or ResCap, respectively. Five or fifteen ARGs were shared between all diet groups, based on MSS and ResCap, respectively. The total number of detected ARGs by MSS or ResCap was not significantly different between the groups. MSS also revealed that vegans have a distinct microbiome composition, compared to other diet groups. Vegans had a lower abundance of Streptococcus thermophilus and Lactococcus lactis compared to pescatarians and a lower abundance of S. thermophilus when compared to omnivores. In summary, our study showed that long-term dietary habits are not associated with a specific resistome signature.}, }
@article {pmid35114943, year = {2022}, author = {Le Roy, CI and Kurilshikov, A and Leeming, ER and Visconti, A and Bowyer, RCE and Menni, C and Falchi, M and Koutnikova, H and Veiga, P and Zhernakova, A and Derrien, M and Spector, TD}, title = {Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {39}, pmid = {35114943}, issn = {1471-2180}, support = {MR/N01183X/1/MRC_/Medical Research Council/United Kingdom ; MR/N030125/1/MRC_/Medical Research Council/United Kingdom ; DP2 OD007444/CD/ODCDC CDC HHS/United States ; DP2 OD007444/OD/NIH HHS/United States ; R01 DK093595/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; RO1 DK093595/NH/NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Bacteria/classification/*genetics/isolation &amp; purification ; Cohort Studies ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; *Metabolome ; Metabolomics/methods ; *Metagenome ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; Probiotics/*administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Surveys and Questionnaires ; United Kingdom ; Yogurt/*microbiology ; }, abstract = {BACKGROUND: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits.<br><br>RESULTS: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17 ± 0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18 ± 11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41 ± 0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30 ± 0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed than an increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.<br><br>CONCLUSIONS: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).}, }
@article {pmid35112151, year = {2022}, author = {Mishra, A and Singh, L and Singh, D}, title = {Unboxing the black box-one step forward to understand the soil microbiome: A systematic review.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35112151}, issn = {1432-184X}, abstract = {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.}, }
@article {pmid35110685, year = {2022}, author = {Miyauchi, E and Taida, T and Kawasumi, M and Ohkusa, T and Sato, N and Ohno, H}, title = {Analysis of colonic mucosa-associated microbiota using endoscopically collected lavage.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1758}, pmid = {35110685}, issn = {2045-2322}, mesh = {Bacteria/genetics/isolation &amp; purification ; Cigarette Smoking ; Colon/*microbiology ; DNA, Bacterial ; *Endoscopy ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The bacterial composition of the gut lumen and mucosa is distinct and the mucosa-associated bacteria are thought to play a more critical role in interactions with the host immune system. However, limited studies of the gut mucosal microbiota in humans have been available due to methodological challenges. Here, we evaluated the potential use of colonic lavage samples for mucosal microbiota analysis in humans. Among the different types of colonic mucosal samples collected from healthy volunteers, the lavage samples contained a higher amount of bacterial DNA and were less contaminated with host DNA compared to mucosal brushing (brush) and biopsy. Although 16S gene amplicon sequencing showed that the bacterial composition of the lavage was intermediate between that of feces and biopsy, mucosal bacteria abundant in the biopsy were also enriched in lavage samples. Furthermore, differences in mucosal microbes between non-smokers and smokers were detectable in lavage samples. Our data emphasize that colonic lavage is suitable for analysis of the mucosal microbiota. Given its minimal invasiveness and high bacterial DNA content, the colonic lavage will promote research on the human mucosal microbiota, especially in gastrointestinal disorders.}, }
@article {pmid35110663, year = {2022}, author = {Ni, J and Yang, H and Chen, L and Xu, J and Zheng, L and Xie, G and Shen, C and Li, W and Liu, Q}, title = {Metagenomic analysis of microbial community structure and function in a improved biofilter with odorous gases.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1731}, pmid = {35110663}, issn = {2045-2322}, mesh = {Ammonia/analysis ; Biodegradation, Environmental ; Biosolids/*microbiology ; Filtration ; Gases/*analysis ; Hydrogen Sulfide/analysis ; Industrial Waste/*analysis ; *Metagenome ; *Metagenomics ; *Microbiota ; Odorants/*analysis ; Phylogeny ; Sewage/*microbiology ; }, abstract = {Biofilters have been broadly applied to degrade the odorous gases from industrial emissions. A industrial scale biofilter was set up to treat the odorous gases. To explore biofilter potentials, the microbial community structure and function must be well defined. Using of improved biofilter, the differences in microbial community structures and functions in biofilters before and after treatment were investigated by metagenomic analysis. Odorous gases have the potential to alter the microbial community structure in the sludge of biofilter. A total of 90,016 genes assigned into various functional metabolic pathways were identified. In the improved biofilter, the dominant phyla were Proteobacteria, Planctomycetes, and Chloroflexi, and the dominant genera were Thioalkalivibrio, Thauera, and Pseudomonas. Several xenobiotic biodegradation-related pathways showed significant changes during the treatment process. Compared with the original biofilter, Thermotogae and Crenarchaeota phyla were significantly enriched in the improved biofilter, suggesting their important role in nitrogen-fixing. Furthermore, several nitrogen metabolic pathway-related genes, such as nirA and nifA, and sulfur metabolic pathway-related genes, such as fccB and phsA, were considered to be efficient genes that were involved in removing odorous gases. Our findings can be used for improving the efficiency of biofilter and helping the industrial enterprises to reduce the emission of waste gases.}, }
@article {pmid35108565, year = {2022}, author = {Mondal, HK and Maji, UJ and Mohanty, S and Sahoo, PK and Maiti, NK}, title = {Alteration of gut microbiota composition and function of Indian major carp, rohu (Labeo rohita) infected with Argulus siamensis.}, journal = {Microbial pathogenesis}, volume = {164}, number = {}, pages = {105420}, doi = {10.1016/j.micpath.2022.105420}, pmid = {35108565}, issn = {1096-1208}, mesh = {Animals ; *Arguloida ; *Carps ; *Fish Diseases/parasitology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbiome homeostasis is critical in preventing diseases. However, the effect of disease on gut microbiota assembly remains unclear. At present, there are no reports on the composition and functional analysis of intestinal microbiota of Indian major carp, rohu (L. rohita) infected with ectoparasite, Argulus. In this study, we analysed and compared the intestinal microbiota of healthy and Argulus-infected rohu by 16S rRNA amplicon sequencing. Argulus infection could significantly influence the diversity and richness of the gut microbiota. However, abundance of Actinobacteria and Patescibacteria were enriched significantly in Argulus-infected fish. Venn diagram revealed that there were many more unique genera in the infected group as compared to control fish. The genera, Stenotrophomonas and Pirellula were significantly increased in infected fish while the abundance of Reyranella was decreased. LEfSe analysis showed a significant enrichment in abundances of 11 taxa in healthy group and 17 taxa in infected group. Furthermore, genera Rubellimicrobium, Dielma, Hyphomicrobium, Reyranella, Streptomyces and Cloacibacterium performed the best in differentiating between both the groups. Predicted microbiota function by PICRUSt revealed that the gut microbiota of infected fish was mainly associated with enriched synthesis of chitinases, chitin binding proteins, osmoprotectant proteins and sulfatases enzymes. There was a positive association between the structural and functional composition of the gut microbiota. The results indicated that the Argulus infection could affect the intestinal microbiota composition and function of rohu.}, }
@article {pmid35107340, year = {2022}, author = {Baumann, KBL and Thoma, R and Callbeck, CM and Niederdorfer, R and Schubert, CJ and Müller, B and Lever, MA and Bürgmann, H}, title = {Microbial Nitrogen Transformation Potential in Sediments of Two Contrasting Lakes Is Spatially Structured but Seasonally Stable.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0101321}, pmid = {35107340}, issn = {2379-5042}, mesh = {Eutrophication ; *Lakes/microbiology ; *Microbiota ; Nitrates/analysis ; Nitrogen ; }, abstract = {The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates from pore water concentration gradients in sediments. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in sediments were associated with distinct microbial community compositions and significant differences in abundances of various N transformation genes. For both characteristics, we observed a more pronounced spatial than seasonal variability within each lake. The eutrophic Lake Baldegg showed a higher denitrification potential with higher nosZ gene (N2O reductase) abundances and higher nirS:nirK (nitrite reductase) ratios, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for nitrification. Specifically, it harbored a high abundance of Nitrospira, including some with the potential for comammox. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding how the lacustrine sedimentary N cycle responds to variations in trophic conditions. IMPORTANCE Anthropogenic nitrogen (N) inputs can lead to eutrophication in surface waters, especially in N-limited coastal ecosystems. Lakes effectively remove reactive N by transforming it to N2 through microbial denitrification or anammox. The rates and distributions of these microbial processes are affected by factors such as the amount and quality of settling organic material and nitrate concentrations. However, the microbial communities mediating these N transformation processes in freshwater lake sediments remain largely unknown. We provide the first seasonally and spatially resolved metagenomic analysis of the N cycle in sediments of two lakes with different trophic states. We show that lakes with different trophic states select for distinct communities of N-cycling microorganisms with contrasting functional potentials for N transformation.}, }
@article {pmid35103093, year = {2022}, author = {Zhao, G and Xiang, Y and Wang, X and Dai, B and Zhang, X and Ma, L and Yang, H and Lyu, W}, title = {Exploring the Possible Link between the Gut Microbiome and Fat Deposition in Pigs.}, journal = {Oxidative medicine and cellular longevity}, volume = {2022}, number = {}, pages = {1098892}, pmid = {35103093}, issn = {1942-0994}, mesh = {Abdominal Fat/*metabolism/pathology ; Acetyl-CoA Carboxylase/genetics/metabolism ; Animals ; Archaea/genetics/isolation &amp; purification/metabolism ; Bacteria/genetics/isolation &amp; purification/metabolism ; Colon/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Glutathione Peroxidase/blood ; Liver/metabolism ; Malondialdehyde/blood ; Metagenomics ; Muscle, Skeletal/pathology/physiology ; Oxidative Stress/genetics ; PPAR gamma/genetics/metabolism ; Swine ; }, abstract = {Excessive lipid accumulation and high oxidative stress have become a serious health and economic problem in the pig industry. Fatness characteristics are crucial in pig production since they are closely related to meat quality. The gut microbiome is well acknowledged as a key element in fat deposition. But the link between gut microbiota and fat accumulation in pigs remains elusive. To examine whether there is a link between pigs' gut microbiome, lipogenic properties, and oxidative stress, we selected 5 high-fat pigs and 5 low-fat pigs from 60 250-day-old Jinhua pigs in the present study and collected the colon content, serum sample, and liver and abdominal fat segments from each pig for metagenomic analysis, the oxidative stress assay, and RT-qPCR analysis, respectively. The backfat thickness and fat content of the longissimus dorsi muscle were considerably higher in the high-fat pigs than in the low-fat pigs (P < 0.05). An obvious difference in GSH-Px and MDA in the serum between the high- and low-fat pigs was observed. After RT-qPCR analysis, we found the gene expression of ACC1 and SREBP1 in the liver and FAS, PPARγ, and LPL in the abdominal fat were significantly higher in high-fat pigs than in low-fat pigs (P < 0.05). Additionally, metagenomic sequencing revealed that high-fat pigs had a higher abundance of Archaeal species with methanogenesis functions, leading to more-efficient fat deposition, while low-fat pigs had higher abundances of butyrate-producing bacteria species that improved the formation of SCFAs, especially butyrate, thus alleviating fat deposition in pigs. Furthermore, a total of 17 CAZyme families were identified to give significant enrichments in different fat phenotypes of pigs. This study would provide a detailed understanding of how the gut microbiome influences fat deposition in pigs, as well as a hint for improving growth performance and fatness traits by manipulating the gut microbiome.}, }
@article {pmid35102501, year = {2022}, author = {Gurbanov, R and Kabaoğlu, U and Yağcı, T}, title = {Metagenomic analysis of intestinal microbiota in wild rats living in urban and rural habitats.}, journal = {Folia microbiologica}, volume = {67}, number = {3}, pages = {469-477}, pmid = {35102501}, issn = {1874-9356}, support = {2019-01. BŞEÜ.01-01//Scientific Research Project fund of Bilecik Şeyh Edebali University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mammals/genetics ; Metagenome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rats ; }, abstract = {Mammals have a symbiotic relationship with various microorganisms called microbiota throughout their lives. These microorganisms are known to affect the host's physiology, health, and even mental balance. The development of the gut microbiota is regulated by a complex interaction between host and environmental factors, including diet and lifestyle. Herein, it is aimed to elucidate the differences in the gut microbiota of rats living in urban and rural habitats. The taxonomic changes in the gut microbiota of wild rats belonging to Rattus rattus species caught from urban and rural areas of Western Anatolian (Bilecik province) were examined comparatively by 16S rRNA next-generation sequencing technique. Laboratory rats were used as reference animals. The alpha diversities were found lower in the rural rats with respect to the urban rats, whereas the highest alpha diversity was calculated for laboratory rats. The lower Firmicutes to Bacteroidetes ratios (F/B ratio) were accounted for both rural and laboratory rats compared with urban rats. The Proteobacteria to Actinobacteria ratio (P/A ratio) was lower for rural rats, but higher for laboratory rats, compared with urban rats. The heatmap analyses of taxonomic units in the microbiota of each group demonstrated distinct patterns at the species and genus levels. The study provided metagenomic data on the gut microbiota of rats residing in urban and rural habitats, offering a different perspective on future environmental biomonitoring studies.}, }
@article {pmid35102136, year = {2022}, author = {Siranosian, BA and Brooks, EF and Andermann, T and Rezvani, AR and Banaei, N and Tang, H and Bhatt, AS}, title = {Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {586}, pmid = {35102136}, issn = {2041-1723}, support = {P01 CA049605/CA/NCI NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; /CC/CDC HHS/United States ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Bacteria/*metabolism ; Bacterial Infections/*transmission ; Cross Infection/microbiology/transmission ; Drug Resistance, Microbial/drug effects/genetics ; Enterococcus faecium/drug effects/isolation &amp; purification ; Escherichia coli/drug effects/isolation &amp; purification ; Female ; *Gastrointestinal Microbiome/drug effects ; Hematopoietic Stem Cell Transplantation ; *Hospitalization ; Hospitals ; Humans ; Length of Stay ; Male ; Metagenome/genetics ; Metagenomics ; Middle Aged ; Phylogeny ; Probiotics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into the bloodstream to cause infections, the mechanisms by which HCT patients acquire pathogens in their microbiome have not yet been described. Here, we use linked-read and short-read metagenomic sequencing to analyze 401 stool samples collected from 149 adults undergoing HCT and hospitalized in the same unit over three years, many of whom were roommates. We use metagenomic assembly and strain-specific comparison methods to search for high-identity bacterial strains, which may indicate transmission between the gut microbiomes of patients. Overall, the microbiomes of patients who share time and space in the hospital do not converge in taxonomic composition. However, we do observe six pairs of patients who harbor identical or nearly identical strains of the pathogen Enterococcus faecium, or the gut commensals Akkermansia muciniphila and Hungatella hathewayi. These shared strains may result from direct transmission between patients who shared a room and bathroom, acquisition from a common hospital source, or transmission from an unsampled intermediate. We also identify multiple patients with identical strains of species commonly found in commercial probiotics, including Lactobacillus rhamnosus and Streptococcus thermophilus. In summary, our findings indicate that sharing of identical pathogens between the gut microbiomes of multiple patients is a rare phenomenon. Furthermore, the observed potential transmission of commensal, immunomodulatory microbes suggests that exposure to other humans may contribute to microbiome reassembly post-HCT.}, }
@article {pmid35100347, year = {2022}, author = {Ruuskanen, MO and Erawijantari, PP and Havulinna, AS and Liu, Y and Méric, G and Tuomilehto, J and Inouye, M and Jousilahti, P and Salomaa, V and Jain, M and Knight, R and Lahti, L and Niiranen, TJ}, title = {Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults.}, journal = {Diabetes care}, volume = {45}, number = {4}, pages = {811-818}, pmid = {35100347}, issn = {1935-5548}, mesh = {Adult ; Cohort Studies ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/epidemiology ; Female ; Finland/epidemiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Middle Aged ; }, abstract = {OBJECTIVE: To examine the previously unknown long-term association between gut microbiome composition and incident type 2 diabetes in a representative population cohort.<br><br>RESEARCH DESIGN AND METHODS: We collected fecal samples from 5,572 Finns (mean age 48.7 years; 54.1% women) in 2002 who were followed up for incident type 2 diabetes until 31 December 2017. The samples were sequenced using shotgun metagenomics. We examined associations between gut microbiome composition and incident diabetes using multivariable-adjusted Cox regression models. We first used the eastern Finland subpopulation to obtain initial findings and validated these in the western Finland subpopulation.<br><br>RESULTS: Altogether, 432 cases of incident diabetes occurred over the median follow-up of 15.8 years. We detected four species and two clusters consistently associated with incident diabetes in the validation models. These four species were Clostridium citroniae (hazard ratio [HR] 1.21; 95% CI 1.04-1.42), C. bolteae (HR 1.20; 95% CI 1.04-1.39), Tyzzerella nexilis (HR 1.17; 95% CI 1.01-1.36), and Ruminococcus gnavus (HR 1.17; 95% CI 1.01-1.36). The positively associated clusters, cluster 1 (HR 1.18; 95% CI 1.02-1.38) and cluster 5 (HR 1.18; 95% CI 1.02-1.36), mostly consisted of these same species.<br><br>CONCLUSIONS: We observed robust species-level taxonomic features predictive of incident type 2 diabetes over long-term follow-up. These findings build on and extend previous mainly cross-sectional evidence and further support links between dietary habits, metabolic diseases, and type 2 diabetes that are modulated by the gut microbiome. The gut microbiome can potentially be used to improve disease prediction and uncover novel therapeutic targets for diabetes.}, }
@article {pmid35095912, year = {2021}, author = {Yang, K and Deng, X and Jian, S and Zhang, M and Wen, C and Xin, Z and Zhang, L and Tong, A and Ye, S and Liao, P and Xiao, Z and He, S and Zhang, F and Deng, J and Zhang, L and Deng, B}, title = {Gallic Acid Alleviates Gut Dysfunction and Boosts Immune and Antioxidant Activities in Puppies Under Environmental Stress Based on Microbiome-Metabolomics Analysis.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {813890}, pmid = {35095912}, issn = {1664-3224}, mesh = {Age Factors ; Animal Feed ; Animals ; Antioxidants/*pharmacology ; Biomarkers ; Dogs ; Environment ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Gallic Acid/*pharmacology ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome/*drug effects ; Immunologic Factors/*pharmacology ; Lipid Metabolism/drug effects ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; RNA, Ribosomal, 16S ; Stress, Physiological/*drug effects ; }, abstract = {Early-life exposure to environmental stress disrupts the gut barrier and leads to inflammatory responses and changes in gut microbiota composition. Gallic acid (GA), a natural plant polyphenol, has received significant interest for its antioxidant, anti-inflammatory, and antimicrobial properties that support the maintenance of intestinal health. To assess whether dietary supplementation of GA alleviates environmental stress, a total of 19 puppies were randomly allocated to the following three dietary treatments for 2 weeks: 1) basal diet (control (CON)); 2) basal diet + transportation (TS); and 3) basal diet with the addition of 500 mg/kg of GA + transportation (TS+GA). After a 1-week supplementation period, puppies in the TS and TS+GA groups were transported from a stressful environment to another livable location, and puppies in the CON group were then left in the stressful environment. Results indicated that GA markedly reduced the diarrhea rate in puppies throughout the trial period and caused a moderate decline of serum cortisol and HSP-70 levels after transportation. Also, GA alleviated the oxidative stress and inflammatory response caused by multiple environmental stressors. Meanwhile, puppies fed GA had a higher abundance of fecal Firmicutes and Lactobacillus and lower Proteobacteria, Escherichia-Shigella, and Clostridium_sensu_stricto_1 after transportation. As a result, the TS+GA group had the highest total short-chain fatty acids and acetic acid. Also, the fecal and serum metabolomics analyses revealed that GA markedly reversed the abnormalities of amino acid metabolism, lipid metabolism, carbohydrate metabolism, and nucleotide metabolism caused by stresses. Finally, Spearman's correlation analysis was carried out to explore the comprehensive microbiota and metabolite relationships. Overall, dietary supplementation of GA alleviates oxidative stress and inflammatory response in stressed puppies by causing beneficial shifts on gut microbiota and metabolites that may support gut and host health.}, }
@article {pmid35095808, year = {2021}, author = {Wang, N and Li, H and Wang, B and Ding, J and Liu, Y and Wei, Y and Li, J and Ding, GC}, title = {Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {798476}, pmid = {35095808}, issn = {1664-302X}, abstract = {Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.}, }
@article {pmid35094961, year = {2022}, author = {Cantoni, C and Lin, Q and Dorsett, Y and Ghezzi, L and Liu, Z and Pan, Y and Chen, K and Han, Y and Li, Z and Xiao, H and Gormley, M and Liu, Y and Bokoliya, S and Panier, H and Suther, C and Evans, E and Deng, L and Locca, A and Mikesell, R and Obert, K and Newland, P and Wu, Y and Salter, A and Cross, AH and Tarr, PI and Lovett-Racke, A and Piccio, L and Zhou, Y}, title = {Alterations of host-gut microbiome interactions in multiple sclerosis.}, journal = {EBioMedicine}, volume = {76}, number = {}, pages = {103798}, doi = {10.1016/j.ebiom.2021.103798}, pmid = {35094961}, issn = {2352-3964}, support = {R01 NS102633/NS/NINDS NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Chromatography, Liquid ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metagenomics ; *Multiple Sclerosis/etiology ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Multiple sclerosis (MS) has a complex genetic, immune and metabolic pathophysiology. Recent studies implicated the gut microbiome in MS pathogenesis. However, interactions between the microbiome and host immune system, metabolism and diet have not been studied over time in this disorder.<br><br>METHODS: We performed a six-month longitudinal multi-omics study of 49 participants (24 untreated relapse remitting MS patients and 25 age, sex, race matched healthy control individuals. Gut microbiome composition and function were characterized using 16S and metagenomic shotgun sequencing. Flow cytometry was used to characterize blood immune cell populations and cytokine profiles. Circulating metabolites were profiled by untargeted UPLC-MS. A four-day food diary was recorded to capture the habitual dietary pattern of study participants.<br><br>FINDINGS: Together with changes in blood immune cells, metagenomic analysis identified a number of gut microbiota decreased in MS patients compared to healthy controls, and microbiota positively or negatively correlated with degree of disability in MS patients. MS patients demonstrated perturbations of their blood metabolome, such as linoleate metabolic pathway, fatty acid biosynthesis, chalcone, dihydrochalcone, 4-nitrocatechol and methionine. Global correlations between multi-omics demonstrated a disrupted immune-microbiome relationship and a positive blood metabolome-microbiome correlation in MS. Specific feature association analysis identified a potential correlation network linking meat servings with decreased gut microbe B. thetaiotaomicron, increased Th17 cell and greater abundance of meat-associated blood metabolites. The microbiome and metabolome profiles remained stable over six months in MS and control individuals.<br><br>INTERPRETATION: Our study identified multi-system alterations in gut microbiota, immune and blood metabolome of MS patients at global and individual feature level. Multi-OMICS data integration deciphered a potential important biological network that links meat intakes with increased meat-associated blood metabolite, decreased polysaccharides digesting bacteria, and increased circulating proinflammatory marker.<br><br>FUNDING: This work was supported by the Washington University in St. Louis Institute of Clinical and Translational Sciences, funded, in part, by Grant Number # UL1 TR000448 from the National Institutes of Health, National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award (Zhou Y, Piccio, L, Lovett-Racke A and Tarr PI); R01 NS10263304 (Zhou Y, Piccio L); the Leon and Harriet Felman Fund for Human MS Research (Piccio L and Cross AH). Cantoni C. was supported by the National MS Society Career Transition Fellowship (TA-180531003) and by donations from Whitelaw Terry, Jr. / Valerie Terry Fund. Ghezzi L. was supported by the Italian Multiple Sclerosis Society research fellowship (FISM 2018/B/1) and the National Multiple Sclerosis Society Post-Doctoral Fellowship (FG-190734474). Anne Cross was supported by The Manny &amp; Rosalyn Rosenthal-Dr. John L. Trotter MS Center Chair in Neuroimmunology of the Barnes-Jewish Hospital Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.}, }
@article {pmid35087228, year = {2022}, author = {Mills, RH and Dulai, PS and Vázquez-Baeza, Y and Sauceda, C and Daniel, N and Gerner, RR and Batachari, LE and Malfavon, M and Zhu, Q and Weldon, K and Humphrey, G and Carrillo-Terrazas, M and Goldasich, LD and Bryant, M and Raffatellu, M and Quinn, RA and Gewirtz, AT and Chassaing, B and Chu, H and Sandborn, WJ and Dorrestein, PC and Knight, R and Gonzalez, DJ}, title = {Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.}, journal = {Nature microbiology}, volume = {7}, number = {2}, pages = {262-276}, pmid = {35087228}, issn = {2058-5276}, support = {P30 DK120515/DK/NIDDK NIH HHS/United States ; P30 NS047101/NS/NINDS NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacterial Proteins/classification/genetics ; Bacteroides/enzymology/*pathogenicity ; Cohort Studies ; Colitis, Ulcerative/*microbiology/*physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Longitudinal Studies ; Male ; Metagenome ; Metagenomics/*methods ; Mice ; Middle Aged ; Peptide Hydrolases/classification/*genetics ; Proteomics/*methods ; Severity of Illness Index ; }, abstract = {Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.}, }
@article {pmid35087123, year = {2022}, author = {Domènech, L and Willis, J and Alemany-Navarro, M and Morell, M and Real, E and Escaramís, G and Bertolín, S and Sánchez Chinchilla, D and Balcells, S and Segalàs, C and Estivill, X and Menchón, JM and Gabaldón, T and Alonso, P and Rabionet, R}, title = {Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1448}, pmid = {35087123}, issn = {2045-2322}, mesh = {Adult ; Brain-Gut Axis/*immunology ; Case-Control Studies ; DNA, Bacterial/isolation &amp; purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Healthy Volunteers ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Obsessive-Compulsive Disorder/immunology/*microbiology ; Oropharynx/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although the etiology of obsessive-compulsive disorder (OCD) is largely unknown, it is accepted that OCD is a complex disorder. There is a known bi-directional interaction between the gut microbiome and brain activity. Several authors have reported associations between changes in gut microbiota and neuropsychiatric disorders, including depression or autism. Furthermore, a pediatric-onset neuropsychiatric OCD-related syndrome occurs after streptococcal infection, which might indicate that exposure to certain microbes could be involved in OCD susceptibility. However, only one study has investigated the microbiome of OCD patients to date. We performed 16S ribosomal RNA gene-based metagenomic sequencing to analyze the stool and oropharyngeal microbiome composition of 32 OCD cases and 32 age and gender matched controls. We estimated different α- and β-diversity measures and performed LEfSe and Wilcoxon tests to assess differences in bacterial distribution. OCD stool samples showed a trend towards lower bacterial α-diversity, as well as an increase of the relative abundance of Rikenellaceae, particularly of the genus Alistipes, and lower relative abundance of Prevotellaceae, and two genera within the Lachnospiraceae: Agathobacer and Coprococcus. However, we did not observe a different Bacteroidetes to Firmicutes ratio between OCD cases and controls. Analysis of the oropharyngeal microbiome composition showed a lower Fusobacteria to Actinobacteria ratio in OCD cases. In conclusion, we observed an imbalance in the gut and oropharyngeal microbiomes of OCD cases, including, in stool, an increase of bacteria from the Rikenellaceae family, associated with gut inflammation, and a decrease of bacteria from the Coprococcus genus, associated with DOPAC synthesis.}, }
@article {pmid35086715, year = {2022}, author = {He, Q and Yang, C and Kang, X and Chen, Y and Zhang, T and Zhang, H and Kwok, LY}, title = {Intake of Bifidobacterium lactis Probio-M8 fermented milk protects against alcoholic liver disease.}, journal = {Journal of dairy science}, volume = {105}, number = {4}, pages = {2908-2921}, doi = {10.3168/jds.2021-21265}, pmid = {35086715}, issn = {1525-3198}, mesh = {Animals ; *Bifidobacterium animalis/metabolism ; *Gastrointestinal Microbiome ; *Liver Diseases, Alcoholic/prevention &amp; control/veterinary ; Milk ; *Probiotics ; Rats ; *Rodent Diseases ; }, abstract = {Alcoholic liver disease (ALD) is a liver disease caused by long-term heavy drinking, which is characterized by increased inflammation and oxidative stress in the liver and gut dysbiosis. The purpose of this study was to investigate the protective effect of administering ordinary and probiotic- (containing the Bifidobacterium animalis ssp. lactis Probio-M8 strain; M8) fermented milk to rats. Several biochemical parameters and the fecal metagenomes were monitored before (d 0) and after (d 42) the intervention. Our results confirmed that alcohol could cause significant changes in the liver levels of the proinflammatory cytokine IL-1β, antioxidation indicators, and liver function-related indicators; meanwhile, the gut bacterial and viral microbiota were disrupted with significant reduction in microbial diversity and richness. Feeding the rats with Probio-M8-fermented milk effectively maintained the gut microbiota stability, reduced liver inflammation and oxidative stress, and mitigated liver damages in ALD. Moreover, the Probio-M8-fermented milk reversed alcohol-induced dysbiosis by restoring the gut microbiota diversity, richness, and composition. Four predicted fecal metabolites (inositol, tryptophan, cortisol, and vitamin K2) increased after the intervention, which might help regulate liver metabolism and alleviate ALD-related symptoms. In short, our data supported that consuming Probio-M8-fermented milk effectively mitigated ALD. The protective effect against ALD could be related to changes in the gut microbiome after probiotic-fermented milk consumption. However, such observation and the causal relationship among probiotic milk consumption, changes in gut microbiome, and disease alleviation would still need to be further confirmed. Nevertheless, this study has shown in a rat model that consuming probiotic-fermented milk could protect against ALD.}, }
@article {pmid35086016, year = {2022}, author = {Rocchetti, G and Luisa Callegari, M and Senizza, A and Giuberti, G and Ruzzolini, J and Romani, A and Urciuoli, S and Nediani, C and Lucini, L}, title = {Oleuropein from olive leaf extracts and extra-virgin olive oil provides distinctive phenolic profiles and modulation of microbiota in the large intestine.}, journal = {Food chemistry}, volume = {380}, number = {}, pages = {132187}, doi = {10.1016/j.foodchem.2022.132187}, pmid = {35086016}, issn = {1873-7072}, mesh = {Intestine, Large ; Iridoid Glucosides ; *Microbiota ; Olea ; Olive Oil ; Plant Extracts ; *Plant Oils ; }, abstract = {The interest in the modulation of gut microbiota by polyphenols from olives and derived products is increasing. In this work, phenolic leaf extracts (PLE) were in vitro faecal fermented to evaluate the changes in phenolic profiles and the impact on microbiota, using a commercial extra-virgin olive oil (EVOO) as reference. The in vitro fermentation decreased oleuropein content in PLE, determining an increase of hydroxytyrosol and other phenolic metabolites. An increase (p < 0.05) of hydroxytyrosol (LogFC = 6.02; VIP score = 1.05) was also observed in fermented EVOO. Besides, PLE significantly (p < 0.05) changed amino acids (LogFC = 6.1) and fatty acids (LogFC = 5.9) profile of the faeces. Metagenomic sequencing revealed that Coriobacteriaceae at the family level, and Collinsella at the genus level, were the most affected by PLE fermentation. These findings support the modulation of the gut microbiota exerted by phenolics from PLE and EVOO.}, }
@article {pmid35085655, year = {2022}, author = {Malla, MA and Dubey, A and Raj, A and Kumar, A and Upadhyay, N and Yadav, S}, title = {Emerging frontiers in microbe-mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {299}, number = {}, pages = {118851}, doi = {10.1016/j.envpol.2022.118851}, pmid = {35085655}, issn = {1873-6424}, mesh = {Agriculture ; Humans ; *Microbiota ; *Pesticides/analysis ; Soil ; Soil Microbiology ; }, abstract = {The overuse of pesticides for augmenting agriculture productivity always comes at the cost of environment, biodiversity, and human health and has put the land, water, and environmental footprints under severe threat throughout the globe. Underpinning and maximizing the microbiome functions in pesticide-contaminated environments has become a prerequisite for a sustainable environment and resilient agriculture. It is imperative to elucidate the metabolic network of the microbial communities and environmental variables at the contaminated site to predict the best strategy for remediation and soil microbe-pesticide interactions. High throughput next-generation sequencing and in silico analysis allow us to identify and discern the members and characteristics of core microbiomes at the contaminated site. Integration of modern high throughput multi-omics investigations and informatics pipelines provide novel approaches and pathways to capitalize on the core microbiomes for enhancing environmental functioning and mitigation. The role of eco-genomics tools in visualising the microbial network, taxonomy, functional potential, and environmental variables in contaminated habitats is discussed in this review. The integrated role of the potential microbe identification as individual or consortia, mechanistic approach for pesticide degradation, identification of responsible enzymes/genes, and in silico approach is emphasized for the prospects of the area.}, }
@article {pmid35083969, year = {2022}, author = {Fishbein, SR and Robinson, JI and Hink, T and Reske, KA and Newcomer, EP and Burnham, CD and Henderson, JP and Dubberke, ER and Dantas, G}, title = {Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35083969}, issn = {2050-084X}, support = {R01 DK111930/DK/NIDDK NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; R01 AT009741/AT/NCCIH NIH HHS/United States ; R01 OH011578/OH/NIOSH CDC HHS/United States ; }, mesh = {Clostridioides difficile/*genetics/*growth &amp; development ; Clostridium Infections/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; Metagenomics ; Ribotyping ; Symbiosis ; }, abstract = {Clostridioides difficile infection (CDI) imposes a substantial burden on the health care system in the United States. Understanding the biological basis for the spectrum of C. difficile-related disease manifestations is imperative to improving treatment and prevention of CDI. Here, we investigate the correlates of asymptomatic C. difficile colonization using a multi-omics approach. We compared the fecal microbiome and metabolome profiles of patients with CDI versus asymptomatically colonized patients, integrating clinical and pathogen factors into our analysis. We found that CDI patients were more likely to be colonized by strains with the binary toxin (CDT) locus or strains of ribotype 027, which are often hypervirulent. We find that microbiomes of asymptomatically colonized patients are significantly enriched for species in the class Clostridia relative to those of symptomatic patients. Relative to CDI microbiomes, asymptomatically colonized patient microbiomes were enriched with sucrose degradation pathways encoded by commensal Clostridia, in addition to glycoside hydrolases putatively involved in starch and sucrose degradation. Fecal metabolomics corroborates the carbohydrate degradation signature: we identify carbohydrate compounds enriched in asymptomatically colonized patients relative to CDI patients. Further, we reveal that across C. difficile isolates, the carbohydrates sucrose, rhamnose, and lactulose do not serve as robust growth substrates in vitro, consistent with their enriched detection in our metagenomic and metabolite profiling of asymptomatically colonized individuals. We conclude that pathogen genetic variation may be strongly related to disease outcome. More interestingly, we hypothesize that in asymptomatically colonized individuals, carbohydrate metabolism by other commensal Clostridia may prevent CDI by inhibiting C. difficile proliferation. These insights into C. difficile colonization and putative commensal competition suggest novel avenues to develop probiotic or prebiotic therapeutics against CDI.}, }
@article {pmid35082799, year = {2021}, author = {Han, Z and Cen, C and Ou, Q and Pan, Y and Zhang, J and Huo, D and Chen, K}, title = {The Potential Prebiotic Berberine Combined With Methimazole Improved the Therapeutic Effect of Graves' Disease Patients Through Regulating the Intestinal Microbiome.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {826067}, pmid = {35082799}, issn = {1664-3224}, mesh = {Berberine/administration &amp; dosage/*therapeutic use ; Biomarkers ; Disease Management ; Drug Therapy, Combination ; Dysbiosis ; Gastrointestinal Microbiome/*drug effects ; Graves Disease/diagnosis/etiology/*therapy ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Methimazole/administration &amp; dosage/*therapeutic use ; Models, Biological ; Prebiotics/*administration &amp; dosage ; Thyroid Function Tests ; Treatment Outcome ; }, abstract = {Graves' disease, a typical metabolism disorder, causes diffuse goiter accompanied by ocular abnormalities and ocular dysfunction. Although methimazole (MI) is a commonly used drug for the treatment of GD, the efficacy of methimazole is only limited to the control of clinical indicators, and the side effects of MI should be seriously considered. Here, we designed a 6-month clinical trial that divided the patients into two groups: a methimazole group (n=8) and a methimazole combined with potential prebiotic berberine group (n=10). The effects of both treatments on thyroid function and treatment outcomes in patients with GD were assessed by thyroid index measurements and gut microbiota metagenomic sequencing. The results showed that the addition of berberine restored the patients' TSH and FT3 indices to normal levels, whereas MI alone restored only FT3. In addition, TRAb was closer to the healthy threshold at the end of treatment with the drug combination. MI alone failed to modulate the gut microbiota of the patients. However, the combination of berberine with methimazole significantly altered the microbiota structure of the patients, increasing the abundance of the beneficial bacteria Lactococcus lactis while decreasing the abundance of the pathogenic bacteria Enterobacter hormaechei and Chryseobacterium indologenes. Furthermore, further mechanistic exploration showed that the addition of berberine resulted in a significant upregulation of the synthesis of enterobactin, which may have increased iron functioning and thus restored thyroid function. In conclusion, methimazole combined with berberine has better efficacy in patients with GD, suggesting the potential benefit of berberine combined with methimazole in modulating the composition of intestinal microbes in the treatment of GD, providing new strong evidence for the effectiveness of combining Chinese and Western drugs from the perspective of modulating the intestinal microbiota.}, }
@article {pmid35082169, year = {2022}, author = {Liu, Q and Mak, JWY and Su, Q and Yeoh, YK and Lui, GC and Ng, SSS and Zhang, F and Li, AYL and Lu, W and Hui, DS and Chan, PK and Chan, FKL and Ng, SC}, title = {Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome.}, journal = {Gut}, volume = {71}, number = {3}, pages = {544-552}, doi = {10.1136/gutjnl-2021-325989}, pmid = {35082169}, issn = {1468-3288}, mesh = {COVID-19/*complications/diagnosis/microbiology ; Follow-Up Studies ; Gastrointestinal Microbiome/*physiology ; Humans ; Metagenomics/*methods ; Prospective Studies ; *SARS-CoV-2 ; Severity of Illness Index ; }, abstract = {BACKGROUND: Long-term complications after COVID-19 are common, but the potential cause for persistent symptoms after viral clearance remains unclear.<br><br>OBJECTIVE: To investigate whether gut microbiome composition is linked to post-acute COVID-19 syndrome (PACS), defined as at least one persistent symptom 4 weeks after clearance of the SARS-CoV-2 virus.<br><br>METHODS: We conducted a prospective study of 106 patients with a spectrum of COVID-19 severity followed up from admission to 6 months and 68 non-COVID-19 controls. We analysed serial faecal microbiome of 258 samples using shotgun metagenomic sequencing, and correlated the results with persistent symptoms at 6 months.<br><br>RESULTS: At 6 months, 76% of patients had PACS and the most common symptoms were fatigue, poor memory and hair loss. Gut microbiota composition at admission was associated with occurrence of PACS. Patients without PACS showed recovered gut microbiome profile at 6 months comparable to that of non-COVID-19 controls. Gut microbiome of patients with PACS were characterised by higher levels of Ruminococcus gnavus, Bacteroides vulgatus and lower levels of Faecalibacterium prausnitzii. Persistent respiratory symptoms were correlated with opportunistic gut pathogens, and neuropsychiatric symptoms and fatigue were correlated with nosocomial gut pathogens, including Clostridium innocuum and Actinomyces naeslundii (all p<0.05). Butyrate-producing bacteria, including Bifidobacterium pseudocatenulatum and Faecalibacterium prausnitzii showed the largest inverse correlations with PACS at 6 months.<br><br>CONCLUSION: These findings provided observational evidence of compositional alterations of gut microbiome in patients with long-term complications of COVID-19. Further studies should investigate whether microbiota modulation can facilitate timely recovery from post-acute COVID-19 syndrome.}, }
@article {pmid35077538, year = {2022}, author = {Agostinetto, G and Brusati, A and Sandionigi, A and Chahed, A and Parladori, E and Balech, B and Bruno, A and Pescini, D and Casiraghi, M}, title = {ExTaxsI: an exploration tool of biodiversity molecular data.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35077538}, issn = {2047-217X}, mesh = {*Biodiversity ; Genomics ; *Metadata ; Metagenomics ; }, abstract = {BACKGROUND: The increasing availability of multi-omics data is leading to regularly revised estimates of existing biodiversity data. In particular, the molecular data enable novel species to be characterized and the information linked to those already observed to be increased with new genomics data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy-to-use IT tools have become a key point to design future research. The more users are able to access biodiversity-related information, the greater the ability of the scientific community to expand its knowledge in this area.<br><br>RESULTS: In this article we focus on the development of ExTaxsI (Exploring Taxonomy Information), an IT tool that can retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. We use 3 case studies to show how an efficient organization of the available data can lead to obtaining new information that is fundamental as a starting point for new research. Using this approach highlights the limits in the distribution of data availability, a key factor to consider in the experimental design phase of broad-spectrum studies such as metagenomics.<br><br>CONCLUSIONS: ExTaxsI can easily retrieve molecular data and its metadata with an explorable visualization, with the aim of helping researchers to improve experimental designs and highlight the main gaps in the coverage of available data.}, }
@article {pmid35067915, year = {2022}, author = {Shahraki, MF and Atanaki, FF and Ariaeenejad, S and Ghaffari, MR and Norouzi-Beirami, MH and Maleki, M and Salekdeh, GH and Kavousi, K}, title = {A computational learning paradigm to targeted discovery of biocatalysts from metagenomic data: A case study of lipase identification.}, journal = {Biotechnology and bioengineering}, volume = {119}, number = {4}, pages = {1115-1128}, doi = {10.1002/bit.28037}, pmid = {35067915}, issn = {1097-0290}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Lipase/chemistry/genetics ; *Metagenome ; *Metagenomics/methods ; Temperature ; }, abstract = {The growing adoption of enzymes as biocatalysts in various industries has accentuated the demand for acquiring access to the great natural diversity and, in the meantime, the advent and advancements of metagenomics and high-throughput sequencing technologies have offered an unprecedented opportunity to explore this extensive resource. Lipases, enzymes responsible for the biological turnover of lipids, are among the most commercialized biocatalysts with numerous applications in different domains and therefore are of high industrial value. The relatively costly and time-consuming wet-lab experimental pipelines commonly used for novel enzyme discovery, highlight the necessity of agile in silico approaches to keep pace with the exponential growth of available sequencing data. In the present study, an in-depth analysis of a tannery wastewater metagenome, including taxonomic and enzymatic profiling, was performed. Using sequence homology-based screening methods and supervised machine learning-based regression models aimed at prediction of lipases' pH and temperature optima, the metagenomic data set was screened for lipolytic enzymes, which led to the isolation of alkaline and highly thermophilic novel lipase. Moreover, MeTarEnz (metagenomic targeted enzyme miner) software was developed and made freely accessible (at https://cbb.ut.ac.ir/MeTarEnz) as a part of this study. MeTarEnz offers several functions to automate the process of targeted enzyme mining from high-throughput sequencing data. This study highlights the competence of computational approaches in exploring vast biodiversity within environmental niches, while providing a set of practical in silico tools as well as a generalized methodology to facilitate the sequence-based mining of biocatalysts.}, }
@article {pmid35067170, year = {2022}, author = {Jin, H and You, L and Zhao, F and Li, S and Ma, T and Kwok, LY and Xu, H and Sun, Z}, title = {Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2021790}, pmid = {35067170}, issn = {1949-0984}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; Bacteriophages/classification/genetics/isolation &amp; purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota ; Phylogeny ; }, abstract = {A large number of microbial genomes have already been identified from the human gut microbiome, but the understanding of the role of the low-abundance species at the individual level remains challenging, largely due to the relatively shallow sequencing depth used in most studies. To improve genome assembling performance, a HiSeq-PacBio hybrid, ultra-deep metagenomic sequencing approach was used to reconstruct metagenomic-assembled genomes (MAGs) from 12 fecal samples. Such approach combined third-generation sequencing with ultra-deep second-generation sequencing to improve the sequencing coverage of the low-abundance subpopulation in the gut microbiome. Our study generated a total of 44 megabase-scale scaffolds, achieving four single-scaffolds of complete (circularized, no gaps) MAGs (CMAGs) that were the first circular genomes of their species. Moreover, 475 high-quality MAGs were assembled across all samples. Among them, 234 MAGs were currently uncultured, including 24 MAGs that were not found in any public genome database. Additionally, 287 and 77 MAGs were classified as low-abundance (0.1-1%) and extra-low-abundance (<0.1%) gut species in each individual, respectively. Our results also revealed individual-specific genomic features in the MAG profiles, including microbial genome growth rate, selective pressure, and frequency of chromosomal mobile genetic elements. Finally, thousands of extrachromosomal mobile genetic elements were identified from the metagenomic data, including 5097 bacteriophages and 79 novel plasmid genomes. Overall, our strategy represents an important step toward comprehensive genomic and functional characterization of the human gut microbiome at an individual level.}, }
@article {pmid35066694, year = {2022}, author = {Liu, J and Luo, W and Chen, Q and Chen, X and Zhou, G and Sun, H}, title = {Curcumin sensitizes response to cytarabine in acute myeloid leukemia by regulating intestinal microbiota.}, journal = {Cancer chemotherapy and pharmacology}, volume = {89}, number = {2}, pages = {243-253}, pmid = {35066694}, issn = {1432-0843}, mesh = {Animals ; Antineoplastic Combined Chemotherapy Protocols/administration &amp; dosage/*pharmacology ; Cholesterol/biosynthesis ; Curcumin/administration &amp; dosage ; Cytarabine/administration &amp; dosage ; Drug Resistance, Neoplasm ; Drug Synergism ; Gastrointestinal Microbiome/*drug effects ; HL-60 Cells ; Humans ; Leukemia, Myeloid, Acute/*drug therapy/microbiology ; Male ; Metabolomics ; Metagenomics ; Mice ; Xenograft Model Antitumor Assays ; }, abstract = {PURPOSE: To address whether Curcumin has synergistic effect with cytarabine (Ara-C) in treating acute myeloid leukemia (AML).<br><br>METHODS: A xenograft AML mouse model was established by injecting HL-60 cells into tail vein of mice to assess the function of Curcumin. Mononuclear cells (MNCs) isolated from AML mice and AML cell lines were used to examine the effect of Curcumin. Metagenomics and metabolomics were used to evaluate the alteration of intestinal microbiota and the change of metabolites in MNCs.<br><br>RESULTS: Curcumin treatment sensitized response to Ara-C in MNCs of AML mice, but had no direct effect on AML cell lines. Metagenomics revealed an alteration of intestinal microbiota with Curcumin treatment, which contributes to sensitized response to Ara-C. Curcumin treatment led to enhanced intestinal intact to sensitize response to Ara-C in AML mice, through reducing mucus degrading bacteria. Metabolomics demonstrated that Curcumin treatment led to decreased cholesterol in MNCs of AML mice. Further study proved that Curcumin treatment resulted in inhibition of SQLE, a key enzyme of cholesterol biosynthesis, to increase sensitivity to Ara-C.<br><br>CONCLUSION: Curcumin sensitizes response to Ara-C through regulating microbiota, highlighting the importance of intestinal intact strengthening in chemoresistant therapy. Moreover, aiming at cholesterol synthesis is promising in AML treatment.}, }
@article {pmid35066408, year = {2022}, author = {Graham, EH and Clarke, JL and Fernando, SC and Herr, JR and Adamowicz, MS}, title = {The application of the skin virome for human identification.}, journal = {Forensic science international. Genetics}, volume = {57}, number = {}, pages = {102662}, doi = {10.1016/j.fsigen.2022.102662}, pmid = {35066408}, issn = {1878-0326}, mesh = {DNA ; *Forensic Anthropology ; Genome, Viral ; Humans ; Metagenome ; Metagenomics ; *Virome ; }, abstract = {The use of skin virome offers a unique approach for human identification purposes in instances where a viable and statistically relevant human DNA profile is unavailable. The skin virome may act as an alternative DNA profile and/or an additional form of probative genetic material. To date, no study has attempted to investigate the human virome over a time series across various physical locations of the body to identify its diagnostic potential as a tool for human identification. For this study, we set out to evaluate the stability, diversity, and individualization of the human skin virome. An additional goal was to identify putative viral signatures that can be used in conjunction with traditional forensic STR loci. In order to accomplish this, human viral metagenomes were collected and sequenced from 42 individuals at three anatomical locations (left hand, right hand, and scalp) across multiple collection periods over a 6-month window of time. Assembly dependent and independent bioinformatic approaches, along with a database centered assessment of viral identification, resulted in three sets of stable putative viral markers. In total, with the three sets combined, we identified 59 viral biomarker regions, consisting of viral species and uncharacterized viral genome assemblies, that were stable over the sampling period. Additionally, we found the abundance profiles of these 59 viral biomarkers, based on presence or absence, to be significantly different across subjects (P < 0.001). Here we demonstrate that not only is the human virome applicable to be used for human identification, but we have identified many viral signatures that can putatively be used for forensic applications, thus providing a foundation to the novel field of forensic virology.}, }
@article {pmid35064149, year = {2022}, author = {Altshuler, I and Raymond-Bouchard, I and Magnuson, E and Tremblay, J and Greer, CW and Whyte, LG}, title = {Unique high Arctic methane metabolizing community revealed through in situ 13CH4-DNA-SIP enrichment in concert with genome binning.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1160}, pmid = {35064149}, issn = {2045-2322}, mesh = {Arctic Regions ; *Carbon Cycle ; Carbon Isotopes ; Genome, Bacterial ; Greenhouse Gases/*metabolism ; Methane/chemistry/isolation &amp; purification/*metabolism ; Microbiota/*genetics ; Permafrost/*microbiology ; }, abstract = {Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.}, }
@article {pmid35059329, year = {2021}, author = {Zuppi, M and Hendrickson, HL and O'Sullivan, JM and Vatanen, T}, title = {Phages in the Gut Ecosystem.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {822562}, pmid = {35059329}, issn = {2235-2988}, mesh = {Bacteria ; *Bacteriophages ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Viruses ; }, abstract = {Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored environment, from the deep sea to the Sahara Desert. Phages are abundant within the human biome and are gaining increasing recognition as potential modulators of the gut ecosystem. For example, they have been connected to gastrointestinal diseases and the treatment efficacy of Fecal Microbiota Transplant. The ability of phages to modulate the human gut microbiome has been attributed to the predation of bacteria or the promotion of bacterial survival by the transfer of genes that enhance bacterial fitness upon infection. In addition, phages have been shown to interact with the human immune system with variable outcomes. Despite the increasing evidence supporting the importance of phages in the gut ecosystem, the extent of their influence on the shape of the gut ecosystem is yet to be fully understood. Here, we discuss evidence for phage modulation of the gut microbiome, postulating that phages are pivotal contributors to the gut ecosystem dynamics. We therefore propose novel research questions to further elucidate the role(s) that they have within the human ecosystem and its impact on our health and well-being.}, }
@article {pmid35055056, year = {2022}, author = {Kawalec, A and Zwolińska, D}, title = {Emerging Role of Microbiome in the Prevention of Urinary Tract Infections in Children.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055056}, issn = {1422-0067}, mesh = {Age Factors ; Child ; Child, Preschool ; Diet ; Disease Management ; Disease Susceptibility ; Humans ; Immunologic Factors/therapeutic use ; Metagenome ; Metagenomics/methods ; *Microbiota ; Molecular Diagnostic Techniques ; Probiotics/administration &amp; dosage ; Urinary Tract Infections/diagnosis/epidemiology/*etiology/*prevention &amp; control ; Vaccines/therapeutic use ; }, abstract = {The microbiome of the urinary tract plays a significant role in maintaining health through the impact on bladder homeostasis. Urobiome is of great importance in maintaining the urothelial integrity and preventing urinary tract infection (UTI), as well as promoting local immune function. Dysbiosis in this area has been linked to an increased risk of UTIs, nephrolithiasis, and dysfunction of the lower urinary tract. However, the number of studies in the pediatric population is limited, thus the characteristic of the urobiome in children, its role in a child's health, and pediatric urologic diseases are not completely understood. This review aims to characterize the healthy urobiome in children, the role of dysbiosis in urinary tract infection, and to summarize the strategies to modification and reshape disease-prone microbiomes in pediatric patients with recurrent urinary tract infections.}, }
@article {pmid35055048, year = {2022}, author = {Costa, A and Rani, B and Bastiaanssen, TFS and Bonfiglio, F and Gunnigle, E and Provensi, G and Rossitto, M and Boehme, M and Strain, C and Martínez, CS and Blandina, P and Cryan, JF and Layé, S and Corradetti, R and Passani, MB}, title = {Diet Prevents Social Stress-Induced Maladaptive Neurobehavioural and Gut Microbiota Changes in a Histamine-Dependent Manner.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055048}, issn = {1422-0067}, support = {AMBROSIAC//JPI-Healthy Diet for Healthy Life Project/ ; FRM PRINSS DEQ20170336724//Fondation pour la Recherche Médicale/ ; }, mesh = {Animals ; Behavior, Animal ; Biomarkers ; Body Weight ; Cytokines/metabolism ; *Diet ; *Dysbiosis ; Fatty Acids/metabolism ; *Gastrointestinal Microbiome ; Gene Expression ; Hippocampus/metabolism/physiopathology ; Histamine/*metabolism ; Locomotion ; Male ; Metagenome ; Metagenomics ; Mice ; Mice, Knockout ; Models, Animal ; *Social Behavior ; *Stress, Psychological ; }, abstract = {Exposure to repeated social stress may cause maladaptive emotional reactions that can be reduced by healthy nutritional supplementation. Histaminergic neurotransmission has a central role in orchestrating specific behavioural responses depending on the homeostatic state of a subject, but it remains to be established if it participates in the protective effects against the insults of chronic stress afforded by a healthy diet. By using C57BL/6J male mice that do not synthesize histamine (Hdc-/-) and their wild type (Hdc+/+) congeners we evaluated if the histaminergic system participates in the protective action of a diet enriched with polyunsaturated fatty acids and vitamin A on the deleterious effect of chronic stress. Behavioural tests across domains relevant to cognition and anxiety were performed. Hippocampal synaptic plasticity, cytokine expression, hippocampal fatty acids, oxylipins and microbiota composition were also assessed. Chronic stress induced social avoidance, poor recognition memory, affected hippocampal long-term potentiation, changed the microbiota profile, brain cytokines, fatty acid and oxylipins composition of both Hdc-/- and Hdc+/+ mice. Dietary enrichment counteracted stress-induced deficits only in Hdc+/+ mice as histamine deficiency prevented almost all the diet-related beneficial effects. Interpretation: Our results reveal a previously unexplored and novel role for brain histamine as a mediator of many favorable effects of the enriched diet. These data present long-reaching perspectives in the field of nutritional neuropsychopharmacology.}, }
@article {pmid35055031, year = {2022}, author = {Martin, S and Foulon, A and El Hage, W and Dufour-Rainfray, D and Denis, F}, title = {Is There a Link between Oropharyngeal Microbiome and Schizophrenia? A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055031}, issn = {1422-0067}, mesh = {Animals ; Antipsychotic Agents/administration &amp; dosage/adverse effects/therapeutic use ; *Disease Susceptibility ; Dysbiosis ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/drug effects ; Neuroinflammatory Diseases/etiology/metabolism ; Oropharynx/*microbiology ; Periodontal Diseases/complications/etiology ; Saliva/microbiology ; Schizophrenia/drug therapy/*etiology/metabolism ; }, abstract = {The study aimed to examine the impact of the oropharyngeal microbiome in the pathophysiology of schizophrenia and to clarify whether there might be a bidirectional link between the oral microbiota and the brain in a context of dysbiosis-related neuroinflammation. We selected nine articles including three systemic reviews with several articles from the same research team. Different themes emerged, which we grouped into 5 distinct parts concerning the oropharyngeal phageome, the oropharyngeal microbiome, the salivary microbiome and periodontal disease potentially associated with schizophrenia, and the impact of drugs on the microbiome and schizophrenia. We pointed out the presence of phageoma in patients suffering from schizophrenia and that periodontal disease reinforces the role of inflammation in the pathophysiology of schizophrenia. Moreover, saliva could be an interesting substrate to characterize the different stages of schizophrenia. However, the few studies we have on the subject are limited in scope, and some of them are the work of a single team. At this stage of knowledge, it is difficult to conclude on the existence of a bidirectional link between the brain and the oral microbiome. Future studies on the subject will clarify these questions that for the moment remain unresolved.}, }
@article {pmid35055002, year = {2022}, author = {Zhang, X and Xiong, Z and Li, M and Zheng, N and Zhao, S and Wang, J}, title = {Activity- and Enrichment-Based Metaproteomics Insights into Active Urease from the Rumen Microbiota of Cattle.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055002}, issn = {1422-0067}, support = {CAAS-ZDXT2019004//Scientific Research Project for Major Achievements of the Agricultural Science and Technology Innovation Program/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition/ ; }, mesh = {Amino Acid Sequence ; Animals ; Cattle ; Enzyme Activation ; *Metagenomics/methods ; *Microbiota ; Models, Molecular ; Protein Conformation ; *Proteomics/methods ; Rumen/*microbiology ; Structure-Activity Relationship ; Urease/chemistry/*metabolism ; }, abstract = {Regulation of microbial urease activity plays a crucial role in improving the utilization efficiency of urea and reducing nitrogen emissions to the environment for ruminant animals. Dealing with the diversity of microbial urease and identifying highly active urease as the target is the key for future regulation. However, the identification of active urease in the rumen is currently limited due to large numbers of uncultured microorganisms. In the present study, we describe an activity- and enrichment-based metaproteomic analysis as an approach for the discovery of highly active urease from the rumen microbiota of cattle. We conducted an optimization method of protein extraction and purification to obtain higher urease activity protein. Cryomilling was the best choice among the six applied protein extraction methods (ultrasonication, bead beating, cryomilling, high-pressure press, freeze-thawing, and protein extraction kit) for obtaining protein with high urease activity. The extracted protein by cryomilling was further enriched through gel filtration chromatography to obtain the fraction with the highest urease activity. Then, by using SDS-PAGE, the gel band including urease was excised and analyzed using LC-MS/MS, searching against a metagenome-derived protein database. Finally, we identified six microbial active ureases from 2225 rumen proteins, and the identified ureases were homologous to those of Fibrobacter and Treponema. Moreover, by comparing the 3D protein structures of the identified ureases and known ureases, we found that the residues in the β-turn of flap regions were nonconserved, which might be crucial in influencing the flexibility of flap regions and urease activity. In conclusion, the active urease from rumen microbes was identified by the approach of activity- and enrichment-based metaproteomics, which provides the target for designing a novel efficient urease inhibitor to regulate rumen microbial urease activity.}, }
@article {pmid35051998, year = {2022}, author = {Hiraoka, S and Sumida, T and Hirai, M and Toyoda, A and Kawagucci, S and Yokokawa, T and Nunoura, T}, title = {Diverse DNA modification in marine prokaryotic and viral communities.}, journal = {Nucleic acids research}, volume = {50}, number = {3}, pages = {1531-1550}, pmid = {35051998}, issn = {1362-4962}, mesh = {DNA/genetics ; DNA Methylation/genetics ; *DNA Modification Methylases/genetics ; *Epigenomics ; Methyltransferases/genetics ; Prokaryotic Cells/metabolism ; }, abstract = {DNA chemical modifications, including methylation, are widespread and play important roles in prokaryotes and viruses. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. Here, using single-molecule real-time sequencing, we conducted culture-independent 'metaepigenomic' analyses (an integrated analysis of metagenomics and epigenomics) of marine microbial communities. A total of 233 and 163 metagenomic-assembled genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTase genes were not genetically linked with the endonuclease genes predicted to be involved in defense mechanisms against extracellular DNA. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, 5 of which showed novel specificities and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative specificities in MTases that are highly conserved in Alphaproteobacteria, which may enhance our understanding of the co-evolutionary history of the methylation systems and the genomes. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses in nature.}, }
@article {pmid35051422, year = {2022}, author = {Volodina, DE and Gureev, AP and Shaforostova, EA and Gryaznova, MV and Ignatyeva, DA and Popov, VN}, title = {Effect of l-carnitine and mildronate on the mitochondrial metabolism of heart and bacterial composition of the gut microbiome in ageing mice.}, journal = {Life sciences}, volume = {293}, number = {}, pages = {120333}, doi = {10.1016/j.lfs.2022.120333}, pmid = {35051422}, issn = {1879-0631}, mesh = {Aging/drug effects/*metabolism ; Animals ; Bifidobacterium/metabolism ; Cardiovascular Agents/*pharmacology ; Carnitine/*pharmacology ; DNA, Mitochondrial/metabolism ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Male ; Methylhydrazines/*pharmacology ; Mice ; Mice, Inbred C57BL ; Mitochondria, Heart/drug effects/*metabolism ; }, abstract = {Ageing is the most significant risk factor for cardiovascular diseases. l-Carnitine has a potent cardioprotective effect and its synthesis decreases during ageing. At the same time, there are pharmaceuticals, such as mildronate which, on the contrary, are aimed at reducing the concentration of l-carnitine in the heart and lead to slows down the oxidation of fatty acids in mitochondria. Despite this, both l-carnitine and mildronate are positioned as cardio protectors. We showed that l-carnitine supplementation to the diet of 15-month-old mice increased expression of the PGC-1α gene, which is responsible for the regulation of fatty acid oxidation, and the Nrf2 gene, which is responsible for protecting mitochondria by regulating the expression of antioxidants and mitophagy, in the heart. Mildronate activated the expression of genes that regulate glucose metabolism. Probably, this metabolic shift may protect the mitochondria of the heart from the accumulation of acyl-carnitine, which occurs during the oxidation of fatty acids under oxygen deficiency. Both pharmaceuticals impacted the gut microbiome bacterial composition. l-Carnitine increased the level of Lachnoanaerobaculum and [Eubacterium] hallii group, mildronate increased the level of Bifidobacterium, Rikinella, Christensenellaceae. Considered, that these bacteria for protection the organism from various pathogens and chronic inflammation. Thus, we suggested that the positive effects of both drugs on the mitochondria metabolism and gut microbiome bacterial composition may contribute to the protection of the heart during ageing.}, }
@article {pmid35051369, year = {2022}, author = {Jin, WB and Li, TT and Huo, D and Qu, S and Li, XV and Arifuzzaman, M and Lima, SF and Shi, HQ and Wang, A and Putzel, GG and Longman, RS and Artis, D and Guo, CJ}, title = {Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome.}, journal = {Cell}, volume = {185}, number = {3}, pages = {547-562.e22}, pmid = {35051369}, issn = {1097-4172}, support = {R21 AI142213/AI/NIAID NIH HHS/United States ; R01 AI095466/AI/NIAID NIH HHS/United States ; DP2 HD101401/HD/NICHD NIH HHS/United States ; R01 DK126871/DK/NIDDK NIH HHS/United States ; R01 AI151599/AI/NIAID NIH HHS/United States ; R01 DK128257/DK/NIDDK NIH HHS/United States ; U01 AI095608/AI/NIAID NIH HHS/United States ; R01 DK114252/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bile Acids and Salts/metabolism ; CRISPR-Cas Systems/genetics ; Clostridium/genetics ; Colitis/chemically induced/microbiology/pathology ; Dextran Sulfate ; Drug Resistance, Microbial/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; *Genes, Bacterial ; Germ-Free Life ; Inflammation/pathology ; Intestines/pathology ; Male ; Metabolome/genetics ; Metagenomics ; Mice, Inbred C57BL ; Mice, Knockout ; Mutagenesis, Insertional/genetics ; Mutation/genetics ; RNA, Ribosomal, 16S/genetics ; Transcription, Genetic ; }, abstract = {Hundreds of microbiota genes are associated with host biology/disease. Unraveling the causal contribution of a microbiota gene to host biology remains difficult because many are encoded by nonmodel gut commensals and not genetically targetable. A general approach to identify their gene transfer methodology and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. We developed a pipeline that identifies the gene transfer methods for multiple nonmodel microbes spanning five phyla, and we demonstrated the utility of their genetic tools by modulating microbiome-derived short-chain fatty acids and bile acids in vitro and in the host. In a proof-of-principle study, by deleting a commensal gene for bile acid synthesis in a complex microbiome, we discovered an intriguing role of this gene in regulating colon inflammation. This technology will enable genetically engineering the nonmodel gut microbiome and facilitate mechanistic dissection of microbiota-host interactions.}, }
@article {pmid35048279, year = {2022}, author = {Serag, AM and Abdel-Sabour, MS and El-Hadidi, M and Maged, M and Magdy, M and Ramadan, MF and Refaat, MH}, title = {Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt.}, journal = {Applied biochemistry and biotechnology}, volume = {194}, number = {5}, pages = {2168-2182}, pmid = {35048279}, issn = {1559-0291}, mesh = {Animals ; Bacteria/genetics ; *Cichlids/genetics/microbiology ; Egypt ; *Gastrointestinal Microbiome/genetics ; Lakes ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nile tilapia, Oreochromis niloticus, is the principal fish bred in Egypt. A pilot study was designed to analyze the bacterial composition of the Nile tilapia fish guts from two saltwater lakes in Northern Egypt. Fish samples were obtained from two Delta lakes: Manzala (ML) and Borollus (BL). DNA was extracted, and the bacterial communities in the stomach content were classified (down to the species level) using the 16S rRNA-based analysis. From the two metagenomics libraries in this study, 1,426,740 reads of the amplicon sequence corresponding to 508 total taxonomic operational units were recorded. The most prevalent bacterial phyla were Proteobacteria, Firmicutes, Actinobacteria, and Synergistetes in all samples. Some of the strains identified belong to classes of pathogenic zoonotic bacteria. A notable difference was observed between gut bacteria of Nile tilapia fish obtained from BL and ML. There is a remarkable indication that Nile tilapia fish living in BL is heavily burdened with pathogenic microbes most remarkably those involved with methylation of mercury and its accumulation in fish organs. These pathogenic microbes could have clinical implications and correlated with many diseases. This result was also consistent with the metagenomic data's functional prediction that indicated that Nile tilapia species harboring these two Egyptian northern lakes may be exposed to numerous anthropogenic pollutants. The findings show that the host environment has a significant impact on the composition of its microbiota. The first step towards exploring the better management of this profit-making fish is recognizing the structure of the microbiome.}, }
@article {pmid35044669, year = {2022}, author = {Kumar, RS and Mishra, N and Kumar, A}, title = {Characterization of Tobacco Microbiome by Metagenomics Approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2413}, number = {}, pages = {229-244}, pmid = {35044669}, issn = {1940-6029}, mesh = {Humans ; Metagenomics ; *Microbiota/genetics ; *Mouth Neoplasms/etiology ; RNA, Ribosomal, 16S/genetics ; Tobacco/genetics ; *Tobacco Products ; Tobacco Use ; }, abstract = {Chronic consumption of tobacco in all forms, either smoked/smokeless forms, causes major health hazards to humans that include cancer, cardiovascular, lung diseases, diabetes, fertility issues, etc. Among tobacco-mediated cancers, the prominent one being the oral cancers are caused due to chronic tobacco chewing. The biochemicals present in tobacco are involved in carcinogenesis, and their presence is partly mediated by the existence of microbes in tobacco products. The microbial characterization has been evolved from classical microscopical observation to the recent development of 16S rRNA sequencing by next-generation sequencing methods. The metagenomics approach using 16S rRNA-based next-generation sequencing methods enables the detection and characterization of the complete microbial community of tobacco, including both cultivable and non-cultivable microorganisms. Identification of microbes will help in devising strategies to limit the carcinogenic compounds present in tobacco.}, }
@article {pmid35041771, year = {2022}, author = {Ahearn-Ford, S and Berrington, JE and Stewart, CJ}, title = {Development of the gut microbiome in early life.}, journal = {Experimental physiology}, volume = {107}, number = {5}, pages = {415-421}, doi = {10.1113/EP089919}, pmid = {35041771}, issn = {1469-445X}, support = {221745/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Enterocolitis, Necrotizing ; Feces ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; RNA, Ribosomal, 16S/genetics ; }, abstract = {NEW FINDINGS: What is the topic of this review? The importance of the early life gut microbiome, with a focus on preterm infants and microbially related diseases. Current techniques to study the preterm gut microbiome are appraised, and the potential of recent methodological advancements is discussed. What advances does it highlight? Recent findings in the field achieved by the application of advanced technologies, the applicability of intestinally derived organoid models to study host-microbiome interactions in the preterm gut, and recent developments in enhancing the physiological relevance of such models. Preterm intestinally derived organoids may provide novel insights into the mechanisms underlying preterm disease, as well as diagnosis and treatment opportunities. These models have huge translational potential, offering a step towards precision medicine.<br><br>ABSTRACT: Accumulating evidence affirms the importance of the gut microbiome in both health and disease. In early life, there exists a critical period in which the composition of gut microbes is particularly malleable and subject to a wide range of influencing factors. Disturbances to microbial communities during this time may be beneficial or detrimental to short and long-term health outcomes. For infants born prematurely, naïve immune systems, immature gastrointestinal tracts and additional clinical needs put this population at high risk of abnormal microbial colonisation, resulting in increased susceptibility to diseases including necrotising enterocolitis (NEC) and late-onset sepsis (LOS). Traditional cell culture methods, gnotobiotic animals, molecular sequencing techniques (16S rRNA gene sequencing and metagenomics) and advanced 'omics' technologies (transcriptomics, proteomics and metabolomics) have been fundamental in exploring the associations between diet, gut microbes, microbial functions and disease. Despite significant investment and ongoing research efforts, prevention and treatment strategies in NEC and LOS remain limited. Recent endeavours have focused on searching for new, more physiologically relevant models to simulate the preterm intestine. Preterm intestinally derived organoids represent a promising in vitro approach in the study of host-microbiome interactions in the preterm infant gut, offering new and exciting possibilities in this field.}, }
@article {pmid35040752, year = {2022}, author = {Chen, Y and Wang, H and Lu, W and Wu, T and Yuan, W and Zhu, J and Lee, YK and Zhao, J and Zhang, H and Chen, W}, title = {Human gut microbiome aging clocks based on taxonomic and functional signatures through multi-view learning.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2025016}, pmid = {35040752}, issn = {1949-0984}, mesh = {*Aging ; Bacteria/*classification/genetics/isolation &amp; purification ; Biomarkers/analysis ; Cohort Studies ; *Gastrointestinal Microbiome ; Humans ; *Machine Learning ; Metagenomics ; }, abstract = {The human gut microbiome is a complex ecosystem that is closely related to the aging process. However, there is currently no reliable method to make full use of the metagenomics data of the gut microbiome to determine the age of the host. In this study, we considered the influence of geographical factors on the gut microbiome, and a total of 2604 filtered metagenomics data from the gut microbiome were used to construct an age prediction model. Then, we developed an ensemble model with multiple heterogeneous algorithms and combined species and pathway profiles for multi-view learning. By integrating gut microbiome metagenomics data and adjusting host confounding factors, the model showed high accuracy (R2 = 0.599, mean absolute error = 8.33 years). Besides, we further interpreted the model and identify potential biomarkers for the aging process. Among these identified biomarkers, we found that Finegoldia magna, Bifidobacterium dentium, and Clostridium clostridioforme had increased abundance in the elderly. Moreover, the utilization of amino acids by the gut microbiome undergoes substantial changes with increasing age which have been reported as the risk factors for age-associated malnutrition and inflammation. This model will be helpful for the comprehensive utilization of multiple omics data, and will allow greater understanding of the interaction between microorganisms and age to realize the targeted intervention of aging.}, }
@article {pmid35039616, year = {2022}, author = {Zheng, X and Jahn, MT and Sun, M and Friman, VP and Balcazar, JL and Wang, J and Shi, Y and Gong, X and Hu, F and Zhu, YG}, title = {Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes.}, journal = {The ISME journal}, volume = {16}, number = {5}, pages = {1397-1408}, pmid = {35039616}, issn = {1751-7370}, support = {RSG\R1\180213//Royal Society/ ; }, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; DNA Viruses ; Metagenomics ; *Microbiota/genetics ; *Pesticides/analysis ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; *Viruses/genetics ; }, abstract = {Viruses significantly influence local and global biogeochemical cycles and help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance and degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched in organochlorine pesticide (OCP) contaminated soil in China and if viral AMGs include genes linked to OCP biodegradation. Using metagenomics, we found that OCP-contaminated soils displayed a lower bacterial, but higher diversity of viruses that harbored a higher relative abundance of AMGs linked to pesticide degradation and metabolism. Furthermore, the diversity and relative abundance of AMGs significantly increased along with the severity of pesticide contamination, and several biodegradation genes were identified bioinformatically in viral metagenomes. Functional assays were conducted to experimentally demonstrate that virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for the degradation of L-2-haloacid pesticide precursors, improving bacterial growth at sub-inhibitory pesticide concentrations. Taken together, these results demonstrate that virus-encoded AMGs are linked to bacterial metabolism and biodegradation, being more abundant and diverse in soils contaminated with pesticides. Moreover, our findings highlight the importance of virus-encoded accessory genes for bacterial ecology in stressful environments, providing a novel avenue for using viruses in the bioremediation of contaminated soils.}, }
@article {pmid35039534, year = {2022}, author = {Lee, SJ and Rho, M}, title = {Multimodal deep learning applied to classify healthy and disease states of human microbiome.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {824}, pmid = {35039534}, issn = {2045-2322}, support = {2017M3A9F3041232//National Research Foundation of Korea/ ; 2020-0-01373//Institute of Information &amp; Communications Technology Planning &amp; Evaluation (IITP)/ ; }, mesh = {Colorectal Neoplasms/diagnosis/*microbiology ; *Deep Learning ; Diabetes Mellitus, Type 2/diagnosis/*microbiology ; Genome, Microbial/*genetics ; *Healthy Volunteers ; Humans ; Inflammatory Bowel Diseases/diagnosis/*microbiology ; Liver Cirrhosis/diagnosis/*microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {Metagenomic sequencing methods provide considerable genomic information regarding human microbiomes, enabling us to discover and understand microbial diseases. Compositional differences have been reported between patients and healthy people, which could be used in the diagnosis of patients. Despite significant progress in this regard, the accuracy of these tools needs to be improved for applications in diagnostics and therapeutics. MDL4Microbiome, the method developed herein, demonstrated high accuracy in predicting disease status by using various features from metagenome sequences and a multimodal deep learning model. We propose combining three different features, i.e., conventional taxonomic profiles, genome-level relative abundance, and metabolic functional characteristics, to enhance classification accuracy. This deep learning model enabled the construction of a classifier that combines these various modalities encoded in the human microbiome. We achieved accuracies of 0.98, 0.76, 0.84, and 0.97 for predicting patients with inflammatory bowel disease, type 2 diabetes, liver cirrhosis, and colorectal cancer, respectively; these are comparable or higher than classical machine learning methods. A deeper analysis was also performed on the resulting sets of selected features to understand the contribution of their different characteristics. MDL4Microbiome is a classifier with higher or comparable accuracy compared with other machine learning methods, which offers perspectives on feature generation with metagenome sequences in deep learning models and their advantages in the classification of host disease status.}, }
@article {pmid35039079, year = {2022}, author = {Adu-Oppong, B and Thänert, R and Wallace, MA and Burnham, CD and Dantas, G}, title = {Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {6}, pmid = {35039079}, issn = {2049-2618}, mesh = {Dysbiosis ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Urinary Tract Infections/diagnosis/microbiology ; }, abstract = {BACKGROUND: The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic patients in routine standard-of-care urine tests. Here, we used shotgun metagenomic sequencing to characterize the microbial composition of asymptomatic volunteers in a set of 30 longitudinally collected urine specimens. Using permutation tests, we established a range of asymptomatic microbiota states, and use these to contextualize the microbiota of 122 urine specimens collected from patients with suspected UTIs diagnostically categorized by standard-of-care urinalysis within that range. Finally, we used a standard-of-care culture protocol to evaluate the efficiency of culture-based recovery of the urinary microbiota.<br><br>RESULTS: The majority of genitourinary microbiota in individals suspected to have UTI overlapped with the spectrum of asymptomatic microbiota states. Longitudinal characterization of the genitourinary microbiome in urine specimens collected from asymptomatic volunteers revealed fluctuations of microbial functions and taxonomy over time. White blood cell counts from urinalysis suggested that urine specimens categorized as 'insignificant', 'contaminated', or 'no-growth' by conventional culture methods frequently showed signs of urinary tract inflammation, but this inflammation is not associated with genitourinary microbiota dysbiosis. Comparison of directly sequenced urine specimens with standard-of-care culturing confirmed that culture-based diagnosis biases genitourinary microbiota recovery towards the traditional uropathogens Escherichia coli and Klebsiella pneumoniae.<br><br>CONCLUSION: Here, we utilize shotgun metagenomic sequencing to establish a baseline of asymptomatic genitourinary microbiota states. Using this baseline we establish substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Our results establish that bacterial presence alone does not explain the onset of clinical symptoms. Video Abstract.}, }
@article {pmid35038012, year = {2022}, author = {Zhou, SP and Zhou, HY and Sun, JC and Liu, C and Ke, X and Zou, SP and Xue, YP and Zheng, YG}, title = {Bacterial dynamics and functions driven by bulking agents to enhance organic degradation in food waste in-situ rapid biological reduction (IRBR).}, journal = {Bioprocess and biosystems engineering}, volume = {45}, number = {4}, pages = {689-700}, pmid = {35038012}, issn = {1615-7605}, mesh = {Bacteria ; Food ; *Microbiota ; *Refuse Disposal/methods ; Triticum ; }, abstract = {This study investigated the effects of different bulking agents (i.e., sawdust, wheat straw, rice straw, and corncob) on bacterial structure and functions for organic degradation during food waste in-situ rapid biological reduction (IRBR) inoculated with microbial agent. Results showed that the highest organic degradation (409.5 g/kg total solid) and volatile solids removal efficiency (41.0%) were achieved when wheat straw was used, largely because the degradation of readily degradable substrates and cellulose was promoted by this bulking agent. Compared with other three bulking agents, the utilization of wheat straw was conducive to construct a more suitable environmental condition (moisture content of 18.0-28.2%, pH of 4.91-5.87) for organic degradation during IRBR process, by virtue of its excellent structural and physiochemical properties. Microbial community analysis suggested that the high-moisture environment in rice straw treatment promoted the growth of Staphylococcus and inhibited the activity of the inoculum. By contrast, lowest bacterial richness was observed in corncob treatment due to the faster water loss. Compared with these two bulking agents, sawdust and wheat straw treatment led to a more stable bacterial community structure, and the inoculated Bacillus gradually became the dominant genus (36.6-57.8%) in wheat straw treatment. Predicted metagenomics analysis showed that wheat straw treatment exhibited the highest carbohydrate metabolism activity which improved the pyruvate, amino sugar and nucleotide sugar metabolism, and thereby promoted the organic degradation and humic substrate production. These results indicated that wheat straw was a more desirable bulking agent, and revealed the potential microbial organics degradation mechanism in IRBR process.}, }
@article {pmid35034639, year = {2022}, author = {Amundson, KK and Borton, MA and Daly, RA and Hoyt, DW and Wong, A and Eder, E and Moore, J and Wunch, K and Wrighton, KC and Wilkins, MJ}, title = {Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {5}, pmid = {35034639}, issn = {2049-2618}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Canada ; *Hydraulic Fracking ; *Microbiota/genetics ; Predatory Behavior ; }, abstract = {BACKGROUND: Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation.<br><br>RESULTS: We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems.<br><br>CONCLUSIONS: These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. Video Abstract.}, }
@article {pmid35032344, year = {2022}, author = {Rasmussen, JA and Villumsen, KR and von Gersdorff Jørgensen, L and Forberg, T and Zuo, S and Kania, PW and Buchmann, K and Kristiansen, K and Bojesen, AM and Limborg, MT}, title = {Integrative analyses of probiotics, pathogenic infections and host immune response highlight the importance of gut microbiota in understanding disease recovery in rainbow trout (Oncorhynchus mykiss).}, journal = {Journal of applied microbiology}, volume = {132}, number = {4}, pages = {3201-3216}, doi = {10.1111/jam.15433}, pmid = {35032344}, issn = {1365-2672}, support = {DNRF143//Danmarks Grundforskningsfond/ ; 34009-17-1218//Miljøstyrelsen/ ; 8022-00005B//Det Frie Forskningsråd/ ; }, mesh = {Animals ; *Fish Diseases/microbiology ; *Gastrointestinal Microbiome ; Immunity ; *Oncorhynchus mykiss/microbiology ; *Probiotics ; *Yersinia Infections/microbiology/veterinary ; Yersinia ruckeri ; }, abstract = {AIMS: Given the pivotal role played by the gut microbiota in regulating the host immune system, great interest has arisen in the possibility of controlling fish health by modulating the gut microbiota. Hence, there is a need to better understand of the host-microbiota interactions after disease responses to optimize the use of probiotics to strengthen disease resilience and recovery.<br><br>METHODS AND RESULTS: We tested the effects of a probiotic feed additive in rainbow trout and challenged the fish with the causative agent for enteric red mouth disease, Yersinia ruckeri. We evaluated the survival, host immune gene expression and the gut microbiota composition. Results revealed that provision of probiotics and exposure to Y. ruckeri induced immune gene expression in the host, which were associated with changes in the gut microbiota. Subsequently, infection with Y. ruckeri had very little effect on microbiota composition when probiotics were applied, indicating that probiotics increased stabilisation of the microbiota. Our analysis revealed potential biomarkers for monitoring infection status and fish health. Finally, we used modelling approaches to decipher interactions between gut bacteria and the host immune gene responses, indicating removal of endogenous bacteria elicited by non-specific immune responses.<br><br>CONCLUSIONS: We discuss the relevance of these results emphasizing the importance of host-microbiota interactions, including the protective potential of the gut microbiota in disease responses.<br><br>Our results highlight the functional consequences of probiotic-induced changes in the gut microbiota post infection and the resulting host immune response.}, }
@article {pmid35027090, year = {2022}, author = {Rajala, P and Cheng, DQ and Rice, SA and Lauro, FM}, title = {Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {4}, pmid = {35027090}, issn = {2049-2618}, mesh = {Bacteria/genetics/metabolism ; Biofilms ; Corrosion ; *Microbiota ; *Steel/chemistry ; Sulfates/metabolism ; }, abstract = {BACKGROUND: Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity, and high hydrostatic pressure increase the costs and logistical challenges associated with monitoring corrosion. Moreover, there is currently only a rudimentary understanding of the role of microbially induced corrosion, which has rarely been studied in the deep-sea. We report here an integrative study of the biofilms growing on the surface of corroding mooring chain links that had been deployed for 10 years at ~2 km depth and developed a model of microbially induced corrosion based on flux-balance analysis.<br><br>METHODS: We used optical emission spectrometry to analyze the chemical composition of the mooring chain and energy-dispersive X-ray spectrometry coupled with scanning electron microscopy to identify corrosion products and ultrastructural features. The taxonomic structure of the microbiome was determined using shotgun metagenomics and was confirmed by 16S amplicon analysis and quantitative PCR of the dsrB gene. The functional capacity was further analyzed by generating binned, genomic assemblies and performing flux-balance analysis on the metabolism of the dominant taxa.<br><br>RESULTS: The surface of the chain links showed intensive and localized corrosion with structural features typical of microbially induced corrosion. The microbiome on the links differed considerably from that of the surrounding sediment, suggesting selection for specific metal-corroding biofilms dominated by sulfur-cycling bacteria. The core metabolism of the microbiome was reconstructed to generate a mechanistic model that combines biotic and abiotic corrosion. Based on this metabolic model, we propose that sulfate reduction and sulfur disproportionation might play key roles in deep-sea corrosion.<br><br>CONCLUSIONS: The corrosion rate observed was higher than what could be expected from abiotic corrosion mechanisms under these environmental conditions. High corrosion rate and the form of corrosion (deep pitting) suggest that the corrosion of the chain links was driven by both abiotic and biotic processes. We posit that the corrosion is driven by deep-sea sulfur-cycling microorganisms which may gain energy by accelerating the reaction between metallic iron and elemental sulfur. The results of this field study provide important new insights on the ecophysiology of the corrosion process in the deep sea.}, }
@article {pmid35026256, year = {2022}, author = {Wang, J and Zhang, Y and Ding, Y and Song, H and Liu, T}, title = {Analysis of microbial community resistance mechanisms in groundwater contaminated with SAs and high NH4+-Fe-Mn.}, journal = {The Science of the total environment}, volume = {817}, number = {}, pages = {153036}, doi = {10.1016/j.scitotenv.2022.153036}, pmid = {35026256}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; *Groundwater/chemistry ; *Microbiota ; Rivers ; Sulfonamides ; }, abstract = {The resistance mechanism of microbial communities in contaminated groundwater under the combined stress of sulfonamide antibiotics (SAs), NH4+, and Fe-Mn exceeding the standard levels was studied in an agricultural area along the Songhua River in Northeast China with developed livestock and poultry breeding. Representative points were selected in the study area to explore the response of environmental parameters and microbial communities, and microscopic experiments with different SA concentrations were conducted with background groundwater. The results showed a complex relationship between microbial communities and environmental factors. The environmental factors SM, SM2, SMX, DOC, NO3-, Fe, Mn, and HCO3- significantly affected the microbial community, with SMX, DOC, and Mn having the greatest effect. Three types of antibiotics with similar properties had different effects on the microbial community, and these effects were not simply additive or superimposed. After adding SAs, Proteobacteria with multi-resistance (99.85%) became the dominant phylum, and Acinetobacter (98.68%) became the dominant genus with SA resistance. SAs have a significant influence on bacterial chemotaxis, transporters, substance transport, and metabolism. Microorganisms resist the influence of SAs via a series of resistance mechanisms, such as enhancing the synthesis of relevant enzymes, generating new biochemical reactions, and reducing the transport of harmful substances through cell membranes. We also found that the proportion of exogenous compound degradation and metabolism-related functional genes in the presence of high SA concentrations increased significantly, which may be related to the degradation of SAs by microorganisms.}, }
@article {pmid35021085, year = {2022}, author = {Gulyaeva, A and Garmaeva, S and Ruigrok, RAAA and Wang, D and Riksen, NP and Netea, MG and Wijmenga, C and Weersma, RK and Fu, J and Vila, AV and Kurilshikov, A and Zhernakova, A}, title = {Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts.}, journal = {Cell reports}, volume = {38}, number = {2}, pages = {110204}, doi = {10.1016/j.celrep.2021.110204}, pmid = {35021085}, issn = {2211-1247}, mesh = {Adult ; Aged ; Bacteria/genetics/virology ; Bacteriophages/*genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Genome, Viral ; Humans ; Inflammatory Bowel Diseases/virology ; Male ; Metagenome/*genetics ; Metagenomics/methods ; Middle Aged ; Netherlands ; Obesity/virology ; Phylogeny ; }, abstract = {The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.}, }
@article {pmid35020412, year = {2022}, author = {Du, Y and Laperriere, SM and Fuhrman, J and Sun, F}, title = {Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {29}, number = {2}, pages = {106-120}, pmid = {35020412}, issn = {1557-8666}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bias ; Chromosomes/genetics ; Computational Biology ; High-Throughput Nucleotide Sequencing/statistics &amp; numerical data ; Linear Models ; Logistic Models ; Metagenome ; Metagenomics/*statistics &amp; numerical data ; Microbiota/genetics ; Regression Analysis ; Software ; Yeasts/genetics ; }, abstract = {High-throughput chromosome conformation capture (Hi-C) has recently been applied to natural microbial communities and revealed great potential to study multiple genomes simultaneously. Several extraneous factors may influence chromosomal contacts rendering the normalization of Hi-C contact maps essential for downstream analyses. However, the current paucity of metagenomic Hi-C normalization methods and the ignorance for spurious interspecies contacts weaken the interpretability of the data. Here, we report on two types of biases in metagenomic Hi-C experiments: explicit biases and implicit biases, and introduce HiCzin, a parametric model to correct both types of biases and remove spurious interspecies contacts. We demonstrate that the normalized metagenomic Hi-C contact maps by HiCzin result in lower biases, higher capability to detect spurious contacts, and better performance in metagenomic contig clustering.}, }
@article {pmid35019688, year = {2022}, author = {Lin, B and Wang, M and Gao, R and Ye, Z and Yu, Y and He, W and Qiao, N and Ma, Z and Ji, C and Shi, C and Zhou, X and Wang, Y and Zeng, F and Zhang, L and Gong, W and Cao, Z and Zhou, P and Melnikov, V and Ye, H and Li, Y and Zhang, Z and He, M and Qin, H and Zhang, Y}, title = {Characteristics of Gut Microbiota in Patients with GH-Secreting Pituitary Adenoma.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0042521}, pmid = {35019688}, issn = {2165-0497}, mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Case-Control Studies ; DNA, Bacterial/genetics ; Dysbiosis/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Growth Hormone/metabolism ; Growth Hormone-Secreting Pituitary Adenoma/metabolism/*microbiology ; Humans ; Insulin-Like Growth Factor I/metabolism ; Male ; Metagenomics ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prior study has demonstrated that gut microbiota at the genus level is significantly altered in patients with growth hormone (GH)-secreting pituitary adenoma (GHPA). Yet, no studies exist describing the state of gut microbiota at species level in GHPA. We performed a study using 16S rRNA amplicon sequencing in a cohort of patients with GH-secreting pituitary adenoma (GHPA, n = 28) and healthy controls (n = 67). Among them, 9 patients and 10 healthy controls were randomly chosen and enrolled in metagenomics shotgun sequencing, generating 280,426,512 reads after aligning to NCBI GenBank DataBase to acquire taxa information at the species level. Weighted UniFrac analysis revealed that microbial diversity was notably decreased in patients with GHPA, consistent with a previous study. With 16S rRNA sequencing, after correction for false-discovery rate (FDR), rank-sum test at the genus level revealed that the relative abundance of Oscillibacter and Enterobacter was remarkably increased in patients and Blautia and Romboutsia genera predominated in the controls, augmented by additional LEfSe (linear discriminant analysis effect size) analysis. As for further comparison at the species level with metagenomics sequencing, rank-sum test together with LEfSe analysis confirmed the enrichment of Alistipes shahii and Odoribacter splanchnicus in the patient group. Notably, LEfSe analysis with metagenomics also demonstrated that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND, derived from Enterobacter, were both significantly enriched in patients. Functional analysis showed that amino acid metabolism pathway was remarkably enriched in GHPA, while carbohydrate metabolism pathway was notably enriched in controls. Further, significant positive correlations were observed between Enterobacter and baseline insulin-like growth factor 1 (IGF-1), indicating that Enterobacter may be strongly associated with GH/IGF-1 axis in GHPA. Our data extend our insight into the GHPA microbiome, which may shed further light on GHPA pathogenesis and facilitate the exploration of novel therapeutic targets based on microbiota manipulation. IMPORTANCE Dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extraintestinal diseases. Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of GH and IGF-1, causing increased morbidity and mortality. Researches have reported that the GH/IGF-1 axis exerts its own influence on the intestinal microflora. Here, the results showed that compared with healthy controls, GHPA patients not only decreased the alpha diversity of the intestinal flora but also significantly changed their beta diversity. Further, metagenomics shotgun sequencing in the present study exhibited that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND were enriched in patients. Also, we were pleasantly surprised to find that the Enterobacter genus was strongly positively correlated with baseline IGF-1 levels. Collectively, our work provides the first glimpse of the dysbiosis of the gut microbiota at species level, providing a better understanding of the pathophysiological process of GHPA.}, }
@article {pmid35019672, year = {2022}, author = {Sun, Z and Zhang, M and Li, M and Bhaskar, Y and Zhao, J and Ji, Y and Cui, H and Zhang, H and Sun, Z}, title = {Interactions between Human Gut Microbiome Dynamics and Sub-Optimal Health Symptoms during Seafaring Expeditions.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0092521}, pmid = {35019672}, issn = {2165-0497}, mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Cohort Studies ; Diet ; *Expeditions/psychology ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Health Status ; Humans ; Male ; Metagenomics ; Microbiota ; Military Personnel/psychology ; Young Adult ; }, abstract = {During long ocean voyages, crew members are subject to complex pressures from their living and working environment, which lead to chronic diseases-like sub-optimal health status. Although the association between dysbiotic gut microbiome and chronic diseases has been broadly reported, the correlation between the sub-optimal health status and gut microbiome remains elusive. Here, the health status of 77 crew members (20-35 years old Chinese, male) during a 135-day sea expedition was evaluated using the shotgun metagenomics of stool samples and health questionnaires taken before and after the voyage. We found five core symptoms (e.g., abnormal defecation frequency, insomnia, poor sleep quality, nausea, and overeating) in 55 out of 77 crew members suffering from sub-optimal health status, and this was termed "seafaring syndrome" (SS) in this study. Significant correlation was found between the gut microbiome and SS rather than any single symptom. For example, SS was proven to be associated with individual perturbation in the gut microbiome, and the microbial dynamics between SS and non-SS samples were different during the voyage. Moreover, the microbial signature for SS was identified using the variation of 19 bacterial species and 26 gene families. Furthermore, using a Random Forest model, SS was predicted with high accuracy (84.4%, area under the concentration-time curve = 0.91) based on 28 biomarkers from pre-voyage samples, and the prediction model was further validated by another 30-day voyage cohort (accuracy = 83.3%). The findings in this study provide insights to help us discover potential predictors or even therapeutic targets for dysbiosis-related diseases. IMPORTANCE Systemic and chronic diseases are important health problems today and have been proven to be strongly associated with dysbiotic gut microbiome. Studying the association between the gut microbiome and sub-optimal health status of humans in extreme environments (such as ocean voyages) will give us a better understanding of the interactions between observable health signs and a stable versus dysbiotic gut microbiome states. In this paper, we illustrated that ocean voyages could trigger different symptoms for different crew member cohorts due to individual differences; however, the co-occurrence of high prevalence symptoms indicated widespread perturbation of the gut microbiome. By investigating the microbial signature and gut microbiome dynamics, we demonstrated that such sub-optimal health status can be predicted even before the voyage. We termed this phenomenon as "seafaring syndrome." This study not only provides the potential strategy for health management in extreme environments but also can assist the prediction of other dysbiosis-related diseases.}, }
@article {pmid35017031, year = {2022}, author = {Boeri, L and Donnaloja, F and Campanile, M and Sardelli, L and Tunesi, M and Fusco, F and Giordano, C and Albani, D}, title = {Using integrated meta-omics to appreciate the role of the gut microbiota in epilepsy.}, journal = {Neurobiology of disease}, volume = {164}, number = {}, pages = {105614}, doi = {10.1016/j.nbd.2022.105614}, pmid = {35017031}, issn = {1095-953X}, mesh = {Epilepsy/*microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Metagenomics ; }, abstract = {The way the human microbiota may modulate neurological pathologies is a fascinating matter of research. Epilepsy is a common neurological disorder, which has been largely investigated in correlation with microbiota health and function. However, the mechanisms that regulate this apparent connection are scarcely defined, and extensive effort has been conducted to understand the role of microbiota in preventing and reducing epileptic seizures. Intestinal bacteria seem to modulate the seizure frequency mainly by releasing neurotransmitters and inflammatory mediators. In order to elucidate the complex microbial contribution to epilepsy pathophysiology, integrated meta-omics could be pivotal. In fact, the combination of two or more meta-omics approaches allows a multifactorial study of microbial activity within the frame of disease or drug treatments. In this review, we provide information depicting and supporting the use of multi-omics to study the microbiota-epilepsy connection. We described different meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics), focusing on current technical challenges in stool collection procedures, sample extraction methods and data processing. We further discussed the current advantages and limitations of using the integrative approach of multi-omics in epilepsy investigations.}, }
@article {pmid35013454, year = {2022}, author = {Casimiro-Soriguer, CS and Loucera, C and Peña-Chilet, M and Dopazo, J}, title = {Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {450}, pmid = {35013454}, issn = {2045-2322}, support = {PAIDI2020- DOC_00350//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; PID2020-117979RB-I00//Ministerio de Ciencia e Innovación/ ; IMP/0019//Instituto de Salud Carlos III/ ; 813533//H2020 Marie Skłodowska-Curie Actions/ ; 676559//H2020 Research Infrastructures/ ; }, mesh = {Adenoma/*microbiology ; Colorectal Neoplasms/*microbiology ; *Gastrointestinal Microbiome ; Humans ; *Machine Learning ; Metagenomics/*methods ; }, abstract = {Gut microbiome is gaining interest because of its links with several diseases, including colorectal cancer (CRC), as well as the possibility of being used to obtain non-intrusive predictive disease biomarkers. Here we performed a meta-analysis of 1042 fecal metagenomic samples from seven publicly available studies. We used an interpretable machine learning approach based on functional profiles, instead of the conventional taxonomic profiles, to produce a highly accurate predictor of CRC with better precision than those of previous proposals. Moreover, this approach is also able to discriminate samples with adenoma, which makes this approach very promising for CRC prevention by detecting early stages in which intervention is easier and more effective. In addition, interpretable machine learning methods allow extracting features relevant for the classification, which reveals basic molecular mechanisms accounting for the changes undergone by the microbiome functional landscape in the transition from healthy gut to adenoma and CRC conditions. Functional profiles have demonstrated superior accuracy in predicting CRC and adenoma conditions than taxonomic profiles and additionally, in a context of explainable machine learning, provide useful hints on the molecular mechanisms operating in the microbiota behind these conditions.}, }
@article {pmid35013297, year = {2022}, author = {Yan, W and Hall, AB and Jiang, X}, title = {Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {1}, pmid = {35013297}, issn = {2055-5008}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Phase Variation ; }, abstract = {Antibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.}, }
@article {pmid35013099, year = {2022}, author = {Zhao, H and Jin, K and Jiang, C and Pan, F and Wu, J and Luan, H and Zhao, Z and Chen, J and Mou, T and Wang, Z and Lu, J and Lu, S and Hu, S and Xu, Y and Huang, M}, title = {A pilot exploration of multi-omics research of gut microbiome in major depressive disorders.}, journal = {Translational psychiatry}, volume = {12}, number = {1}, pages = {8}, pmid = {35013099}, issn = {2158-3188}, mesh = {Brain ; *Depressive Disorder, Major ; *Gastrointestinal Microbiome ; Gray Matter ; Humans ; *Microbiota ; }, abstract = {The pathophysiology of major depressive disorder (MDD) remains obscure. Recently, the microbiota-gut-brain (MGB) axis's role in MDD has an increasing attention. However, the specific mechanism of the multi-level effects of gut microbiota on host metabolism, immunity, and brain structure is unclear. Multi-omics approaches based on the analysis of different body fluids and tissues using a variety of analytical platforms have the potential to provide a deeper understanding of MGB axis disorders. Therefore, the data of metagenomics, metabolomic, inflammatory factors, and MRI scanning are collected from the two groups including 24 drug-naïve MDD patients and 26 healthy controls (HCs). Then, the correlation analysis is performed in all omics. The results confirmed that there are many markedly altered differences, such as elevated Actinobacteria abundance, plasma IL-1β concentration, lipid, vitamin, and carbohydrate metabolism disorder, and diminished grey matter volume (GMV) of inferior frontal gyrus (IFG) in the MDD patients. Notably, three kinds of discriminative bacteria, Ruminococcus bromii, Lactococcus chungangensis, and Streptococcus gallolyticus have an extensive correlation with metabolome, immunology, GMV, and clinical symptoms. All three microbiota are closely related to IL-1β and lipids (as an example, phosphoethanolamine (PEA)). Besides, Lactococcus chungangensis is negatively related to the GMV of left IFG. Overall, this study demonstrate that the effects of gut microbiome exert in MDD is multifactorial.}, }
@article {pmid35010887, year = {2021}, author = {Pinart, M and Dötsch, A and Schlicht, K and Laudes, M and Bouwman, J and Forslund, SK and Pischon, T and Nimptsch, K}, title = {Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis.}, journal = {Nutrients}, volume = {14}, number = {1}, pages = {}, pmid = {35010887}, issn = {2072-6643}, support = {01EA1906B//Federal Ministry of Food and Agriculture/ ; }, mesh = {Bacteria/*classification/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Obesity/*microbiology ; }, abstract = {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, I2 = 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, I2 = 81%) and non-significantly lower Bacteroidetes (-4.79, 95% CI -10.77, 1.20, I2 = 86%). At the genus level, lower relative proportions of Bifidobacterium and Eggerthella and higher Acidaminococcus, Anaerococcus, Catenibacterium, Dialister, Dorea, Escherichia-Shigella, Eubacterium, Fusobacterium, Megasphera, Prevotella, Roseburia, Streptococcus, and Sutterella 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.}, }
@article {pmid35007432, year = {2021}, author = {Ibrahim, A and Maatouk, M and Rajaonison, A and Zgheib, R and Haddad, G and Bou Khalil, J and Raoult, D and Bittar, F}, title = {Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0106921}, pmid = {35007432}, issn = {2165-0497}, mesh = {Actinomycetaceae/classification/genetics/*growth &amp; development/metabolism ; Bacteria/classification/genetics/*growth &amp; development/metabolism ; Coculture Techniques/instrumentation/*methods ; Culture Media/metabolism ; Humans ; Microbiota ; Polymerase Chain Reaction ; }, abstract = {The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a large proportion of the microbial kingdom (>26%). CPR are characterized by their obligate symbiotic or exoparasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the coculture of CPR with a suitable bacterial host. Based on various sputum samples, we tried to enrich CPR (Saccharibacteria members) and to cocultivate them with pure hosts (Schaalia odontolytica). This protocol was monitored by TaqMan real-time quantitative PCR (qPCR) using a system specific for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in coculturing and sequencing the complete genomes of two new Saccharibacteria species, "Candidatus Minimicrobia naudis" and "Candidatus Minimicrobia vallesae." In addition, we noticed a decrease in the CT values of Saccharibacteria and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members, and in the future, their currently unknown characteristics may be revealed. IMPORTANCE In this study, the first TaqMan real-time quantitative PCR (qPCR) system, targeting Saccharibacteria phylum, has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific, and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol facilitates subsequent studies of the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.}, }
@article {pmid34999397, year = {2022}, author = {Chang, HM and Chen, SS and Hsiao, SS and Chang, WS and Chien, IC and Duong, CC and Nguyen, TXQ}, title = {Water reclamation and microbial community investigation: Treatment of tetramethylammonium hydroxide wastewater through an anaerobic osmotic membrane bioreactor hybrid system.}, journal = {Journal of hazardous materials}, volume = {427}, number = {}, pages = {128200}, doi = {10.1016/j.jhazmat.2021.128200}, pmid = {34999397}, issn = {1873-3336}, mesh = {Anaerobiosis ; Bioreactors ; Membranes, Artificial ; *Microbiota ; Osmosis ; Quaternary Ammonium Compounds ; RNA, Ribosomal, 16S/genetics ; Waste Water ; Water ; *Water Purification ; }, abstract = {Tetramethylammonium hydroxide (TMAH) is a toxic photoresist developer used in the photolithography process in thin-film transistor liquid crystal display (TFT-LCD) production, and it can be removed through anaerobic treatment. TMAH cannot be released into the environment because of its higher toxicity. A tight membrane, such as a forward osmosis (FO) membrane, together with an anaerobic biological process can ensure that no TMAH is released into the environment. Thus, for the first time, an anaerobic osmotic membrane bioreactor (AnOMBR) hybrid system was developed in this study to treat a low-strength TMAH wastewater and to simultaneously investigate its microbial community. Microfiltration extraction was used to mitigate the salinity accumulation, and a periodically physical water cleaning was utilized to mitigate the FO membrane fouling. The diluted draw solute (MgSO4) was reconcentrated and reused by a membrane distillation (MD) process in the AnOMBR to achieve 99.99% TMAH removal in this AnOMBR-MD hybrid system, thereby ensuring that no TMAH is released into the natural environment. Moreover, the membrane fouling in the feed and draw sides were analyzed through the fluorescence excitation-emission matrix (FEEM) spectrophotometry to confirm that the humic acid-like materials were the primary membrane fouling components in this AnOMBR. Additionally, 16S rRNA metagenomics analysis indicated that Methanosaeta was the predominant contributor to methanogenesis and proliferated during the long-term operation. The methane yield was increased from 0.2 to 0.26 L CH4/g COD when the methanogen species acclimatized to the saline system.}, }
@article {pmid34998910, year = {2022}, author = {Liew, WP and Sabran, MR and Than, LT and Abd-Ghani, F}, title = {Metagenomic and proteomic approaches in elucidating aflatoxin B1 detoxification mechanisms of probiotic Lactobacillus casei Shirota towards intestine.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {160}, number = {}, pages = {112808}, doi = {10.1016/j.fct.2022.112808}, pmid = {34998910}, issn = {1873-6351}, mesh = {Aflatoxin B1/*toxicity ; Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inflammation/*drug therapy/etiology/genetics/microbiology ; Intestines/drug effects/metabolism/microbiology ; Lactobacillus casei/*physiology ; Male ; Metagenomics ; Probiotics/*administration &amp; dosage ; Proteomics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The modulation of gut microbiota and proteome due to aflatoxin B1 (AFB1) by probiotics remains unclear. This study investigated the alterations of gut microbiota and proteome in AFB1-exposed rats treated with probiotic Lactobacillus casei Shirota (Lcs). Forty male Sprague Dawley rats were randomly divided into five groups (n = 8) comprised control, AFB1, AFB1+activated charcoal, AFB1+Lcs, and Lcs groups. The rats were subjected to different treatments via oral gavage for four weeks. Urine and serum were collected for the measurement of AFB1 biomarkers and organs were harvested for histological analysis. Metagenomic sequencing was performed on fecal samples to profile gut microbiota. Besides, AFB1 most affected organ i.e. jejunum was subjected to proteomic analysis. The results indicated that Lcs intervention significantly reduced AFB1 biomarkers. H&amp;E-stained intestine showed Lcs alleviated AFB1-induced inflammation and abnormal cell growth, particularly at the jejunum. Although AFB1 increased potentially pathogenic bacteria and reduced beneficial bacteria abundance in feces, the microbiota composition was normalized with Lcs treatment. The gut proteome analysis of the jejunum sample showed several pathways of AFB1 toxicity, wherein Lcs treatment demonstrated its protective effect. It is concluded that metagenomic and proteomic approaches are useful tools to understand AFB1-Lcs interaction and detoxification mechanism in the gut.}, }
@article {pmid34998802, year = {2022}, author = {Pratt, M and Forbes, JD and Knox, NC and Van Domselaar, G and Bernstein, CN}, title = {Colorectal Cancer Screening in Inflammatory Bowel Diseases-Can Characterization of GI Microbiome Signatures Enhance Neoplasia Detection?.}, journal = {Gastroenterology}, volume = {162}, number = {5}, pages = {1409-1423.e1}, doi = {10.1053/j.gastro.2021.12.287}, pmid = {34998802}, issn = {1528-0012}, mesh = {Colonoscopy ; *Colorectal Neoplasms/diagnosis/epidemiology ; Early Detection of Cancer/methods ; Humans ; *Inflammatory Bowel Diseases/diagnosis ; *Microbiota ; }, abstract = {Current noninvasive methods for colorectal cancer (CRC) screening are not optimized for persons with inflammatory bowel diseases (IBDs), requiring patients to undergo frequent interval screening via colonoscopy. Although colonoscopy-based screening reduces CRC incidence in IBD patients, rates of interval CRC remain relatively high, highlighting the need for more targeted approaches. In recent years, the discovery of disease-specific microbiome signatures for both IBD and CRC has begun to emerge, suggesting that stool-based biomarker detection using metagenomics and other culture-independent technologies may be useful for personalized, early, noninvasive CRC screening in IBD patients. Here we discuss the utility of the stool microbiome as a noninvasive CRC screening tool. Comparing the performance of multiple microbiome-based CRC classifiers, including several multi-cohort meta-analyses, we find that noninvasive detection of colorectal adenomas and carcinomas from microbial biomarkers is an active area of study with promising early results.}, }
@article {pmid34996363, year = {2022}, author = {Jia, B and Chang, X and Fu, Y and Heng, W and Ye, Z and Liu, P and Liu, L and Al Shoffe, Y and Watkins, CB and Zhu, L}, title = {Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {18}, pmid = {34996363}, issn = {1471-2180}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Fungi/classification/genetics/isolation &amp; purification/metabolism ; Gene Ontology ; Iron/analysis/metabolism ; Metagenomics ; *Microbiota ; Minerals/analysis/metabolism ; Plant Leaves/metabolism/microbiology/ultrastructure ; Plant Necrosis and Chlorosis/*microbiology ; Plant Roots/growth &amp; development/microbiology ; Pyrus/metabolism/*microbiology/ultrastructure ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Water/analysis ; }, abstract = {BACKGROUND: Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant.<br><br>RESULTS: The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani.<br><br>CONCLUSIONS: It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.}, }
@article {pmid34995620, year = {2022}, author = {Liu, J and Liu, Y and Dong, W and Li, J and Yu, S and Wang, J and Zuo, R}, title = {Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics.}, journal = {Chemosphere}, volume = {293}, number = {}, pages = {133509}, doi = {10.1016/j.chemosphere.2021.133509}, pmid = {34995620}, issn = {1879-1298}, mesh = {Metagenomics ; *Microbiota ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; *Soil Pollutants/analysis ; Waste Disposal Facilities ; }, abstract = {Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.}, }
@article {pmid34989986, year = {2022}, author = {Philips, CA and Augustine, P and Ganesan, K and Ranade, S and Chopra, V and Patil, K and Shende, S and Ahamed, R and Kumbar, S and Rajesh, S and George, T and Mohanan, M and Mohan, N and Phadke, N and Rani, M and Narayanan, A and Jagan, SM}, title = {The role of gut microbiota in clinical complications, disease severity, and treatment response in severe alcoholic hepatitis.}, journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology}, volume = {41}, number = {1}, pages = {37-51}, pmid = {34989986}, issn = {0975-0711}, mesh = {*Acute Kidney Injury ; *End Stage Liver Disease ; *Gastrointestinal Microbiome ; Granulocyte Colony-Stimulating Factor/therapeutic use ; *Hepatitis, Alcoholic/microbiology ; Humans ; Male ; Severity of Illness Index ; }, abstract = {BACKGROUND: Dysbiotic gut bacteria engage in the development and progression of severe alcoholic hepatitis (SAH). We aimed to characterize bacterial communities associated with clinical events (CE), identify significant bacteria linked to CE, and define bacterial relationships associated with specific CE and outcomes at baseline and after treatment in SAH.<br><br>METHODS: We performed 16-s rRNA sequencing on stool samples (n=38) collected at admission and the last follow-up within 90 days in SAH patients (n=26; 12 corticosteroids; 14 granulocyte colony-stimulating factor, [G-CSF]). Validated pipelines were used to plot bacterial communities, profile functional metabolism, and identify significant taxa and functional metabolites. Conet/NetworkX® was utilized to identify significant non-random patterns of bacterial co-presence and mutual exclusion for clinical events.<br><br>RESULTS: All the patients were males with median discriminant function (DF) 64, Child-Turcotte-Pugh (CTP) 12, and model for end-stage liver disease (MELD) score 25.5. At admission, 27%, 42%, and 58% had acute kidney injury (AKI), hepatic encephalopathy (HE), and infections respectively; 38.5% died at end of follow-up. Specific bacterial families were associated with HE, sepsis, disease severity, and death. Lachnobacterium and Catenibacterium were associated with HE, and Pediococcus with death after steroid treatment. Change from Enterococcus (promotes AH) to Barnesiella (inhibits E. faecium) was significant after G-CSF. Phenylpropanoid-biosynthesis (innate-immunity) and glycerophospholipid-metabolism (cellular-integrity) pathways in those without infections and the death, respectively, were upregulated. Mutual interactions between Enterococcus cecorum, Acinetobacter schindleri, and Mitsuokella correlated with admission AKI.<br><br>CONCLUSIONS: Specific gut microbiota, their interactions, and metabolites are associated with complications of SAH and treatment outcomes. Microbiota-based precision medicine as adjuvant treatment may be a new therapeutic area.}, }
@article {pmid34989406, year = {2022}, author = {Ferravante, C and Sanna, G and Melone, V and Fromentier, A and Rocco, T and D'Agostino, Y and Lamberti, J and Alexandrova, E and Pecoraro, G and Pagliano, P and Astorri, R and Manzin, A and Weisz, A and Giurato, G and Galdiero, M and Rizzo, F and Franci, G}, title = {Nasopharyngeal virome analysis of COVID-19 patients during three different waves in Campania region of Italy.}, journal = {Journal of medical virology}, volume = {94}, number = {5}, pages = {2275-2283}, pmid = {34989406}, issn = {1096-9071}, support = {//PRIN 2017 "Natural and pharmacological inhibition of the early phase of viral replication (VirSudNet)" N° 2017M8R7N9/ ; //Ministero dell'Istruzione, Università e Ricerca, progr. POC R&amp;I 2014-2020 and PON R&amp;I 2014-2020 'Dottorati innovativi con caratterizzazione industriale' XXXV Ciclo (Fellowships DOT1328517, CUP D52G19000580006 to V.M. and DOT1318705, CUP: E66C18000940007 to C.F.). TR and YD'A are fellows of Rete Oncologica Campana and EA is a fellow of Fondazione U. Veronesi./ ; //CF, JL, VM are PhD student of the Research Doctorate in Veterinary Sciences of the University of Napoli 'Federico II', in 'Molecular and Translational Oncology and Innovative Medical-Surgical Technologies', University of Catanzaro "Magna Graecia" and in 'Translational Medicine for Development and Active Ageing' of the University of Salerno./ ; //Regione Campania (grants 'GENOMAeSALUTE', POR Campania FESR 2014/2020, azione 1.5; CUP: B41C17000080007 and 'Monitoring the spread and genomic variability of the Covid 19 virus in Campania using NGS technology,' POR Campania FESR 2014/2020, CUP: B14I20001980006)/ ; }, mesh = {*COVID-19/epidemiology/therapy/virology ; Humans ; Italy/epidemiology ; *Nasopharynx/virology ; Pandemics ; SARS-CoV-2 ; Virome ; }, abstract = {From December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has spread rapidly, leading to a global pandemic. Little is known about possible relationships between SARS-CoV-2 and other viruses in the respiratory system affecting patient prognosis and outcomes. This study aims to characterize respiratory virome profiles in association with SARS-CoV-2 infection and disease severity, through the analysis in 89 nasopharyngeal swabs collected in a patient's cohort from the Campania region (Southern Italy). Results show coinfections with viral species belonging to Coronaviridae, Retroviridae, Herpesviridae, Poxviridae, Pneumoviridae, Pandoraviridae, and Anelloviridae families and only 2% of the cases (2/89) identified respiratory viruses.}, }
@article {pmid34987055, year = {2022}, author = {Joseph, TA and Chlenski, P and Litman, A and Korem, T and Pe'er, I}, title = {Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.}, journal = {Genome research}, volume = {32}, number = {3}, pages = {558-568}, pmid = {34987055}, issn = {1549-5469}, support = {U54 CA209997/CA/NCI NIH HHS/United States ; }, mesh = {Case-Control Studies ; Genome, Bacterial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Patterns of sequencing coverage along a bacterial genome-summarized by a peak-to-trough ratio (PTR)-have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce Compute PTR (CoPTR): a tool for computing PTRs from complete reference genomes and assemblies. Using simulations and data from growth experiments in simple and complex communities, we show that CoPTR is more accurate than the current state of the art while also providing more PTR estimates overall. We further develop a theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with inflammatory bowel disease. We show that growth rates are personalized, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by showing how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome.}, }
@article {pmid34986315, year = {2022}, author = {Mejia, ME and Ottinger, S and Vrbanac, A and Babu, P and Zulk, JJ and Moorshead, D and Bode, L and Nizet, V and Patras, KA}, title = {Human Milk Oligosaccharides Reduce Murine Group B Streptococcus Vaginal Colonization with Minimal Impact on the Vaginal Microbiota.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0088521}, pmid = {34986315}, issn = {2379-5042}, support = {T32 GM136554/GM/NIGMS NIH HHS/United States ; Seed grant//UCSD Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence/ ; Junior Faculty Seed Grant//Caroline Wiess Law Fund for Research in Molecular Medicine/ ; NGP10103//Burroughs Wellcome Fund (BWF)/ ; T32GM136554//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Female ; Humans ; Infant, Newborn ; Mice ; *Microbiota ; Milk, Human ; Oligosaccharides/therapeutic use ; Pregnancy ; *Premature Birth ; RNA, Ribosomal, 16S ; Streptococcus agalactiae ; }, abstract = {Group B Streptococcus (GBS) colonizes the vaginal mucosa of a significant percentage of healthy women and is a leading cause of neonatal bacterial infections. Currently, pregnant women are screened in the last month of pregnancy, and GBS-positive women are given antibiotics during parturition to prevent bacterial transmission to the neonate. Recently, human milk oligosaccharides (HMOs) isolated from breastmilk were found to inhibit GBS growth and biofilm formation in vitro, and women that make certain HMOs are less likely to be vaginally colonized with GBS. Using in vitro human vaginal epithelial cells and a murine vaginal colonization model, we tested the impact of HMO treatment on GBS burdens and the composition of the endogenous microbiota by 16S rRNA amplicon sequencing. HMO treatment reduced GBS vaginal burdens in vivo with minimal alterations to the vaginal microbiota. HMOs displayed potent inhibitory activity against GBS in vitro, but HMO pretreatment did not alter adherence of GBS or the probiotic Lactobacillus rhamnosus to human vaginal epithelial cells. In addition, disruption of a putative GBS glycosyltransferase (Δsan_0913) rendered the bacterium largely resistant to HMO inhibition in vitro and in vivo but did not compromise its adherence, colonization, or biofilm formation in the absence of HMOs. We conclude that HMOs are a promising therapeutic bioactive to limit GBS vaginal colonization with minimal impacts on the vaginal microenvironment. IMPORTANCE During pregnancy, GBS ascension into the uterus can cause fetal infection or preterm birth. In addition, GBS exposure during labor creates a risk of serious disease in the vulnerable newborn and mother postpartum. Current recommended prophylaxis consists of administering broad-spectrum antibiotics to GBS-positive mothers during labor. Although antibiotics have significantly reduced GBS neonatal disease, there are several unintended consequences, including altered neonatal gut bacteria and increased risk for other types of infection. Innovative preventions displaying more targeted antimicrobial activity, while leaving the maternal microbiota intact, are thus appealing. Using a mouse model, we found that human milk oligosaccharides (HMOs) reduce GBS burdens without perturbing the vaginal microbiota. We conclude that HMOs are a promising alternative to antibiotics to reduce GBS neonatal disease.}, }
@article {pmid34970896, year = {2021}, author = {Peng, X and Zhao, Y and Lin, T and Shu, X and Hou, L and Gao, L and Wang, H and Ge, N and Yue, J}, title = {[Research of relationship between frailty and gut microbiota on middle-aged and the aged patients with diabetes].}, journal = {Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi}, volume = {38}, number = {6}, pages = {1126-1133}, doi = {10.7507/1001-5515.202101083}, pmid = {34970896}, issn = {1001-5515}, mesh = {Aged ; *Diabetes Mellitus ; *Epstein-Barr Virus Infections ; *Frailty ; *Gastrointestinal Microbiome ; Herpesvirus 4, Human ; Humans ; Middle Aged ; }, abstract = {Gut microbiota plays an important role in development of diabetes with frailty. Therefore, it is of great significance to study the structural and functional characteristics of gut microbiota in Chinese with frailty. Totally 30 middle-aged and the aged participants in communities with diabetes were enrolled in this study, and their feces were collected. At the same time, we developed a metagenome analysis to explore the different of the structural and functional characteristics between diabetes with frailty and diabetes without frailty. The results showed the alpha diversity of intestinal microbiota in diabetes with frailty was lower. Collinsella and Butyricimonas were more abundant in diabetes with frailty. The functional characteristics showed that histidine metabolism, Epstein-Barr virus infection, sulfur metabolism, and biosynthesis of type Ⅱ polyketide products were upregulated in diabetes with frailty. Otherwise, butanoate metabolism and phenylalanine metabolism were down-regulated in diabetes with frailty. This research provides theoretical basic for exploring the mechanism of the gut microbiota on the occurrence and development of diabetes with frailty, and provides a basic for prevention and intervention of it.}, }
@article {pmid34970508, year = {2021}, author = {Jiang, Q and Liu, X and Yang, Q and Chen, L and Yang, D}, title = {Salivary Microbiome in Adenoid Cystic Carcinoma Detected by 16S rRNA Sequencing and Shotgun Metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {774453}, pmid = {34970508}, issn = {2235-2988}, mesh = {*Carcinoma, Adenoid Cystic ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Salivary Gland Neoplasms ; }, abstract = {Microorganisms are confirmed to be closely related to the occurrence and development of cancers in human beings. However, there has been no published report detailing relationships between the oral microbiota and salivary adenoid cystic carcinoma (SACC). In this study, unstimulated saliva was collected from 13 SACC patients and 10 healthy controls. The microbial diversities, compositions and functions were comprehensively analyzed after 16S rRNA sequencing and whole-genome shotgun metagenomic sequencing. The alpha diversity showed no significant difference between SACC patients and healthy controls, while beta diversity showed a separation trend. The SACC patients showed higher abundances of Streptococcus and Rothia, while Prevotella and Alloprevotella were more abundant in healthy controls. The prevalent KEGG pathways, carbohydrate-active enzymes, antibiotic resistances and virulence factors as well as the biomarkers in SACC were determined by functional gene analysis. Our study preliminarily investigated the salivary microbiome of SACC patients compared with healthy controls and might be the basis for further studies on novel diagnostic and treatment strategies.}, }
@article {pmid34969979, year = {2022}, author = {Valles-Colomer, M and Bacigalupe, R and Vieira-Silva, S and Suzuki, S and Darzi, Y and Tito, RY and Yamada, T and Segata, N and Raes, J and Falony, G}, title = {Variation and transmission of the human gut microbiota across multiple familial generations.}, journal = {Nature microbiology}, volume = {7}, number = {1}, pages = {87-96}, pmid = {34969979}, issn = {2058-5276}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/*genetics ; Bacterial Physiological Phenomena/genetics ; Child ; Child, Preschool ; Cohort Studies ; *Family ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics/physiology ; Humans ; *Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Although the composition and functional potential of the human gut microbiota evolve over the lifespan, kinship has been identified as a key covariate of microbial community diversification. However, to date, sharing of microbiota features within families has mostly been assessed between parents and their direct offspring. Here we investigate the potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (n = 102) spanning 3 to 5 generations over the same female bloodline. We observe microbiome community composition associated with kinship, with seven low abundant genera displaying familial distribution patterns. While kinship and current cohabitation emerge as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother-daughter pairs, decreasing with increasing daughter's age and being higher among cohabiting pairs than those living apart. Although rare, we detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.}, }
@article {pmid34966824, year = {2021}, author = {Gao, B and Zhao, X and Liu, X and Yang, X and Zhang, A and Huang, H and Liou, YL and Xu, D}, title = {Imbalance of the Gut Microbiota May Be Associated with Missed Abortions: A Perspective Study from a General Hospital of Hunan Province.}, journal = {Journal of immunology research}, volume = {2021}, number = {}, pages = {5571894}, pmid = {34966824}, issn = {2314-7156}, mesh = {Abortion, Missed/*etiology ; Adult ; Biodiversity ; China ; Computational Biology/methods ; Disease Susceptibility ; Dysbiosis/*complications/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Mycoplasma ; Pregnancy ; Risk Factors ; }, abstract = {OBJECTIVE: To conduct a preliminary investigation that shows the possible correlation between the change of gut microbiota and missed abortions (MAs), which further provides a new potential insight for the prevention and therapy of MAs.<br><br>METHOD: One hundred women, including 50 patients with MAs (case group) and 50 normal pregnant women (control group), were enrolled in the study. Fecal specimens were collected in the first trimester. Bacterial DNA was extracted, hybridized with primers of specific genes, and then detected by bacterial chip. The composition and the relative abundance of the gut microbiota were compared and analyzed. Furthermore, Kyoto Encyclopedia of Genes and Genomes enrichment analysis was used to explore the relative pathways.<br><br>RESULTS: (1) The α-diversity and β-diversity of the gut microbiota in patients with MAs were significantly lower than that those in normal pregnant women (P < 0.05). At the phylum level, Firmicutes, Proteobacteria, Actinomycetes, and Bacteroidetes accounted for the main proportion of intestinal flora in the 2 groups. Only Actinobacteria was high in the case group. Significant differences were found between the two groups at the phylum level (P < 0.05). Prevotella, Lactobacillus, and Paracoccus were significantly more abundant in the control group than in the case group at the genus level (P < 0.05). (2) KEGG pathway enrichment analysis found significant differences in 27 signaling pathways and metabolic pathways between the two groups of differentially expressed genes (all adjusted P < 0.05). (3) The positive rate of M. hominins (MH) detection in the control group was significantly higher in the MA group (χ 2 = 7.853, P = 0.004).<br><br>CONCLUSION: The high abundance of Actinobacteria in the MA group was the first time found and reported in the study. The dysbiosis of the gut microbiota correlates with MAs. This study provided insights into the potential change of gut microbiota of MAs and the potential underlying mechanisms through certain impaired lipid metabolism and aroused inflammation pathways. Comprehensive insights regarding gut microbiota may facilitate improved understanding and the development of novel therapeutic and preventive strategies for MAs.}, }
@article {pmid34965016, year = {2021}, author = {Yu, JS and Youn, GS and Choi, J and Kim, CH and Kim, BY and Yang, SJ and Lee, JH and Park, TS and Kim, BK and Kim, YB and Roh, SW and Min, BH and Park, HJ and Yoon, SJ and Lee, NY and Choi, YR and Kim, HS and Gupta, H and Sung, H and Han, SH and Suk, KT and Lee, DY}, title = {Lactobacillus lactis and Pediococcus pentosaceus-driven reprogramming of gut microbiome and metabolome ameliorates the progression of non-alcoholic fatty liver disease.}, journal = {Clinical and translational medicine}, volume = {11}, number = {12}, pages = {e634}, pmid = {34965016}, issn = {2001-1326}, mesh = {Animals ; Benzofurans/metabolism ; Cellular Reprogramming/*immunology/physiology ; Diet, Western/adverse effects ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/*immunology/physiology ; Lactobacillus/*metabolism/pathogenicity ; Metabolome/*immunology/physiology ; Mice ; Non-alcoholic Fatty Liver Disease/*drug therapy/physiopathology ; Pediococcus pentosaceus/*metabolism/pathogenicity ; Quinolines/metabolism ; }, abstract = {BACKGROUND: Although microbioa-based therapies have shown putative effects on the treatment of non-alcoholic fatty liver disease (NAFLD), it is not clear how microbiota-derived metabolites contribute to the prevention of NAFLD. We explored the metabolomic signature of Lactobacillus lactis and Pediococcus pentosaceus in NAFLD mice and its association in NAFLD patients.<br><br>METHODS: We used Western diet-induced NAFLD mice, and L. lactis and P. pentosaceus were administered to animals in the drinking water at a concentration of 109 CFU/g for 8 weeks. NAFLD severity was determined based on liver/body weight, pathology and biochemistry markers. Caecal samples were collected for the metagenomics by 16S rRNA sequencing. Metabolite profiles were obtained from caecum, liver and serum. Human stool samples (healthy control [n = 22] and NAFLD patients [n = 23]) were collected to investigate clinical reproducibility for microbiota-derived metabolites signature and metabolomics biomarker.<br><br>RESULTS: L. lactis and P. pentosaceus supplementation effectively normalized weight ratio, NAFLD activity score, biochemical markers, cytokines and gut-tight junction. While faecal microbiota varied according to the different treatments, key metabolic features including short chain fatty acids (SCFAs), bile acids (BAs) and tryptophan metabolites were analogously restored by both probiotic supplementations. The protective effects of indole compounds were validated with in vitro and in vivo models, including anti-inflammatory effects. The metabolomic signatures were replicated in NAFLD patients, accompanied by the comparable levels of Firmicutes/Bacteroidetes ratio, which was significantly higher (4.3) compared with control (0.6). Besides, the consequent biomarker panel with six stool metabolites (indole, BAs, and SCFAs) showed 0.922 (area under the curve) in the diagnosis of NAFLD.<br><br>CONCLUSIONS: NAFLD progression was robustly associated with metabolic dys-regulations in the SCFAs, bile acid and indole compounds, and NAFLD can be accurately diagnosed using the metabolites. L. lactis and P. pentosaceus ameliorate NAFLD progression by modulating gut metagenomic and metabolic environment, particularly tryptophan pathway, of the gut-liver axis.}, }
@article {pmid34964297, year = {2021}, author = {Becsei, Á and Solymosi, N and Csabai, I and Magyar, D}, title = {Detection of antimicrobial resistance genes in urban air.}, journal = {MicrobiologyOpen}, volume = {10}, number = {6}, pages = {e1248}, pmid = {34964297}, issn = {2045-8827}, mesh = {*Air Microbiology ; Bacteria/*genetics ; Cities ; Drug Resistance, Bacterial/*genetics ; *Genes, Bacterial ; Metagenome ; *Microbiota ; Sensitivity and Specificity ; }, abstract = {To understand antibiotic resistance in pathogenic bacteria, we need to monitor environmental microbes as reservoirs of antimicrobial resistance genes (ARGs). These bacteria are present in the air and can be investigated with the whole metagenome shotgun sequencing approach. This study aimed to investigate the feasibility of a method for metagenomic analysis of microbial composition and ARGs in the outdoor air. Air samples were collected with a Harvard impactor in the PM10 range at 50 m from a hospital in Budapest. From the DNA yielded from samples of PM10 fraction single-end reads were generated with an Ion Torrent sequencer. During the metagenomic analysis, reads were classified taxonomically. The core bacteriome was defined. Reads were assembled to contigs and the ARG content was analyzed. The dominant genera in the core bacteriome were Bacillus, Acinetobacter, Leclercia and Paenibacillus. Among the identified ARGs best hits were vanRA, Bla1, mphL, Escherichia coli EF-Tu mutants conferring resistance to pulvomycin; BcI, FosB, and mphM. Despite the low DNA content of the samples of PM10 fraction, the number of detected airborne ARGs was surprisingly high.}, }
@article {pmid34961896, year = {2021}, author = {Johny, TK and Puthusseri, RM and Bhat, SG}, title = {Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {87}, pmid = {34961896}, issn = {1432-072X}, support = {MOES/10-MLR/2/2007//centre for marine living resources &amp; ecology- ministry of earth sciences, government of india/ ; MOES/10-MLRTD/03/2013//centre for marine living resources &amp; ecology- ministry of earth sciences, government of india/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Fishes ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Fish gut microbiota, encompassing a colossal reserve of microbes represents a dynamic ecosystem, influenced by a myriad of environmental and host factors. The current study presents a comprehensive insight into Sardinella longiceps gut microbiome using whole metagenome shotgun sequencing. Taxonomic profiling identified the predominance of phylum Proteobacteria, comprising of Photobacterium, Vibrio and Shewanella sp. Functional annotation revealed the dominance of Clustering based subsystems, Carbohydrate, and Amino acids and derivatives. Analysis of Virulence, disease and defense subsystem identified genes conferring resistance to antibiotics and toxic compounds, like multidrug resistance efflux pumps and resistance genes for fluoroquinolones and heavy metals like cobalt, zinc, cadmium and copper. The presence of overlapping genetic mechanisms of resistance to antibiotics and heavy metals, like the efflux pumps is a serious cause of concern as it is likely to aggravate co-selection pressure, leading to an increased dissemination of these resistance genes to fish and humans.}, }
@article {pmid34960807, year = {2021}, author = {Folgueiras-González, A and van den Braak, R and Deijs, M and Kuller, W and Sietsma, S and Thuring, V and van der Hoek, L and de Groof, A}, title = {Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960807}, issn = {1999-4915}, mesh = {Animals ; Astroviridae/isolation &amp; purification ; Enteroviruses, Porcine/*isolation &amp; purification ; Female ; Intestines/*virology ; Male ; Metagenomics ; Rotavirus/*isolation &amp; purification ; Sapovirus/*isolation &amp; purification ; Swine ; Swine Diseases/*virology ; Virome/*physiology ; Wasting Syndrome/*veterinary/virology ; Weaning ; }, abstract = {A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20-30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.}, }
@article {pmid34960726, year = {2021}, author = {Redila, CD and Prakash, V and Nouri, S}, title = {Metagenomics Analysis of the Wheat Virome Identifies Novel Plant and Fungal-Associated Viral Sequences.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960726}, issn = {1999-4915}, mesh = {Base Sequence ; Fungal Viruses/classification/*genetics/*isolation &amp; purification ; Fungi/virology ; Genome, Viral ; Metagenomics ; Phylogeny ; Plant Diseases/*virology ; Triticum/microbiology ; *Virome ; Viruses/classification/*genetics/*isolation &amp; purification ; }, abstract = {Wheat viruses including wheat streak mosaic virus, Triticum mosaic virus, and barley yellow dwarf virus cost substantial losses in crop yields every year. Although there have been extensive studies conducted on these known wheat viruses, currently, there is limited knowledge about all components of the wheat (Triticum aestivum L.) virome. Here, we determined the composition of the wheat virome through total RNA deep sequencing of field-collected leaf samples. Sequences were de novo assembled after removing the host reads, and BLASTx searches were conducted. In addition to the documented wheat viruses, novel plant and fungal-associated viral sequences were identified. We obtained the full genome sequence of the first umbra-like associated RNA virus tentatively named wheat umbra-like virus in cereals. Moreover, a novel bi-segmented putative virus tentatively named wheat-associated vipovirus sharing low but significant similarity with both plant and fungal-associated viruses was identified. Additionally, a new putative fungal-associated tobamo-like virus and novel putative Mitovirus were discovered in wheat samples. The discovery and characterization of novel viral sequences associated with wheat is important to determine if these putative viruses may pose a threat to the wheat industry or have the potential to be used as new biological control agents for wheat pathogens either as wild-type or recombinant viruses.}, }
@article {pmid34960693, year = {2021}, author = {Paim, WP and Maggioli, MF and Falkenberg, SM and Ramachandran, A and Weber, MN and Canal, CW and Bauermann, FV}, title = {Virome Characterization in Commercial Bovine Serum Batches-A Potentially Needed Testing Strategy for Biological Products.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960693}, issn = {1999-4915}, mesh = {Animals ; Bacteriophages/genetics/*isolation &amp; purification ; *Biological Products ; Cattle/*blood ; DNA Viruses/genetics/*isolation &amp; purification ; Drug Contamination ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA Viruses/genetics/*isolation &amp; purification ; Serum/*virology ; *Virome ; }, abstract = {Bovine serum has been widely used as a universal supplement in culture media and other applications, including the manufacture of biological products and the production of synthetic meat. Currently, commercial bovine serum is tested for possible viral contaminants following regional guidelines. Regulatory agencies' established tests focused on detecting selected animal origin viruses and are based on virus isolation, immunofluorescence, and hemadsorption assays. However, these tests may fail to detect new or emerging viruses in biological products. High-throughput sequencing is a powerful option since no prior knowledge of the viral targets is required. In the present study, we evaluate the virome of seven commercial batches of bovine serum from Mexico (one batch), New Zealand (two batches), and the United States (four batches) using a specific preparation and enrichment method for pooled samples and sequencing using an Illumina platform. A variety of circular replicase-encoding single-stranded (CRESS) DNA families (Genomoviridae, Circoviridae, and Smacoviridae) was identified. Additionally, CrAssphage, a recently discovered group of bacteriophage correlated with fecal contamination, was identified in 85% of the tested batches. Furthermore, sequences representing viral families with single-stranded DNA (Parvoviridae), double-stranded DNA (Polyomaviridae and Adenoviridae), single-stranded RNA (Flaviviridae, Picornaviridae, and Retroviridae), and double-stranded RNA (Reoviridae) were identified. These results support that high-throughput sequencing associated with viral enrichment is a robust tool and should be considered an additional layer of safety when testing pooled biologicals to detect viral contaminants overlooked by the current testing protocols.}, }
@article {pmid34960644, year = {2021}, author = {Litov, AG and Belova, OA and Kholodilov, IS and Gadzhikurbanov, MN and Gmyl, LV and Oorzhak, ND and Saryglar, AA and Ishmukhametov, AA and Karganova, GG}, title = {Possible Arbovirus Found in Virome of Melophagus ovinus.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960644}, issn = {1999-4915}, mesh = {Animals ; Arboviruses/*genetics/isolation &amp; purification ; Cell Line ; Diptera/*virology ; Ectoparasitic Infestations/*virology ; Phylogeny ; Reoviridae ; Rhabdoviridae ; Russia ; Sheep ; Sheep Diseases/*parasitology ; *Virome ; }, abstract = {Members of the Lipopteninae subfamily are blood-sucking ectoparasites of mammals. The sheep ked (Melophagus ovinus) is a widely distributed ectoparasite of sheep. It can be found in most sheep-rearing areas and can cause skin irritation, restlessness, anemia, weight loss and skin injuries. Various bacteria and some viruses have been detected in M. ovinus; however, the virome of this ked has never been studied using modern approaches. Here, we study the virome of M. ovinus collected in the Republic of Tuva, Russia. In our research, we were able to assemble full genomes for five novel viruses, related to the Rhabdoviridae (Sigmavirus), Iflaviridae, Reoviridae and Solemoviridae families. Four viruses were found in all five of the studied pools, while one virus was found in two pools. Phylogenetically, all of the novel viruses clustered together with various recently described arthropod viruses. All the discovered viruses were tested on their ability to replicate in the mammalian porcine embryo kidney (PEK) cell line. Aksy-Durug Melophagus sigmavirus RNA was detected in the PEK cell line cultural supernate after the first, second and third passages. Such data imply that this virus might be able to replicate in mammalian cells, and thus, can be considered as a possible arbovirus.}, }
@article {pmid34960634, year = {2021}, author = {do Socorro Fôro Ramos, E and de Oliveira Ribeiro, G and Villanova, F and de Padua Milagres, FA and Brustulin, R and Araújo, ELL and Pandey, RP and Raj, VS and Deng, X and Delwart, E and Luchs, A and da Costa, AC and Leal, É}, title = {Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, pmid = {34960634}, issn = {1999-4915}, mesh = {Acute Disease ; Adenoviridae/genetics ; Adolescent ; Adult ; Aged ; Bacteriophages/genetics ; Brazil/epidemiology ; Child ; Child, Preschool ; Feces/virology ; Female ; Gastroenteritis/epidemiology/*virology ; Humans ; Male ; *Metagenomics ; Middle Aged ; Norovirus/genetics ; Rotavirus/genetics ; Virome/*genetics ; Viruses/classification/*genetics/isolation &amp; purification ; Young Adult ; }, abstract = {Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.}, }
@article {pmid34960001, year = {2021}, author = {Kaashyap, M and Cohen, M and Mantri, N}, title = {Microbial Diversity and Characteristics of Kombucha as Revealed by Metagenomic and Physicochemical Analysis.}, journal = {Nutrients}, volume = {13}, number = {12}, pages = {}, pmid = {34960001}, issn = {2072-6643}, mesh = {Acetobacter/isolation &amp; purification ; Bacteria/classification ; Chemical Phenomena ; Fermentation ; Humans ; Kombucha Tea/*analysis/*microbiology ; Metagenomics/*methods ; *Microbiota ; Phenols/analysis ; Probiotics/analysis ; Proteins/analysis ; RNA, Ribosomal, 16S/genetics ; Tea/chemistry ; Yeasts/classification ; }, abstract = {Kombucha is a fermented tea made from a Symbiotic Culture of Bacteria and Yeast (SCOBY) with a long history of use as a health tonic. It is likely that most health benefits come from the tea and fermentation metabolites from specific microbial communities. Despite its growing importance as a functional health drink, the microbial ecosystem present in kombucha has not been fully documented. To characterize the microbial composition and biochemical properties of 'The Good Brew' original base kombucha, we used metagenomics amplicon (16S rRNA and ITS) sequencing to identify the microbial communities at the taxonomic level. We identified 34 genera with 200 microbial species yet described in kombucha. The dominance of organic acid producing microorganisms Acetobacter, Komagataeibacter and Starmerella are healthy for the human gut and their glucose metabolising activities have a putative role in preventing conditions such as diabetes and obesity. Kombucha contains high protein (3.31 µg/mL), high phenolic content (290.4 mg/100 mL) and low sugars (glucose: 1.87 g/L; sucrose 1.11 g/L; fructose: 0.05 g/L) as compared to green tea. The broad microbial diversity with proven health benefits for the human gut suggests kombucha is a powerful probiotic. These findings are important to improve the commercial value of kombucha and uncover the immense prospects for health benefits.}, }
@article {pmid34954158, year = {2022}, author = {Zhao, X and Liu, M and Yang, S and Gong, H and Ma, J and Li, C and Wang, K}, title = {Performance and microbial community evaluation of full-scale two-phase anaerobic digestion of waste activated sludge.}, journal = {The Science of the total environment}, volume = {814}, number = {}, pages = {152525}, doi = {10.1016/j.scitotenv.2021.152525}, pmid = {34954158}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; Methane ; *Microbiota ; *Sewage ; }, abstract = {"Temperature Staging and Biological Phasing" (TSBP) is an improved two-phase anaerobic digestion (AD) technology. This technology hydrolyzes waste activated sludge (WAS) at 45 °C and converts methane at mesophilic temperature (35-38 °C), with hydraulic retention times of 3-5 d and 14-17 d, respectively. In this study, the performance and microbial community dynamics of full-scale TSBP-based sludge anaerobic digestion system were studied, and the technology was evaluated by energy balance and ecological benefit analysis. The stable operation for 390 d showed that the cumulative biogas yield was about 349,041 m3, the maximum biogas yield rate was 563.68 L/kg VS, and the VS degradation rate of organic matters in the sludge was 47.19%. Proteobacteria and Firmicutes were found to be the dominant bacteria in both thermophilic and mesophilic reactors. Methanobacterium and Methanosarcina were the two most abundant methanogenic genera in the AD samples. The aceticlastic methanogenesis was likely the predominant production pathway of methane in AD processes based on metagenomics. The TSBP system operated stably, and the recovered energy could achieve energy self-sufficiency, which provided technical reference for the anaerobic treatment of sludge.}, }
@article {pmid34952941, year = {2022}, author = {Saheb Kashaf, S and Proctor, DM and Deming, C and Saary, P and Hölzer, M and ,  and Taylor, ME and Kong, HH and Segre, JA and Almeida, A and Finn, RD}, title = {Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions.}, journal = {Nature microbiology}, volume = {7}, number = {1}, pages = {169-179}, pmid = {34952941}, issn = {2058-5276}, support = {ZIA HG000180/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Child ; Child, Preschool ; Colony Count, Microbial/methods ; Female ; *Genome, Microbial ; Humans ; Infant ; Infant, Newborn ; Male ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; Phylogeny ; Skin/*microbiology ; Symbiosis ; Young Adult ; }, abstract = {Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic dermatitis. Previous metagenomic investigations into the role of the skin microbiome in health or disease have found that much of the sequenced data do not match reference genomes, making it difficult to interpret metagenomic datasets. We combined bacterial cultivation and metagenomic sequencing to assemble the Skin Microbial Genome Collection (SMGC), which comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. The metagenomic datasets that we generated were combined with publicly available skin metagenomic datasets to identify members and functions of the human skin microbiome. The SMGC collection includes 174 newly identified bacterial species and 12 newly identified bacterial genera, including the abundant genus 'Candidatus Pellibacterium', which has been newly associated with the skin. The SMGC increases the characterized set of known skin bacteria by 26%. We validated the SMGC metagenome-assembled genomes by comparing them with sequenced isolates obtained from the same samples. We also recovered 12 eukaryotic species and assembled thousands of viral sequences, including newly identified clades of jumbo phages. The SMGC enables classification of a median of 85% of skin metagenomic sequences and provides a comprehensive view of skin microbiome diversity, derived primarily from samples obtained in North America.}, }
@article {pmid34951957, year = {2022}, author = {Bell, HN and Rebernick, RJ and Goyert, J and Singhal, R and Kuljanin, M and Kerk, SA and Huang, W and Das, NK and Andren, A and Solanki, S and Miller, SL and Todd, PK and Fearon, ER and Lyssiotis, CA and Gygi, SP and Mancias, JD and Shah, YM}, title = {Reuterin in the healthy gut microbiome suppresses colorectal cancer growth through altering redox balance.}, journal = {Cancer cell}, volume = {40}, number = {2}, pages = {185-200.e6}, pmid = {34951957}, issn = {1878-3686}, support = {R01 CA148828/CA/NCI NIH HHS/United States ; R01 DK095201/DK/NIDDK NIH HHS/United States ; P30 CA046592/CA/NCI NIH HHS/United States ; R01 CA245546/CA/NCI NIH HHS/United States ; R01 CA248160/CA/NCI NIH HHS/United States ; I01 BX004842/BX/BLRD VA/United States ; R37 CA237421/CA/NCI NIH HHS/United States ; R01 NS099280/NS/NINDS NIH HHS/United States ; P30 DK089503/DK/NIDDK NIH HHS/United States ; P50 CA130810/CA/NCI NIH HHS/United States ; R01 CA244931/CA/NCI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; F31 CA247457/CA/NCI NIH HHS/United States ; U24 DK097153/DK/NIDDK NIH HHS/United States ; T32 GM007315/GM/NIGMS NIH HHS/United States ; R01 CA215607/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Biomarkers ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Colorectal Neoplasms/*metabolism/*pathology ; Disease Models, Animal ; Energy Metabolism ; *Gastrointestinal Microbiome ; Glutathione/metabolism ; Glyceraldehyde/*analogs &amp; derivatives/metabolism/pharmacology ; Host Microbial Interactions ; Humans ; Intestinal Mucosa/metabolism/microbiology/pathology ; Metabolomics/methods ; Metagenomics/methods ; Mice ; Models, Biological ; *Oxidation-Reduction/drug effects ; Oxidative Stress ; Propane/*metabolism/pharmacology ; Signal Transduction ; Xenograft Model Antitumor Assays ; }, abstract = {Microbial dysbiosis is a colorectal cancer (CRC) hallmark and contributes to inflammation, tumor growth, and therapy response. Gut microbes signal via metabolites, but how the metabolites impact CRC is largely unknown. We interrogated fecal metabolites associated with mouse models of colon tumorigenesis with varying mutational load. We find that microbial metabolites from healthy mice or humans are growth-repressive, and this response is attenuated in mice and patients with CRC. Microbial profiling reveals that Lactobacillus reuteri and its metabolite, reuterin, are downregulated in mouse and human CRC. Reuterin alters redox balance, and reduces proliferation and survival in colon cancer cells. Reuterin induces selective protein oxidation and inhibits ribosomal biogenesis and protein translation. Exogenous Lactobacillus reuteri restricts colon tumor growth, increases tumor reactive oxygen species, and decreases protein translation in vivo. Our findings indicate that a healthy microbiome and specifically, Lactobacillus reuteri, is protective against CRC through microbial metabolite exchange.}, }
@article {pmid34949778, year = {2022}, author = {Shi, ZJ and Dimitrov, B and Zhao, C and Nayfach, S and Pollard, KS}, title = {Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.}, journal = {Nature biotechnology}, volume = {40}, number = {4}, pages = {507-516}, pmid = {34949778}, issn = {1546-1696}, support = {DMS-1563159//National Science Foundation (NSF)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Genotype ; Humans ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. To address these issues, we developed the GenoTyper for Prokaryotes (GT-Pro), a suite of methods to catalog SNPs from genomes and use unique k-mers to rapidly genotype these SNPs from metagenomes. Compared to methods that use read alignment, GT-Pro is more accurate and two orders of magnitude faster. Using high-quality genomes, we constructed a catalog of 104 million SNPs in 909 human gut species and used unique k-mers targeting this catalog to characterize the global population structure of gut microbes from 7,459 samples. GT-Pro enables fast and memory-efficient metagenotyping of millions of SNPs on a personal computer.}, }
@article {pmid34946200, year = {2021}, author = {Bordugo, A and Salvetti, E and Rodella, G and Piazza, M and Dianin, A and Amoruso, A and Piacentini, G and Pane, M and Torriani, S and Vitulo, N and Felis, GE}, title = {Assessing Gut Microbiota in an Infant with Congenital Propionic Acidemia before and after Probiotic Supplementation.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, pmid = {34946200}, issn = {2076-2607}, abstract = {Propionic Acidemia (PA) is a rare inherited metabolic disorder caused by the enzymatic block of propionyl-CoA carboxylase with the consequent accumulation of propionic acid, which is toxic for the brain and cardiac cells. Since a considerable amount of propionate is produced by intestinal bacteria, interest arose in the attempt to reduce propionate-producing bacteria through a monthly antibiotic treatment of metronidazole. In the present study, we investigated the gut microbiota structure of an infant diagnosed at 4 days of life through Expanded Newborn Screening (NBS) and treated the child following international guidelines with a special low-protein diet, specific medications and strict biochemical monitoring. Microbiota composition was assessed during the first month of life, and the presence of Bacteroides fragilis, known to be associated with propionate production, was effectively decreased by metronidazole treatment. After five antibiotic therapy cycles, at 4 months of age, the infant was supplemented with a daily mixture of three bifidobacterial strains, known not to be propionate producers. The supplementation increased the population of bifidobacteria, with Bifidobacterium breve as the dominating species; Ruminococcus gnavus, an acetate and formate producer, was also identified. Metabarcoding analysis, compared with low coverage whole metagenome sequencing, proved to capture all the microbial biodiversity and could be the elected tool for fast and cost-effective monitoring protocols to be implemented in the follow up of rare metabolic disorders such as PA. Data obtained could be a possible starting point to set up tailored microbiota modification treatment studies in the attempt to improve the quality of life of people affected by propionic acidemia.}, }
@article {pmid34941731, year = {2021}, author = {Hu, D and Giesy, JP and Guo, M and Ung, WK and Kong, Y and Mok, KM and Lee, SM}, title = {Temporal Patterns of Bacterial and Viral Communities during Algae Blooms of a Reservoir in Macau.}, journal = {Toxins}, volume = {13}, number = {12}, pages = {}, pmid = {34941731}, issn = {2072-6651}, mesh = {Bacteria/*growth &amp; development ; Biodiversity ; Environmental Monitoring ; *Eutrophication ; Macau ; RNA, Ribosomal, 16S ; Viruses/*growth &amp; development ; *Water Microbiology ; }, abstract = {Compositions of microbial communities associated with blooms of algae in a storage reservoir in Macau, China were investigated between 2013 and 2016. Algae were enumerated by visible light microscopy. Profiles of organisms in water were examined by 16S rRNA sequences and viral metagenomics, based on next generation sequencing. Results of 16S rRNA sequencing indicated that majority of the identified organisms were bacteria closely related to Proteobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria. Metagenomics sequences demonstrated that the dominant virus was Phycodnavirus, accounting for 70% of the total population. Patterns of relative numbers of bacteria in the microbial community and their temporal changes were determined through alpha diversity indices, principal coordinates analysis (PCoA), relative abundance, and visualized by Venn diagrams. Ways in which the bacterial and viral communities are influenced by various water-related variables were elucidated based on redundancy analysis (RDA). Relationships of the relative numbers of bacteria with trophic status in a reservoir used for drinking water in Macau, provided insight into associations of Phycodnavirus and Proteobacteria with changes in blooms of algae.}, }
@article {pmid34940122, year = {2021}, author = {Ghannoum, MA and McCormick, TS and Retuerto, M and Bebek, G and Cousineau, S and Hartman, L and Barth, C and Schrom, K}, title = {Evaluation of Microbiome Alterations Following Consumption of BIOHM, a Novel Probiotic.}, journal = {Current issues in molecular biology}, volume = {43}, number = {3}, pages = {2135-2146}, doi = {10.3390/cimb43030148}, pmid = {34940122}, issn = {1467-3045}, support = {R01 AI145289/AI/NIAID NIH HHS/United States ; AI145289//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Candida albicans ; Dysbiosis/*microbiology ; Healthy Volunteers ; Humans ; Metagenomics/methods ; Microbial Interactions ; *Microbiota ; Mycobiome ; Probiotics/*administration &amp; dosage ; RNA, Ribosomal, 16S ; }, abstract = {Gastrointestinal microbiome dysbiosis may result in harmful effects on the host, including those caused by inflammatory bowel diseases (IBD). The novel probiotic BIOHM, consisting of Bifidobacterium breve, Saccharomyces boulardii, Lactobacillus acidophilus, L. rhamnosus, and amylase, was developed to rebalance the bacterial-fungal gut microbiome, with the goal of reducing inflammation and maintaining a healthy gut population. To test the effect of BIOHM on human subjects, we enrolled a cohort of 49 volunteers in collaboration with the Fermentation Festival group (Santa Barbara, CA, USA). The profiles of gut bacterial and fungal communities were assessed via stool samples collected at baseline and following 4 weeks of once-a-day BIOHM consumption. Mycobiome analysis following probiotic consumption revealed an increase in Ascomycota levels in enrolled individuals and a reduction in Zygomycota levels (p value < 0.01). No statistically significant difference in Basidiomycota was detected between pre- and post-BIOHM samples and control abundance profiles (p > 0.05). BIOHM consumption led to a significant reduction in the abundance of Candida genus in tested subjects (p value < 0.013), while the abundance of C. albicans also trended lower than before BIOHM use, albeit not reaching statistical significance. A reduction in the abundance of Firmicutes at the phylum level was observed following BIOHM use, which approached levels reported for control individuals reported in the Human Microbiome Project data. The preliminary results from this clinical study suggest that BIOHM is capable of significantly rebalancing the bacteriome and mycobiome in the gut of healthy individuals, suggesting that further trials examining the utility of the BIOHM probiotic in individuals with gastrointestinal symptoms, where dysbiosis is considered a source driving pathogenesis, are warranted.}, }
@article {pmid34939673, year = {2022}, author = {Rahaman, MM and Sarkar, MMH and Rahman, MS and Islam, MR and Islam, I and Saha, O and Akter, S and Banu, TA and Jahan, I and Habib, MA and Goswami, B and Bari, L and Malek, MA and Khan, MS}, title = {Genomic characterization of the dominating Beta, V2 variant carrying vaccinated (Oxford-AstraZeneca) and nonvaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole-genome approach.}, journal = {Journal of medical virology}, volume = {94}, number = {4}, pages = {1670-1688}, doi = {10.1002/jmv.27537}, pmid = {34939673}, issn = {1096-9071}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/genetics ; Bacterial Infections/epidemiology/microbiology/virology ; Bangladesh/epidemiology ; COVID-19/epidemiology/microbiology/prevention &amp; control/*virology ; ChAdOx1 nCoV-19/*administration &amp; dosage ; Coinfection/epidemiology/microbiology/virology ; Drug Resistance, Bacterial/genetics ; Female ; Genome, Bacterial/genetics ; Genome, Viral/genetics ; Humans ; Male ; *Metagenomics ; Microbiota/genetics ; Middle Aged ; Mutation ; Phylogeny ; SARS-CoV-2/classification/*genetics/isolation &amp; purification ; Selection, Genetic ; Vaccination ; Viral Proteins/genetics ; Young Adult ; }, abstract = {Bangladesh is experiencing a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approaches. Screening for SARS-CoV-2 by reverse transcriptase polymerase chain reaction and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated = 10, nonvaccinated = 7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the coinfected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta, V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthily, the receptor binding domain (RBD) region of S protein of all the isolates harbored similar substitutions including K417N, E484K, and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F, and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS = 0.621). Furthermore, we found different bacterial coinfections like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and nonvaccinated patients in Bangladesh.}, }
@article {pmid34938813, year = {2021}, author = {Wang, S and Chen, H and Wen, X and Mu, J and Sun, M and Song, X and Liu, B and Chen, J and Fan, X}, title = {The Efficacy of Fecal Microbiota Transplantation in Experimental Autoimmune Encephalomyelitis: Transcriptome and Gut Microbiota Profiling.}, journal = {Journal of immunology research}, volume = {2021}, number = {}, pages = {4400428}, pmid = {34938813}, issn = {2314-7156}, mesh = {Animals ; Biomarkers ; Disease Management ; Disease Models, Animal ; Disease Susceptibility/immunology ; Encephalomyelitis, Autoimmune, Experimental/diagnosis/*etiology/*therapy ; *Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Intestinal Mucosa/metabolism/pathology ; Metagenomics/methods ; Mice ; Phylogeny ; RNA, Ribosomal, 16S ; Severity of Illness Index ; Spinal Cord/immunology/metabolism/pathology ; *Transcriptome ; Treatment Outcome ; }, abstract = {OBJECTIVE: To study the protective effect of fecal microbiota transplantation (FMT) on experimental autoimmune encephalomyelitis (EAE) and reveal its potential intestinal microflora-dependent mechanism through analyses of the intestinal microbiota and spinal cord transcriptome in mice.<br><br>METHOD: We measured the severity of disease by clinical EAE scores and H&amp;E staining. Gut microbiota alteration in the gut and differentially expressed genes (DEGs) in the spinal cord were analyzed through 16S rRNA and transcriptome sequencing. Finally, we analyzed associations between the relative abundance of intestinal microbiota constituents and DEGs.<br><br>RESULTS: We observed that clinical EAE scores were lower in the EAE+FMT group than in the EAE group. Meanwhile, mice in the EAE+FMT group also had a lower number of infiltrating cells. The results of 16S rRNA sequence analysis showed that FMT increased the relative abundance of Firmicutes and Proteobacteria and reduced the abundance of Bacteroides and Actinobacteria. Meanwhile, FMT could modulate gut microbiota balance, especially via increasing the relative abundance of g_Adlercreutzia, g_Sutterella, g_Prevotella_9, and g_Tyzzerella_3 and decreasing the relative abundance of g_Turicibacter. Next, we analyzed the transcriptome of mouse spinal cord tissue and found that 1476 genes were differentially expressed between the EAE and FMT groups. The analysis of these genes showed that FMT mainly participated in the inflammatory response. Correlation analysis between gut microbes and transcriptome revealed that the relative abundance of Adlercreutzia was correlated with the expression of inflammation-related genes negatively, including Casp6, IL1RL2 (IL-36R), IL-17RA, TNF, CCL3, CCR5, and CCL8, and correlated with the expression of neuroprotection-related genes positively, including Snap25, Edil3, Nrn1, Cpeb3, and Gpr37.<br><br>CONCLUSION: Altogether, FMT may selectively regulate gene expression to improve inflammation and maintain the stability of the intestinal environment in a gut microbiota-dependent manner.}, }
@article {pmid34925329, year = {2021}, author = {Guo, Y and Huang, X and Sun, X and Yu, Y and Wang, Y and Zhang, B and Cao, J and Wen, S and Li, Y and Wang, X and Cai, S and Xia, W and Wei, F and Duan, J and Dong, H and Guo, S and Zhang, F and Zheng, D and Sun, Z}, title = {The Underrated Salivary Virome of Men Who Have Sex With Men Infected With HIV.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {759253}, pmid = {34925329}, issn = {1664-3224}, mesh = {Adult ; Cross-Sectional Studies ; HIV Infections/*virology ; Homosexuality, Male ; Humans ; Male ; Metagenomics ; Saliva/*virology ; *Sexual and Gender Minorities ; Virome ; }, abstract = {Salivary virome is important for oral ecosystem, but there are few reports on people living with HIV. We performed metagenomic sequencing to compare composition and functional genes of salivary virobiota between one HIV-negative and four HIV-positive groups in which participants were all men who have sex with men (MSM) with different immunosuppression statuses (five samples per group) to find the evidence that salivary virobiota plays a role in the pathogenesis of oral disease. Acute-stage subjects achieved a positive result of HIV RNA, but HIV antibody negative or indeterminate, whereas individuals with mild, moderate, and severe immunosuppression exhibited CD4+ T-lymphocyte counts of at least 500, 200-499, and less than 200 cells/μL or opportunistic infection, respectively. The results showed the composition of salivary virus genera in subjects with mild immunosuppression was the most similar to that in healthy people, followed by that in the acute stage; under severe immunosuppression, virus genera were suppressed and more similar to that under moderate immunosuppression. Furthermore, abnormally high abundance of Lymphocryptovirus was particularly obvious in MSM with HIV infection. Analysis of KEGG Pathway revealed that Caulobacter cell cycle, which affects cell duplication, became shorter in HIV-positive subjects. It is worth noting that in acute-stage participants, protein digestion and absorption related to the anti-HIV-1 activity of secretory leukocyte protease inhibitor was increased. Moreover, in the severely immunosuppressed subjects, glutathione metabolism, which is associated with the activation of lymphocytes, was enhanced. Nevertheless, the ecological dysbiosis in HIV-positive salivary virobiota possibly depended on the changes in blood viral load, and salivary dysfunction of MSM infected with HIV may be related to CD4 counts. Ribonucleoside diphosphate reductase subunit M1 in purine metabolism was negatively correlated, though weakly, to CD4 counts, which may be related to the promotion of HIV-1 DNA synthesis in peripheral blood lymphocytes. 7-Cyano-7-deazaguanine synthase in folate biosynthesis was weakly positively correlated with HIV viral load, suggesting that this compound was produced excessively to correct oral dysfunction for maintaining normal cell development. Despite the limited number of samples, the present study provided insight into the potential role of salivary virome in the oral function of HIV infected MSM.}, }
@article {pmid34923897, year = {2022}, author = {Bihl, S and de Goffau, M and Podlesny, D and Segata, N and Shanahan, F and Walter, J and Fricke, WF}, title = {When to suspect contamination rather than colonization - lessons from a putative fetal sheep microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2005751}, pmid = {34923897}, issn = {1949-0984}, mesh = {Animals ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; DNA Contamination ; Female ; Fetus/*microbiology ; *Gastrointestinal Microbiome ; Pregnancy ; Sheep/*microbiology ; }, abstract = {There is an ongoing controversy around the existence of a prenatal, fetal microbiome in humans, livestock, and other animals. The 'in utero microbial colonization' hypothesis challenges the clinical paradigm of the 'sterile womb' but has been criticized for its reliance on DNA-based evidence to detect microbiomes and the failure to conciliate the routine experimental derivation of germ-free animals from surgically resected embryos with a thriving fetal microbiome. In order to avoid the propagation of misinformation in the scientific literature, a critical assessment and careful review of newly published studies, particularly those that challenge the convincing current clinical dogma of the sterile womb, is of critical importance.We read with interest a recent publication that postulated the presence of a fetal microbiome in sheep, but questioned the plausibility of the reported findings and their meaningfulness to prove "microbial colonisation of the fetal gut […] in utero". We reanalyzed the published metagenomic and metatranscriptomic sequence data from the original publication and identified evidence for different types of contamination that affected all samples alike and could explain the reported findings without requiring the existence of a fetal microbiome.Our reanalysis challenges the reported findings as supportive of a prenatal fetal lamb microbiome. The shortcomings of the original analysis and data interpretation highlight common problems of low-biomass microbiome projects. We propose genomic independence of separate biological samples, i.e. distinctive profiles at the microbial strain level, as a potential new microbiome marker to increase confidence in metagenomics analyses of controversial low-biomass microbiomes.}, }
@article {pmid34923019, year = {2022}, author = {Chen, X and Wang, J and Pan, C and Feng, L and Guo, Q and Chen, S and Xie, S}, title = {Metagenomic analysis reveals the response of microbial community in river sediment to accidental antimony contamination.}, journal = {The Science of the total environment}, volume = {813}, number = {}, pages = {152484}, doi = {10.1016/j.scitotenv.2021.152484}, pmid = {34923019}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Antimony/analysis/toxicity ; Genes, Bacterial ; Humans ; Metagenomics ; *Metals, Heavy ; *Microbiota ; Rivers ; }, abstract = {The mining of deposits containing metals like antimony (Sb) causes serious environmental issues that threaten human health and ecological systems. However, information on the effect of Sb on freshwater sediment microorganisms and the mechanism of microbial Sb resistance is still very limited. This was the first attempt to explore microbial communities in river sediments impacted by accidental Sb spill. Metagenomic analysis revealed the high relative abundance of Proteobacteria and Actinobacteria in all the studied river sediments, showing their advantage in resistance to Sb pollution. Under Sb stress, microbial functions related to DNA repair and ion transport were enhanced. Increase in heavy metal resistance genes (HMRGs), particularly Sb transport-related arsB gene, was observed at Sb spill-impacted sites. HMRGs were significantly correlated with ARGs and MGEs, and the abundant MGEs at Sb spill-impacted sites might contribute to the increase in HMRGs and ARGs via horizontal gene transfer. Deinococcus, Sphingopyxis and Paracoccus were identified as potential tolerant genera under Sb pressure and might be related to the transmission of HMRGs and ARGs. This study can add new insights towards the effect of accidental metal spill on sediment microbial community.}, }
@article {pmid34922301, year = {2022}, author = {Gabashvili, E and Kobakhidze, S and Chkhikvishvili, T and Tabatadze, L and Tsiklauri, R and Dadiani, K and Koulouris, S and Kotetishvili, M}, title = {Metagenomic and Recombination Analyses of Antimicrobial Resistance Genes from Recreational Waters of Black Sea Coastal Areas and Other Marine Environments Unveil Extensive Evidence for Their both Intrageneric and Intergeneric Transmission across Genetically Very Diverse Microbial Communities.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100916}, doi = {10.1016/j.margen.2021.100916}, pmid = {34922301}, issn = {1876-7478}, mesh = {Anti-Bacterial Agents/pharmacology ; Black Sea ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Humans ; *Metagenomics ; *Microbiota ; Recombination, Genetic ; }, abstract = {Microbial communities of marine coastal recreation waters have become large reservoirs of AMR genes (ARGs), contributing to the emergence and transmission of various zoonotic, foodborne and other infections that exhibit resistance to various antibiotics. Thus, it is highly imperative to determine ARGs assemblages as well as mechanisms and trajectories of their transmission across these microbial communities for our better understanding of the evolutionary trends of AMR (AMR). In this study, using metagenomics approaches, we screened for ARGs in recreation waters of the Black Sea coastal areas of the Batumi City (Georgia). Also, a large array of the recombination detection algorithms of the SplitsTree, RDP4, and GARD was applied to elucidate genetic recombination of ARGs and trajectories of their transmission across various marine microbial communities. The metagenomics analyses of sea water samples, obtained from across the above marine sites, could identify putative ARGs encoding for multidrug resistance efflux transporters mainly from the Major Facilitator and Resistance Nodulation Division superfamilies. The data, generated by SplitsTree (fit ≥95.619; bootstrap values ≥ 95; Phi p ≤ 0.0494), RDP4 (p ≤ 0.0490), and GARD, provided strong statistical evidence not only for intrageneric recombination of these ARGs, but also for their intergeneric recombination across fairly large and diverse microbial communities of marine environment. These bacteria included both human pathogenic and nonpathogenic species, exhibiting collectively the genera of Vibrio, Aeromonas, Synechococcus, Citromicrobium, Rhodobacteraceae, Pseudoalteromonas, Altererythrobacter, Erythrobacter, Altererythrobacter, Marivivens, Xuhuaishuia, and Loktanella. The above nonpathogenic bacteria are strongly suggested to contribute to ARGs transmission in marine ecosystems.}, }
@article {pmid34920070, year = {2022}, author = {Zhang, L and Wang, Y and Wu, F and Wang, X and Feng, Y and Wang, Y}, title = {MDG, an Ophiopogon japonicus polysaccharide, inhibits non-alcoholic fatty liver disease by regulating the abundance of Akkermansia muciniphila.}, journal = {International journal of biological macromolecules}, volume = {196}, number = {}, pages = {23-34}, doi = {10.1016/j.ijbiomac.2021.12.036}, pmid = {34920070}, issn = {1879-0003}, mesh = {Akkermansia/drug effects ; Animals ; Diet, High-Fat ; Disease Models, Animal ; Drugs, Chinese Herbal ; Gastrointestinal Microbiome/*drug effects ; Lipid Metabolism/drug effects ; Liver/drug effects/metabolism/pathology ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Non-alcoholic Fatty Liver Disease/*drug therapy/etiology/metabolism ; Ophiopogon/*chemistry ; Polysaccharides/chemistry/*pharmacology ; }, abstract = {MDG, a polysaccharide derived from Ophiopogon japonicus, displays a protective effect against obesity and non-alcoholic fatty liver disease (NAFLD). However, there is no definitive evidence proving the specific mechanism of MDG against NAFLD. The results showed MDG supplementation ameliorated lipid accumulation, liver steatosis, and chronic inflammation in high-fat diet-induced NAFLD mice. Besides, MDG increased the abundance and diversity of microbial communities in the gut. These effects were mediated by the colonization of fecal microbiota. Further investigation revealed that Akkermansia muciniphila levels correlated negatively with NAFLD development, and lipid metabolism-related signaling might be the key regulator. Our study suggested that MDG treatment could inhibit obesity and the NAFLD process by modulating lipid-related pathways via altering the structure and diversity of gut microbiota. In addition, Akkermansia miniciphila might be a promising candidate in future research into NAFLD.}, }
@article {pmid34911987, year = {2021}, author = {Soto-Giron, MJ and Kim, JN and Schott, E and Tahmin, C and Ishoey, T and Mincer, TJ and DeWalt, J and Toledo, G}, title = {The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {24017}, pmid = {34911987}, issn = {2045-2322}, mesh = {*Biodiversity ; Computational Biology/methods ; Food Microbiology ; Genetic Variation ; *Host Microbial Interactions ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Molecular Sequence Annotation ; Phylogeny ; Plants, Edible/*microbiology ; }, abstract = {Plant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.}, }
@article {pmid34911583, year = {2021}, author = {Allali, I and Abotsi, RE and Tow, LA and Thabane, L and Zar, HJ and Mulder, NM and Nicol, MP}, title = {Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {241}, pmid = {34911583}, issn = {2049-2618}, support = {U41 HG006941/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Mass Screening ; *Microbiota ; Public Health ; South Africa ; Uganda ; }, abstract = {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.<br><br>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.<br><br>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).<br><br>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.}, }
@article {pmid34910917, year = {2021}, author = {Wurster, JI and Peterson, RL and Brown, CE and Penumutchu, S and Guzior, DV and Neugebauer, K and Sano, WH and Sebastian, MM and Quinn, RA and Belenky, P}, title = {Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis.}, journal = {Cell reports}, volume = {37}, number = {11}, pages = {110113}, pmid = {34910917}, issn = {2211-1247}, support = {P20 GM121344/GM/NIGMS NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; R01 DK125382/DK/NIDDK NIH HHS/United States ; R21 AT010366/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cecum/*metabolism/microbiology ; Diabetes Mellitus, Experimental/complications ; *Drug Resistance, Bacterial ; Dysbiosis/drug therapy/etiology/metabolism/*pathology ; Female ; Gastrointestinal Microbiome ; Hyperglycemia/drug therapy/etiology/metabolism/*pathology ; Male ; *Metabolome ; Metagenome ; Mice ; Mice, Inbred C57BL ; Microbiota ; Salmonella Infections, Animal/drug therapy/metabolism/microbiology/*pathology ; Salmonella enterica ; Transcriptome ; }, abstract = {It is well established in the microbiome field that antibiotic (ATB) use and metabolic disease both impact the structure and function of the gut microbiome. But how host and microbial metabolism interacts with ATB susceptibility to affect the resulting dysbiosis remains poorly understood. In a streptozotocin-induced model of hyperglycemia (HG), we use a combined metagenomic, metatranscriptomic, and metabolomic approach to profile changes in microbiome taxonomic composition, transcriptional activity, and metabolite abundance both pre- and post-ATB challenge. We find that HG impacts both microbiome structure and metabolism, ultimately increasing susceptibility to amoxicillin. HG exacerbates drug-induced dysbiosis and increases both phosphotransferase system activity and energy catabolism compared to controls. Finally, HG and ATB co-treatment increases pathogen susceptibility and reduces survival in a Salmonella enterica infection model. Our data demonstrate that induced HG is sufficient to modify the cecal metabolite pool, worsen the severity of ATB dysbiosis, and decrease colonization resistance.}, }
@article {pmid34908504, year = {2021}, author = {Kang, Y and Ji, X and Guo, L and Xia, H and Yang, X and Xie, Z and Shi, X and Wu, R and Feng, D and Wang, C and Chen, M and Zhang, W and Wei, H and Guan, Y and Ye, K and Zhao, G}, title = {Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0076921}, pmid = {34908504}, issn = {2165-0497}, mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacteriophages/*isolation &amp; purification ; Blood-Brain Barrier/microbiology ; Cerebrospinal Fluid/*microbiology ; DNA, Bacterial/cerebrospinal fluid ; DNA, Viral/cerebrospinal fluid ; Female ; Healthy Volunteers ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/genetics ; Metagenomics ; Microbiota ; Pregnancy ; }, abstract = {Cerebrospinal fluid (CSF) circulating in the human central nervous system has long been considered aseptic in healthy individuals, because normally, the blood-brain barrier can protect against microbial invasions. However, this dogma has been called into question by several reports that microbes were identified in human brains, raising the question of whether there is a microbial community in the CSF of healthy individuals without neurological diseases. Here, we collected CSF samples and other samples, including one-to-one matched oral and skin swab samples (positive controls), from 23 pregnant women aged between 23 and 40 years. Normal saline samples (negative controls), sterile swabs, and extraction buffer samples (contamination controls) were also collected. Twelve of the CSF specimens were also used to evaluate the physiological activities of detected microbes. Metagenomic and metatranscriptomic sequencing was performed in these 116 specimens. A total of 620 nonredundant microbes were detected, which were dominated by bacteria (74.6%) and viruses (24.2%), while in CSF samples, metagenomic sequencing found only 26 nonredundant microbes, including one eukaryote, four bacteria, and 21 viruses (mostly bacteriophages). The beta diversity of microbes compared between CSF metagenomic samples and other types of samples (except negative controls) was significantly different from that of the CSF self-comparison. In addition, there was no active or viable microbe in the matched metagenomic and metatranscriptomic sequencing of CSF specimens after subtracting those also found in normal saline, DNA extraction buffer, and skin swab specimens. In conclusion, our results showed no strong evidence of a colonized microbial community present in the CSF of healthy individuals. IMPORTANCE The microbiome is prevalent throughout human bodies, with profound health implications. However, it remains unclear whether it is present and active in human CSF, which has been long considered aseptic due to the blood-brain barrier. Here, we applied unbiased metagenomic and metatranscriptomic sequencing to detect the presence of a microbiome in CSF collected from 23 pregnant women with matched controls. Analysis of 116 specimens found no strong evidence to support the presence of a colonized microbiome in CSF. Our findings will strengthen our understanding of the internal environment of the CSF in healthy people, which has strong implications for human health, especially for neurological infections and disorders, and will help further disease diagnostics, prevention, and therapeutics in clinical settings.}, }
@article {pmid34906246, year = {2021}, author = {Chaudhari, NM and Overholt, WA and Figueroa-Gonzalez, PA and Taubert, M and Bornemann, TLV and Probst, AJ and Hölzer, M and Marz, M and Küsel, K}, title = {The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {24}, pmid = {34906246}, issn = {2524-6372}, support = {SFB 1076 -Project Number 218627073//deutsche forschungsgemeinschaft/ ; FZT 118 - 202548816//deutsche forschungsgemeinschaft/ ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//deutsche forschungsgemeinschaft/ ; Nachwuchsgruppe Dr. Alexander Probst//ministerium für kultur und wissenschaft des landes nordrhein-westfalen/ ; }, abstract = {BACKGROUND: The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges.<br><br>RESULTS: Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota).<br><br>CONCLUSION: Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.}, }
@article {pmid34906228, year = {2021}, author = {Shin, J and Noh, JR and Choe, D and Lee, N and Song, Y and Cho, S and Kang, EJ and Go, MJ and Ha, SK and Chang, DH and Kim, JH and Kim, YH and Kim, KS and Jung, H and Kim, MH and Sung, BH and Lee, SG and Lee, DH and Kim, BC and Lee, CH and Cho, BK}, title = {Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {240}, pmid = {34906228}, issn = {2049-2618}, mesh = {Aging ; Animals ; *Gastrointestinal Microbiome/genetics ; *Healthy Aging ; Mice ; *Microbiota ; Rejuvenation ; }, abstract = {BACKGROUND: The gut microbiota is associated with diverse age-related disorders. Several rejuvenation methods, such as probiotic administration and faecal microbiota transplantation, have been applied to alter the gut microbiome and promote healthy ageing. Nevertheless, prolongation of the health span of aged mice by remodelling the gut microbiome remains challenging.<br><br>RESULTS: Here, we report the changes in gut microbial communities and their functions in mouse models during ageing and three rejuvenation procedures including co-housing, serum-injection and parabiosis. Our results showed that the compositional structure and gene abundance of the intestinal microbiota changed dynamically during the ageing process. Through the three rejuvenation procedures, we observed that the microbial community and intestinal immunity of aged mice were comparable to those of young mice. The results of metagenomic data analysis underscore the importance of the high abundance of Akkermansia and the butyrate biosynthesis pathway in the rejuvenated mouse group. Furthermore, oral administration of Akkermansia sufficiently ameliorated the senescence-related phenotype in the intestinal systems in aged mice and extended the health span, as evidenced by the frailty index and restoration of muscle atrophy.<br><br>CONCLUSIONS: In conclusion, the changes in key microbial communities and their functions during ageing and three rejuvenation procedures, and the increase in the healthy lifespan of aged mice by oral administration of Akkermansia. Our results provide a rationale for developing therapeutic strategies to achieve healthy active ageing. Video abstract.}, }
@article {pmid34905206, year = {2022}, author = {Raza, A and Wu, Q}, title = {Diagnosis of Viral Diseases Using Deep Sequencing and Metagenomics Analyses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2400}, number = {}, pages = {225-243}, pmid = {34905206}, issn = {1940-6029}, mesh = {Computational Biology ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Plants ; RNA ; *Virus Diseases/diagnosis/genetics ; }, abstract = {Viruses are ubiquitous in nature and exist in a variety of habitats. The advancement in sequencing technologies has revolutionized the understanding of viral biodiversity associated with plant diseases. Deep sequencing combined with metagenomics is a powerful approach that has proven to be revolutionary in the last decade and involves the direct analysis of viral genomes present in a diseased tissue sample. This protocol describes the details of RNA extraction and purification from wild rice plant and their yield, RNA purity, and integrity assessment. As a final step, bioinformatics data analysis including demultiplexing, quality control, de novo transcriptome assembly, taxonomic allocation and read mapping following Illumina HiSeq small and total RNA sequencing are described. Furthermore, the total RNAs extraction protocol and an additional ribosomal rRNAs depletion step which are significantly important for viral genomes construction are provided.}, }
@article {pmid34904945, year = {2021}, author = {Rego, A and Fernandez-Guerra, A and Duarte, P and Assmy, P and Leão, PN and Magalhães, C}, title = {Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes.}, journal = {Microbial genomics}, volume = {7}, number = {12}, pages = {}, pmid = {34904945}, issn = {2057-5858}, mesh = {Arctic Regions ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; *Biosynthetic Pathways ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiota ; Multigene Family ; Oceans and Seas ; Phylogeny ; Secondary Metabolism ; Sequence Analysis, DNA/*methods ; Water Microbiology ; }, abstract = {Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.}, }
@article {pmid34903850, year = {2022}, author = {Gregor, R and Probst, M and Eyal, S and Aksenov, A and Sasson, G and Horovitz, I and Dorrestein, PC and Meijler, MM and Mizrahi, I}, title = {Mammalian gut metabolomes mirror microbiome composition and host phylogeny.}, journal = {The ISME journal}, volume = {16}, number = {5}, pages = {1262-1274}, pmid = {34903850}, issn = {1751-7370}, support = {240356//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 1947/19//Israel Science Foundation (ISF)/ ; P41 GM103484/GM/NIGMS NIH HHS/United States ; 1667/15//Israel Science Foundation (ISF)/ ; 640384//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; GMS10RR029121//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; S10 RR029121/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mammals ; Metabolome ; *Microbiota ; Phylogeny ; }, abstract = {In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.}, }
@article {pmid34903050, year = {2021}, author = {Beller, L and Deboutte, W and Falony, G and Vieira-Silva, S and Tito, RY and Valles-Colomer, M and Rymenans, L and Jansen, D and Van Espen, L and Papadaki, MI and Shi, C and Yinda, CK and Zeller, M and Faust, K and Van Ranst, M and Raes, J and Matthijnssens, J}, title = {Successional Stages in Infant Gut Microbiota Maturation.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0185721}, pmid = {34903050}, issn = {2150-7511}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Infant ; Infant, Newborn/*growth &amp; development ; Male ; }, abstract = {Disturbances in the primary colonization of the infant gut can result in lifelong consequences and have been associated with a range of host conditions. Although early-life factors have been shown to affect infant gut microbiota development, our current understanding of human gut colonization in early life remains limited. To gain more insights into the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (n = 303 total samples). To evaluate the gut microbiota maturation transition toward an adult configuration, we compared the microbiome composition of the infants to that of the Flemish Gut Flora Project (FGFP) population (n = 1,106). We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, the genus predominance was observed to shift from Escherichia over Bifidobacterium to Bacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like constellations, microbiome community typing against the background of the FGFP cohort clustered all infant samples within the (in adults) potentially dysbiotic Bacteroides 2 (Bact2) enterotype. We confirmed the similarities between infant gut microbial colonization and adult dysbiosis. Profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected. IMPORTANCE After birth, microbial colonization of the infant intestinal tract is important for health later in life. However, this initial process is highly dynamic and influenced by many factors. Studying this process in detail requires a dense longitudinal sampling effort. In the current study, the bacterial microbiota of >300 stool samples was analyzed from 8 healthy infants, suggesting that the infant gut microbial population matures along a path involving distinct microbial constellations and that the timing of these transitions is infant specific and can temporarily retrace upon external events. We also showed that the infant microbial populations show similarities to suboptimal bacterial populations in the guts of adults. These insights are crucial for a better understanding of the dynamics and characteristics of a "healthy gut microbial population" in both infants and adults and might allow the identification of intervention targets in cases of microbial disturbances or disease.}, }
@article {pmid34896845, year = {2022}, author = {Lai, J and Li, A and Jiang, J and Yuan, X and Zhang, P and Xi, C and Wu, L and Wang, Z and Chen, J and Lu, J and Lu, S and Mou, T and Zhou, H and Wang, D and Huang, M and Dong, F and Li, MD and Xu, Y and Song, X and Hu, S}, title = {Metagenomic analysis reveals gut bacterial signatures for diagnosis and treatment outcome prediction in bipolar depression.}, journal = {Psychiatry research}, volume = {307}, number = {}, pages = {114326}, doi = {10.1016/j.psychres.2021.114326}, pmid = {34896845}, issn = {1872-7123}, mesh = {*Bipolar Disorder/diagnosis/drug therapy ; Dysbiosis ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Treatment Outcome ; }, abstract = {BACKGROUND: We aimed to characterize gut microbial alterations in depressed patients with bipolar disorder (BD) following quetiapine monotherapy and explored its potential for disease diagnosis and outcome prediction.<br><br>METHODS: Fecal samples were obtained from 60 healthy individuals and 62 patients in acute depressive episodes. All patients received one-month quetiapine treatment after enrollment. The structure of gut microbiota was measured with metagenomic sequencing, and its correlation with clinical profiles and brain function as indicated by resting-state functional magnetic resonance imaging was analyzed. Random forest models based on bacterial species were constructed to distinguish patients from controls, and responders from non-responders, respectively.<br><br>RESULTS: BD patients displayed specific alterations in gut microbial diversity and composition. Quetiapine treatment increased the diversity of microbial communities and changed the composition. The abundance of Clostridium bartlettii was negatively associated with age, baseline depression severity, while positively associated with spontaneous neural oscillation in the hippocampus. Tree-based classification models for (1) patients and controls and (2) responders and non-responders showed an area under the curve of 0.733 and 0.800, respectively.<br><br>CONCLUSION: Our findings add new evidence to the existing literature regarding gut dysbiosis in BD and reveal the potential of microbe-based biomarkers for disease diagnosis and treatment outcome prediction.}, }
@article {pmid34896510, year = {2022}, author = {Zhou, L and Xu, P and Gong, J and Huang, S and Chen, W and Fu, B and Zhao, Z and Huang, X}, title = {Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {152263}, doi = {10.1016/j.scitotenv.2021.152263}, pmid = {34896510}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Ecosystem ; *Estuaries ; Genes, Bacterial ; *Metagenomics ; }, abstract = {Estuaries are resistome hotspots owing to resistome accumulation and propagation at these locations from surrounding rivers, yet the large-scale biogeographic pattern of resistome, especially biocide and metal resistance genes (BMRGs) and its driving mechanisms in estuarine waters remains to be elucidated. Here, a metagenomics-based approach was firstly used to investigate resistome and mobilome profiles in waters from 30 subtropical estuaries, South China. The Pearl River estuaries had a higher diversity and abundance of antibiotic resistance genes (ARGs), BMRGs, and mobile genetic elements (MGEs) when compared with estuaries from east and west regions. Genes resistant to multiple antibiotics, metals, and biocides were the most abundant gene types in the resistome. The abundance of MGEs (e.g., intI1, IS91, and tnpA) was highly associated with the total abundance of resistance genes, suggesting their utility as potential indicators for quantitative estimations of the resistome contamination. Further, MGEs contributed more than bacterial communities in shaping the resistome in subtropical estuaries. Physicochemical factors (e.g., pH) regulated MGE composition and stochastic assembly, which mediated the co-selection of ARGs and BMRGs via horizontal gene transfer. Our findings have important implications and provide a reference on the management of ARGs and BMRGs in subtropical estuarine ecosystems.}, }
@article {pmid34896404, year = {2022}, author = {Demir, M and Lang, S and Hartmann, P and Duan, Y and Martin, A and Miyamoto, Y and Bondareva, M and Zhang, X and Wang, Y and Kasper, P and Bang, C and Roderburg, C and Tacke, F and Steffen, HM and Goeser, T and Kruglov, A and Eckmann, L and Stärkel, P and Fouts, DE and Schnabl, B}, title = {The fecal mycobiome in non-alcoholic fatty liver disease.}, journal = {Journal of hepatology}, volume = {76}, number = {4}, pages = {788-799}, pmid = {34896404}, issn = {1600-0641}, support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Liver ; Mice ; *Mycobiome ; *Non-alcoholic Fatty Liver Disease/etiology ; Saccharomyces cerevisiae ; }, abstract = {BACKGROUND &amp; AIMS: Studies investigating the gut-liver axis have largely focused on bacteria, whereas little is known about commensal fungi. We characterized fecal fungi in patients with non-alcoholic fatty liver disease (NAFLD) and investigated their role in a fecal microbiome-humanized mouse model of Western diet-induced steatohepatitis.<br><br>METHODS: We performed fungal internal transcribed spacer 2 sequencing using fecal samples from 78 patients with NAFLD, 16 controls and 73 patients with alcohol use disorder. Anti-Candida albicans (C. albicans) IgG was measured in blood samples from 17 controls and 79 patients with NAFLD. Songbird, a novel multinominal regression tool, was used to investigate mycobiome changes. Germ-free mice were colonized with feces from patients with non-alcoholic steatohepatitis (NASH), fed a Western diet for 20 weeks and treated with the antifungal amphotericin B.<br><br>RESULTS: The presence of non-obese NASH or F2-F4 fibrosis was associated with a distinct fecal mycobiome signature. Changes were characterized by an increased log-ratio for Mucor sp./Saccharomyces cerevisiae (S. cerevisiae) in patients with NASH and F2-F4 fibrosis. The C. albicans/S. cerevisiae log-ratio was significantly higher in non-obese patients with NASH when compared with non-obese patients with NAFL or controls. We observed a different fecal mycobiome composition in patients with NAFLD and advanced fibrosis compared to those with alcohol use disorder and advanced fibrosis. Plasma anti-C. albicans IgG was increased in patients with NAFLD and advanced fibrosis. Gnotobiotic mice, colonized with human NASH feces and treated with amphotericin B were protected from Western diet-induced steatohepatitis.<br><br>CONCLUSIONS: Non-obese patients with NAFLD and more advanced disease have a different fecal mycobiome composition to those with mild disease. Antifungal treatment ameliorates diet-induced steatohepatitis in mice. Intestinal fungi could be an attractive target to attenuate NASH.<br><br>LAY SUMMARY: Non-alcoholic fatty liver disease is one of the most common chronic liver diseases and is associated with changes in the fecal bacterial microbiome. We show that patients with non-alcoholic fatty liver disease and more severe disease stages have a specific composition of fecal fungi and an increased systemic immune response to Candida albicans. In a fecal microbiome-humanized mouse model of Western diet-induced steatohepatitis, we show that treatment with antifungals reduces liver damage.}, }
@article {pmid34893656, year = {2021}, author = {Cholewińska, P and Wołoszyńska, M and Michalak, M and Czyż, K and Rant, W and Smoliński, J and Wyrostek, A and Wojnarowski, K}, title = {Influence of selected factors on the Firmicutes, Bacteroidetes phyla and the Lactobacillaceae family in the digestive tract of sheep.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23801}, pmid = {34893656}, issn = {2045-2322}, mesh = {Age Factors ; Animals ; Biodiversity ; Body Weight ; Feces/microbiology ; Firmicutes/*physiology ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Lactobacillaceae/*physiology ; Metagenome ; Metagenomics/methods ; Milk ; Sheep ; }, abstract = {In this study, we used 10 healthy sheep, which gave birth to healthy twins. Stool samples were collected from mothers and their offspring 3 times during the study (0, 28 and 56 day postpartum). Milk samples were taken from the mothers at the same time. RT PCR analysis of faeces and milk was performed in order to assess the level of bacteria from the Firmicutes and Bacteroidetes phyla including the family Lactobacillaceae (phylum Firmicutes). The composition of mother's milk was also analyzed and their BCS. The data were compiled statistically. The obtained results showed that the level of the studied groups of bacteria may change due to the change of diet. Additionally, there were significant differences between lambs and mothers in the levels of the studied groups of bacteria. Analysis also shown that in the digestive system of mothers was a smaller disproportion in the level of the studied bacterial phyla than in lambs. The results also indicated the occurrence of differences in the bacterial composition at the individual level, both in ewes and their offspring. Additionally, in the conducted experiment, there were differences in the level of Firmicutes and Bacteroidetes groups depending on the sex.}, }
@article {pmid34893089, year = {2021}, author = {Wang, Z and Usyk, M and Vázquez-Baeza, Y and Chen, GC and Isasi, CR and Williams-Nguyen, JS and Hua, S and McDonald, D and Thyagarajan, B and Daviglus, ML and Cai, J and North, KE and Wang, T and Knight, R and Burk, RD and Kaplan, RC and Qi, Q}, title = {Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {336}, pmid = {34893089}, issn = {1474-760X}, support = {HHSN268201000031C/HL/NHLBI NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; R01 DK120870/DK/NIDDK NIH HHS/United States ; P60 DK020541/DK/NIDDK NIH HHS/United States ; HHSN261201300005I/CA/NCI NIH HHS/United States ; HHSN268201000001I/HL/NHLBI NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; HHSN261201300004I/CA/NCI NIH HHS/United States ; HHSN268201000021C/HL/NHLBI NIH HHS/United States ; R01 DK119268/DK/NIDDK NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; P30 DK020541/DK/NIDDK NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; R01 HL136266/HL/NHLBI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; }, mesh = {Acculturation ; Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/genetics ; Cohort Studies ; Diet ; *Eating ; Emigrants and Immigrants ; *Emigration and Immigration ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Hispanic or Latino ; Humans ; Male ; Metagenomics ; Middle Aged ; Obesity/*microbiology ; RNA, Ribosomal, 16S ; United States ; }, abstract = {BACKGROUND: Obesity and related comorbidities are major health concerns among many US immigrant populations. Emerging evidence suggests a potential involvement of the gut microbiome. Here, we evaluated gut microbiome features and their associations with immigration, dietary intake, and obesity in 2640 individuals from a population-based study of US Hispanics/Latinos.<br><br>RESULTS: The fecal shotgun metagenomics data indicate that greater US exposure is associated with reduced ɑ-diversity, reduced functions of fiber degradation, and alterations in individual taxa, potentially related to a westernized diet. However, a majority of gut bacterial genera show paradoxical associations, being reduced with US exposure and increased with fiber intake, but increased with obesity. The observed paradoxical associations are not explained by host characteristics or variation in bacterial species but might be related to potential microbial co-occurrence, as seen by positive correlations among Roseburia, Prevotella, Dorea, and Coprococcus. In the conditional analysis with mutual adjustment, including all genera associated with both obesity and US exposure in the same model, the positive associations of Roseburia and Prevotella with obesity did not persist, suggesting that their positive associations with obesity might be due to their co-occurrence and correlations with obesity-related taxa, such as Dorea and Coprococcus.<br><br>CONCLUSIONS: Among US Hispanics/Latinos, US exposure is associated with unfavorable gut microbiome profiles for obesity risk, potentially related to westernized diet during acculturation. Microbial co-occurrence could be an important factor to consider in future studies relating individual gut microbiome taxa to environmental factors and host health and disease.}, }
@article {pmid34890483, year = {2021}, author = {Shen, Z and Wang, F and Liang, Y and Li, Y and Liu, Q and Liu, F}, title = {Diversity and functions of microbes in surface sediments under heavy metal pollution of western Chaohu Lake.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/lam.13627}, pmid = {34890483}, issn = {1472-765X}, support = {41371444//the National Science Foundation of China/ ; KJ2017ZD55//the Innovation Team of Scientific Research Platform of Anhui Province, China/ ; }, abstract = {Heavy metal pollution is a global concern. Targeting at the surface sediments in western Chaohu Lake and using metagenome sequencing, we probed into the mechanism of how microbes adapted to heavy metal-polluted sediments under natural conditions. It was found the heavy metal pollution intensity of the three typical sampling places ranked as estuary of Nanfeihe River (NFH) > Zhongmiao Town (HZ) > Hongshizui (HSZ). Totally 129 phyla, 2631 genera and 12 989 species were detected in the sediment samples, and HSZ, HZ and NFH had 35, 51 and 67 exclusive genera, respectively. The bacterial biomass and virus quantity from NFH accounted for 22·84 and 70·69% of total quantities, respectively, and the microbial community compositions in NFH were also different from those in HSZ and HZ. Metagenomics sequencing and functional gene annotation showed NFH contained many functional genes related to nucleic acid transport and metabolism, ribosome structures and biological origin, replication recombining and repair and inorganic ion transport and metabolism. Kyoto Encyclopedia of Genes and Genomes analysis suggested the sediments from NFH were rich in enzymes correlated with heavy metal transport and reduction. Our findings offer some scientific basis for Chaohu Lake control and microbe resource utilization.}, }
@article {pmid34887548, year = {2022}, author = {Conrad, RE and Viver, T and Gago, JF and Hatt, JK and Venter, SN and Rossello-Mora, R and Konstantinidis, KT}, title = {Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations.}, journal = {The ISME journal}, volume = {16}, number = {5}, pages = {1222-1234}, pmid = {34887548}, issn = {1751-7370}, support = {1831582//National Science Foundation (NSF)/ ; 1759831//National Science Foundation (NSF)/ ; }, mesh = {Bacteria/genetics ; *Genome, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.}, }
@article {pmid34887510, year = {2021}, author = {Hrbacek, J and Morais, D and Cermak, P and Hanacek, V and Zachoval, R}, title = {Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23758}, pmid = {34887510}, issn = {2045-2322}, mesh = {Aged ; *Biodiversity ; Comorbidity ; Humans ; Male ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Urinalysis ; Urinary Tract/*microbiology ; }, abstract = {Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n = 35) and expanded quantitative urine culture (EQUC, n = 31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.}, }
@article {pmid34887434, year = {2021}, author = {Goswami, K and Shope, AJ and Tokarev, V and Wright, JR and Unverdorben, LV and Ly, T and Chen See, J and McLimans, CJ and Wong, HT and Lock, L and Clarkson, S and Parvizi, J and Lamendella, R}, title = {Comparative meta-omics for identifying pathogens associated with prosthetic joint infection.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23749}, pmid = {34887434}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Arthritis, Infectious/diagnosis/*etiology ; Biodiversity ; Computational Biology/methods ; Female ; Gene Expression Profiling ; Humans ; Male ; Metagenome ; Metagenomics/*methods ; Middle Aged ; Prosthesis-Related Infections/diagnosis/*etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prosthetic joint infections (PJI) are economically and personally costly, and their incidence has been increasing in the United States. Herein, we compared 16S rRNA amplicon sequencing (16S), shotgun metagenomics (MG) and metatranscriptomics (MT) in identifying pathogens causing PJI. Samples were collected from 30 patients, including 10 patients undergoing revision arthroplasty for infection, 10 patients receiving revision for aseptic failure, and 10 patients undergoing primary total joint arthroplasty. Synovial fluid and peripheral blood samples from the patients were obtained at time of surgery. Analysis revealed distinct microbial communities between primary, aseptic, and infected samples using MG, MT, (PERMANOVA p = 0.001), and 16S sequencing (PERMANOVA p < 0.01). MG and MT had higher concordance with culture (83%) compared to 0% concordance of 16S results. Supervised learning methods revealed MT datasets most clearly differentiated infected, primary, and aseptic sample groups. MT data also revealed more antibiotic resistance genes, with improved concordance results compared to MG. These data suggest that a differential and underlying microbial ecology exists within uninfected and infected joints. This study represents the first application of RNA-based sequencing (MT). Further work on larger cohorts will provide opportunities to employ deep learning approaches to improve accuracy, predictive power, and clinical utility.}, }
@article {pmid34885912, year = {2021}, author = {Marfil-Santana, MD and Martínez-Cárdenas, A and Ruíz-Hernández, A and Vidal-Torres, M and Márquez-Velázquez, NA and Figueroa, M and Prieto-Davó, A}, title = {A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {23}, pages = {}, pmid = {34885912}, issn = {1420-3049}, support = {UNAM-DGAPA-PAPIIT TA200415//National Autonomous University of Mexico/ ; UNAM-DGAPA-PAPIIT IN222220//National Autonomous University of Mexico/ ; Proyecto Semilla FQ//National Autonomous University of Mexico/ ; }, mesh = {Actinobacteria/genetics/*isolation &amp; purification/metabolism ; Geologic Sediments/*microbiology ; Metabolome ; Metabolomics ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world's largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the "El Palmar" natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments' microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from "El Palmar" harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of "El Palmar" microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases' biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from "El Palmar", and show the impact selective media had on the composition of communities of actinobacteria.}, }
@article {pmid34884735, year = {2021}, author = {Hernandez-Baixauli, J and Puigbò, P and Abasolo, N and Palacios-Jordan, H and Foguet-Romero, E and Suñol, D and Galofré, M and Caimari, A and Baselga-Escudero, L and Bas, JMD and Mulero, M}, title = {Alterations in Metabolome and Microbiome Associated with an Early Stress Stage in Male Wistar Rats: A Multi-Omics Approach.}, journal = {International journal of molecular sciences}, volume = {22}, number = {23}, pages = {}, pmid = {34884735}, issn = {1422-0067}, mesh = {Animals ; Biomarkers/blood/urine ; Male ; *Metabolome ; *Microbiota ; Rats, Wistar ; Stress, Psychological/*metabolism/microbiology ; }, abstract = {Stress disorders have dramatically increased in recent decades becoming the most prevalent psychiatric disorder in the United States and Europe. However, the diagnosis of stress disorders is currently based on symptom checklist and psychological questionnaires, thus making the identification of candidate biomarkers necessary to gain better insights into this pathology and its related metabolic alterations. Regarding the identification of potential biomarkers, omic profiling and metabolic footprint arise as promising approaches to recognize early biochemical changes in such disease and provide opportunities for the development of integrative candidate biomarkers. Here, we studied plasma and urine metabolites together with metagenomics in a 3 days Chronic Unpredictable Mild Stress (3d CUMS) animal approach that aims to focus on the early stress period of a well-established depression model. The multi-omics integration showed a profile composed by a signature of eight plasma metabolites, six urine metabolites and five microbes. Specifically, threonic acid, malic acid, alpha-ketoglutarate, succinic acid and cholesterol were proposed as key metabolites that could serve as key potential biomarkers in plasma metabolome of early stages of stress. Such findings targeted the threonic acid metabolism and the tricarboxylic acid (TCA) cycle as important pathways in early stress. Additionally, an increase in opportunistic microbes as virus of the Herpesvirales was observed in the microbiota as an effect of the primary stress stages. Our results provide an experimental biochemical characterization of the early stage of CUMS accompanied by a subsequent omic profiling and a metabolic footprinting that provide potential candidate biomarkers.}, }
@article {pmid34881191, year = {2021}, author = {Afolayan, AO and Biagi, E and Rampelli, S and Candela, M and Brigidi, P and Turroni, S and Ayeni, FA}, title = {The Gut Microbiota of an Individual Varies With Intercontinental Four-Month Stay Between Italy and Nigeria: A Pilot Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {725769}, pmid = {34881191}, issn = {2235-2988}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; Nigeria ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Despite well-established knowledge of the role of diet and the geographic effect on the gut microbiota of human populations, the temporal dynamics of the individual microbiota profile across changes associated with intercontinental short residence are still far from being understood. This pilot study sought to provide insights into the trajectory of the gut microbiota of an individual during a two-month stay in Italy and a subsequent two-month stay in Nigeria, by 16S rRNA gene sequencing and inferred metagenomics. The gut microbiota underwent massive but temporary changes, both taxonomically and based on predicted functionality. The faecal microbiota associated with the short stay in Italy progressively lost diversity and showed a dominance of Firmicutes, while after returning to Nigeria, the microbial community quickly regained the typical profile, in terms of biodiversity and bacterial signatures of traditional lifestyle, i.e., Prevotella and Treponema. Predicted pathways involved in glycolysis, fermentation and N-acetylneuraminate degradation were enriched during the subsequent two-month stay in Nigeria, whereas pathways associated with amino acid and peptidoglycan synthesis and maturation became over-represented during short stay in Italy. Our findings stress the plasticity of the individual gut microbiota even during a short-term travel, with loss/gain of taxonomic and functional features that mirror those of the gut microbiota of indigenous people dwelling therein.}, }
@article {pmid34880054, year = {2022}, author = {Tomofuji, Y and Kishikawa, T and Maeda, Y and Ogawa, K and Nii, T and Okuno, T and Oguro-Igashira, E and Kinoshita, M and Yamamoto, K and Sonehara, K and Yagita, M and Hosokawa, A and Motooka, D and Matsumoto, Y and Matsuoka, H and Yoshimura, M and Ohshima, S and Nakamura, S and Inohara, H and Mochizuki, H and Takeda, K and Kumanogoh, A and Okada, Y}, title = {Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease.}, journal = {Annals of the rheumatic diseases}, volume = {81}, number = {2}, pages = {278-288}, pmid = {34880054}, issn = {1468-2060}, mesh = {Asians ; Autoimmune Diseases/*virology ; *Bacteriophages ; Case-Control Studies ; *Gastrointestinal Microbiome ; Humans ; *Virome ; }, abstract = {OBJECTIVE: The relationship between autoimmune diseases and the gut microbiome has been intensively studied, and several autoimmunity-associated bacterial taxa have been identified. However, much less is known about the roles of the gut virome in autoimmune diseases.<br><br>METHODS: Here, we performed a whole gut virome analysis based on the shotgun sequencing of 476 Japanese which included patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), multiple sclerosis and healthy control subjects.<br><br>RESULTS: Our case-control comparison of the viral abundance revealed that crAss-like phages, which are one of the main components of a healthy gut virome, significantly decreased in the gut of the patients with autoimmune disease, specifically the patients with RA and SLE. In addition, Podoviridae significantly decreased in the gut of the patients with SLE. To understand how these viruses affected the bacteriome, we performed a quantitative virus-bacterium association analysis and clustered regularly interspaced short palindromic repeat-based virus-bacterium interaction analysis. We identified a symbiosis between Podoviridae and Faecalibacterium. In addition, multiple bacterial targets of crAss-like phages were identified (eg, Ruminococcus spp).<br><br>CONCLUSION: Our data suggest that the gut virome can affect our body either directly or via bacteria. Our analyses have elucidated a previously missing part of the autoimmunity-associated gut microbiome and presented new candidates that contribute to the development of autoimmune diseases.}, }
@article {pmid34878610, year = {2021}, author = {Kumar, V and Kumar, S and Singh, D}, title = {Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {1}, pages = {3}, pmid = {34878610}, issn = {1433-4909}, support = {MLP0143//CSIR-Institute of Himalayan Bioresource Technology/ ; }, mesh = {Geologic Sediments ; *Lakes ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.}, }
@article {pmid34876615, year = {2021}, author = {Gao, B and Jose, A and Alonzo-Palma, N and Malik, T and Shankaranarayanan, D and Regunathan-Shenk, R and Raj, DS}, title = {Butyrate producing microbiota are reduced in chronic kidney diseases.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23530}, pmid = {34876615}, issn = {2045-2322}, mesh = {Adolescent ; Bacteria/genetics/metabolism ; Butyrates/*metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Male ; Metagenomics/methods ; Renal Insufficiency, Chronic/*microbiology ; Severity of Illness Index ; }, abstract = {Chronic kidney disease is a major public health concern that affects millions of people globally. Alterations in gut microbiota composition have been observed in patients with chronic kidney disease. Nevertheless, the correlation between the gut microbiota and disease severity has not been investigated. In this study, we performed shot-gun metagenomics sequencing and identified several taxonomic and functional signatures associated with disease severity in patients with chronic kidney disease. We noted that 19 microbial genera were significantly associated with the severity of chronic kidney disease. The butyrate-producing bacteria were reduced in patients with advanced stages of chronic kidney diseases. In addition, functional metagenomics showed that two-component systems, metabolic activity and regulation of co-factor were significantly associated with the disease severity. Our study provides valuable information for the development of microbiota-oriented therapeutic strategies for chronic kidney disease.}, }
@article {pmid34875513, year = {2022}, author = {Iasakov, TR and Kanapatskiy, TA and Toshchakov, SV and Korzhenkov, AA and Ulyanova, MO and Pimenov, NV}, title = {The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation.}, journal = {Marine environmental research}, volume = {173}, number = {}, pages = {105533}, doi = {10.1016/j.marenvres.2021.105533}, pmid = {34875513}, issn = {1879-0291}, mesh = {Anaerobiosis ; Archaea/genetics ; Geologic Sediments ; *Methane ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; Planctomycetes ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.}, }
@article {pmid34873013, year = {2021}, author = {Mao, J and Wang, D and Long, J and Yang, X and Lin, J and Song, Y and Xie, F and Xun, Z and Wang, Y and Wang, Y and Li, Y and Sun, H and Xue, J and Song, Y and Zuo, B and Zhang, J and Bian, J and Zhang, T and Yang, X and Zhang, L and Sang, X and Zhao, H}, title = {Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers.}, journal = {Journal for immunotherapy of cancer}, volume = {9}, number = {12}, pages = {}, pmid = {34873013}, issn = {2051-1426}, mesh = {Biliary Tract Neoplasms/*drug therapy/immunology/microbiology/pathology ; Carcinoma, Hepatocellular/*drug therapy/immunology/microbiology/pathology ; DNA, Bacterial/analysis/*genetics ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Immune Checkpoint Inhibitors/*therapeutic use ; Liver Neoplasms/*drug therapy/immunology/microbiology/pathology ; Male ; Metagenomics ; Middle Aged ; Prognosis ; Programmed Cell Death 1 Receptor/*antagonists &amp; inhibitors ; Survival Rate ; }, abstract = {BACKGROUND: The gut microbiome is associated with the response to immunotherapy for different cancers. However, the impact of the gut microbiome on hepatobiliary cancers receiving immunotherapy remains unknown. This study aims to investigate the relationship between the gut microbiome and the clinical response to anti-programmed cell death protein 1 (PD-1) immunotherapy in patients with advanced hepatobiliary cancers.<br><br>METHODS: Patients with unresectable hepatocellular carcinoma or advanced biliary tract cancers who have progressed from first-line chemotherapy (gemcitabine plus cisplatin) were enrolled. Fresh stool samples were collected before and during anti-PD-1 treatment and analyzed with metagenomic sequencing. Significantly differentially enriched taxa and prognosis associated taxa were identified. The Kyoto Encyclopedia of Genes and Genomes database and MetaCyc database were further applied to annotate the differentially enriched taxa to explore the potential mechanism of the gut microbiome influencing cancer immunotherapy.<br><br>RESULTS: In total, 65 patients with advanced hepatobiliary cancers receiving anti-PD-1 treatment were included in this study. Seventy-four taxa were significantly enriched in the clinical benefit response (CBR) group and 40 taxa were significantly enriched in the non-clinical benefit (NCB) group. Among these taxa, patients with higher abundance of Lachnospiraceae bacterium-GAM79 and Alistipes sp Marseille-P5997, which were significantly enriched in the CBR group, achieved longer progression-free survival (PFS) and overall survival (OS) than patients with lower abundance. Higher abundance of Ruminococcus calidus and Erysipelotichaceae bacterium-GAM147 enriched in the CBR group was also observed in patients with better PFS. In contrast, worse PFS and OS were found in patients with higher abundance of Veillonellaceae, which was significantly enriched in the NCB group. Functional annotation indicated that the taxa enriched in the CBR group were associated with energy metabolism while the taxa enriched in the NCB group were associated with amino acid metabolism, which may modulate the clinical response to immunotherapy in hepatobiliary cancers. In addition, immunotherapy-related adverse events were affected by the gut microbiome diversity and relative abundance.<br><br>CONCLUSIONS: We demonstrate that the gut microbiome is associated with the clinical response to anti-PD-1 immunotherapy in patients with hepatobiliary cancers. Taxonomic signatures enriched in responders are effective biomarkers to predict the clinical response and survival benefit of immunotherapy, which might provide a new therapeutic target to modulate the response to cancer immunotherapy.}, }
@article {pmid34872176, year = {2022}, author = {Chen, X and Hu, X and Lu, Q and Yang, Y and Linghu, S and Zhang, X}, title = {Study on the differences in sludge toxicity and microbial community structure caused by catechol, resorcinol and hydroquinone with metagenomic analysis.}, journal = {Journal of environmental management}, volume = {302}, number = {Pt A}, pages = {114027}, doi = {10.1016/j.jenvman.2021.114027}, pmid = {34872176}, issn = {1095-8630}, mesh = {Bioreactors ; Catechols/toxicity ; Hydroquinones/toxicity ; *Microbiota ; Resorcinols/toxicity ; *Sewage ; }, abstract = {The aerobic biodegradation rate, organic toxicity and microbial community structure of activated sludge acclimated by catechol, resorcinol and hydroquinone were investigated, to study the relationship between microbial structure and sludge organic toxicity caused by phenolic compounds. At the stable operation stage, the degradation rates of the dihydroxy benzenes in a single sequencing batch reactor (SBR) cycle were followed the order: resorcinol (89.71%) > hydroquinone (85.64%) > catechol (59.62%). Sludge toxicity bioassay indicated that the toxicity of sludge was catechol (45.63%) > hydroquinone (40.28%) > resorcinol (38.15%). The accumulation of secondary metabolites such as 5-10 kDa tryptophan and tyrosine protein substances caused the differential sludge toxicity. Microbial metagenomic analysis showed that the toxicity of sludge was significantly related to the microbial community structure. Thauera, Azoarcus, Pseudomonas and other Proteobacteria formed in the sludge during acclimation. Catechol group had the least dominant bacteria and loop ring opening enzyme genes (catA, dmpB, dxnF, hapD) numbers. Therefore, the degradation of catechol was the most difficult than resorcinol and hydroquinone, resulting the highest sludge toxicity.}, }
@article {pmid34867834, year = {2021}, author = {Thomas, P and Sahu, PK}, title = {Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {635810}, pmid = {34867834}, issn = {1664-302X}, abstract = {Seed transmission of endophytic microorganisms is a growing research area in plant biology and microbiology. We employed cultivation versus cultivation-independent approaches on excised embryos from watermelon seeds (6-12 months in storage) and on embryo-derived in vitro seedlings (EIVS) to assess the vertical transmission of endophytic bacteria. Surface-disinfected watermelon seeds bore abundant residual bacteria in the testa and perisperm tissues, predominantly Bacillus spp. propounding the essentiality of excluding all non-embryonic tissues for vertical transmission studies. Tissue homogenates from re-disinfected seed embryos displayed no cultivable bacteria during the 1-week monitoring. Bright-field live microscopy revealed abundant bacteria in tissue homogenates and in embryo sections as intracellular motile particles. Confocal imaging on embryo sections after SYTO-9 staining and eubacterial fluorescent in situ hybridization (FISH) endorsed enormous bacterial colonization. Quantitative Insights Into Microbial Ecology (QIIME)-based 16S rRNA V3-V4 taxonomic profiling excluding the preponderant chloroplast and mitochondrial sequences revealed a high bacterial diversity in watermelon seed embryos mainly Firmicutes barring spore formers followed by Proteobacteria, Bacteroidetes, and Actinobacteria, and other minor phyla. Embryo-base (comprising the radicle plus plumule parts) and embryo-cotyledon parts differed in bacterial profiles with the abundance of Firmicutes in the former and Proteobacteria dominance in the latter. EIVS displayed a higher bacterial diversity over seed embryos indicating the activation from the dormant stage of more organisms in seedlings or their better amenability to DNA techniques. It also indicated embryo-to-seedling bacterial transmission, varying taxonomic abundances for seed embryos and seedlings, and differing phylogenic profiles for root, hypocotyl, and cotyledon/shoot-tip tissues. Investigations on different watermelon cultivars confirmed the embryo transmission of diverse cultivation recalcitrant endophytic bacteria. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes formed the core phyla across different cultivars with 80-90% similarity at genus to phylum levels. Conversely, freshly harvested seeds displayed a dominance of Proteobacteria. The findings revealed that dicot seeds such as in different watermelon cultivars come packaged with abundant and diverse vertical and seedling-transmissible cultivation recalcitrant endophytic bacteria with significant implications for plant biology.}, }
@article {pmid34865800, year = {2021}, author = {Zhang, Z and Han, Z and Wu, Y and Jiang, S and Ma, C and Zhang, Y and Zhang, J}, title = {Metagenomics assembled genome scale analysis revealed the microbial diversity and genetic polymorphism of Lactiplantibacillus plantarum in traditional fermented foods of Hainan, China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {150}, number = {Pt A}, pages = {110785}, doi = {10.1016/j.foodres.2021.110785}, pmid = {34865800}, issn = {1873-7145}, mesh = {*Fermented Foods ; Food Microbiology ; Humans ; Metagenomics ; *Microbiota ; Polymorphism, Genetic ; }, abstract = {Exploring the microbiome in fermented foods and their effects on food quality and sustainability is beneficial to provide data support for understanding how they affects human physiology. Here, metagenomic sequencing and metagenomic assembled genomes (MAGs) were applied to appraise the microbial diversity of fermented Yucha (FYC) and fermented vegetables (FVE). The antibiotic resistance genes (ARGs) enrichment and genetic polymorphism of Lactiplantibacillus plantarum in fermented foods of different regions were compared. The results showed that Lactiplantibacillus plantarum was the dominant species in FYC, while Lactiplantibacillus fermentum in FVE occupied the dominant position. From 32 high-quality MAGs, the central differential Lactic acid bacteria were higher in FVE. By comparing the Lactiplantibacillus plantarum MAGs in Hainan and Other regions, we found that the total Single Nucleotide Polymorphisms of Lactiplantibacillus plantarum in Hainan were significantly higher than other areas. Six non-synonymous mutations were included in the primary differential mutation, especially TrkA family potassium uptake protein and MerR family transcriptional regulator, which may be related to the hypersaline environment and highest ARGs enrichment in Hainan. This research provides valuable insight into our understanding of the microbiome of fermented food. Meanwhile, the analysis of Lactiplantibacillus plantarum genetic polymorphism based on MAGs helps us understand this strain's evolutionary history.}, }
@article {pmid34864967, year = {2021}, author = {Sato, Y and Takebe, H and Tominaga, K and Oishi, K and Kumagai, H and Yoshida, T and Hirooka, H}, title = {Taxonomic and functional characterization of the rumen microbiome of Japanese Black cattle revealed by 16S rRNA gene amplicon and metagenome shotgun sequencing.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {12}, pages = {}, doi = {10.1093/femsec/fiab152}, pmid = {34864967}, issn = {1574-6941}, mesh = {Animals ; Cattle ; Diet ; Genes, rRNA ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rumen ; }, abstract = {This study aimed to determine the taxonomic and functional characteristics of the Japanese Black (JB) steer rumen microbiome. The rumen microbiomes of six JB steers (age 14.7 ± 1.44 months) and six JB sires × Holstein dams crossbred (F1) steers (age 11.1 ± 0.39 months), fed the same diet, were evaluated. Based on 16S rRNA gene sequencing, the beta diversity revealed differences in microbial community structures between the JB and F1 rumen. Shotgun sequencing showed that Fibrobacter succinogenes and two Ruminococcus spp., which are related to cellulose degradation were relatively more abundant in the JB steer rumen than in the F1 rumen. Furthermore, the 16S rRNA gene copy number of F. succinogenes was significantly higher in the JB steer rumen than in the F1 rumen according to quantitative real-time polymerase chain reaction analysis. Genes encoding the enzymes that accelerate cellulose degradation and those associated with hemicellulose degradation were enriched in the JB steer rumen. Although Prevotella spp. were predominant both in the JB and F1 rumen, the genes encoding carbohydrate-active enzymes of Prevotella spp. may differ between JB and F1.}, }
@article {pmid34864203, year = {2022}, author = {Maran, MIJ and Davis G, DJ}, title = {Benefits of merging paired-end reads before pre-processing environmental metagenomics data.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100914}, doi = {10.1016/j.margen.2021.100914}, pmid = {34864203}, issn = {1876-7478}, mesh = {Biodiversity ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: High throughput sequencing of environmental DNA has applications in biodiversity monitoring, taxa abundance estimation, understanding the dynamics of community ecology, and marine species studies and conservation. Environmental DNA, especially, marine eDNA, has a fast degradation rate. Aside from the good quality reads, the data could have a significant number of reads that fall slightly below the default PHRED quality threshold of 30 on sequencing. For quality control, trimming methods are employed, which generally precede the merging of the read pairs. However, in the case of eDNA, a significant percentage of reads within the acceptable quality score range are also dropped.<br><br>METHODS: To infer the ideal merge tool that is sensitive to eDNA, two Hiseq paired-end eDNA datasets were utilized to study the merging by the tools - FLASH (Fast Length Adjustment of SHort reads), PANDAseq, COPE, BBMerge, and VSEARCH without preprocessing. We assessed these tools on the following parameters: Time taken to process, the quality, and the number of merged reads. Trimmomatic, a widely-used preprocessing tool, was also assessed by preprocessing the datasets at different parameters for the two approaches of preprocessing: Sliding Window and Maximum Information. The preprocessed read pairs were then merged using the ideal merge tool identified earlier.<br><br>RESULTS: FLASH is the most efficient merge tool balancing data conservation, quality of reads, and processing time. We compared Trimmomatic's two quality trimming options with increasing strictness with FLASH's direct merge. The raw reads processed with Trimmomatic then merged, yielded a significant drop in reads compared to the direct merge. An average of 29% of reads was dropped when directly merged with FLASH. Maximum Information option resulted in 30.7% to 68.05% read loss with lowest and highest stringency parameters, respectively. The Sliding Window approach conserves approximately 10% more reads at a PHRED score of 25 set as the threshold for a window of size 4. The lowered PHRED cut off conserves about 50% of the reads that could potentially be informative. We noted no significant reduction of data while optimizing the number of reads read in a window with the ideal quality (Q) score.<br><br>CONCLUSIONS: Losing reads can negatively impact the downstream processing of the environmental data, especially for sequence alignment studies. The quality trim-first-merge-later approach can significantly decrease the number of reads conserved. However, direct merging of pair-end reads using FLASH conserved more than 60% of the reads. Therefore, direct merging of the paired-end reads can prevent potential removal of informative reads that do not comply by the trimming tool's strict checks. FLASH to be an efficient tool in conserving reads while carrying out quality trimming in moderation. Overall, our results show that merging paired-end reads of eDNA data before trimming can conserve more reads.}, }
@article {pmid34864063, year = {2022}, author = {Pradhan, S and Ray, P and Aich, P}, title = {Microbiota transplantation from younger to older mice could restore lost immunity to effectively clear salmonella infection in Th2-biased BALB/c mice.}, journal = {Life sciences}, volume = {288}, number = {}, pages = {120201}, doi = {10.1016/j.lfs.2021.120201}, pmid = {34864063}, issn = {1879-0631}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*growth &amp; development ; Cecum/*transplantation ; Fecal Microbiota Transplantation/*methods ; Gastrointestinal Microbiome ; Homeostasis ; Immunity, Innate ; Male ; Metabolome ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Salmonella/drug effects/genetics/*immunology/metabolism ; Salmonella Infections/immunology/metabolism/microbiology/*therapy ; Th2 Cells/*immunology ; }, abstract = {AIMS: The composition, overtly abundance, and diversity of gut microbiota, play a significant role in maintaining physiological homeostasis with age. Reports revealed that the gut microbial profile might be correlated with immunity and metabolism. It is, therefore, tantamount to know if an older individual can achieve the immunity and metabolic profile of a younger individual by receiving the gut microbiome of a younger individual. In the current report, we have studied the effects of cecal microbiota transplantation (CMT) from younger to older mice.<br><br>MATERIALS AND METHODS: In this study, older BALB/c mice (23 weeks) received CMT from younger BALB/c mice (3 weeks).<br><br>KEY FINDINGS: CMT recipient mice showed altered expressions of immune and tight junction protein genes in the colon of mice, while the non-CMT recipient mice did not. Older mice were treated with AVNM to make them compatible with CMT. Further data from metabolite studies revealed that AVNM treatment mainly affected the aromatic amino acid biosynthesis pathway while CMT mostly affected the metabolism of different carbohydrates. We repeated the analysis in C57BL/6 mice without any significant effects of CMT.<br><br>SIGNIFICANCE: Results revealed that mice who received CMT showed more efficient restoration of gut microbiota than non-CMT recipient mice. CMT caused the alleviation of Salmonella infection and efficient recovery of the cecal index in the mice following antibiotics treatment.}, }
@article {pmid34862696, year = {2022}, author = {Jiao, S and Chen, W and Wei, G}, title = {Core microbiota drive functional stability of soil microbiome in reforestation ecosystems.}, journal = {Global change biology}, volume = {28}, number = {3}, pages = {1038-1047}, doi = {10.1111/gcb.16024}, pmid = {34862696}, issn = {1365-2486}, mesh = {Metagenomics ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {Revealing the ecological roles of core microbiota in the maintenance of the functional stability of soil microbiomes is crucial for sustainable ecosystem functioning; however, there is a dearth of whole-soil profile studies on the fundamental topic in microbial ecology, especially in the context of ecological restoration. Here, we explored whether core microbiota influence the temporal changes in the functional stability of soil microbiomes throughout the soil profile (i.e., soil depths of 0-300 cm) during natural succession in restored ex-arable ecosystems, via high-throughput amplicon and metagenomic sequencing. We revealed that core microbiota were essential for the maintenance of the functional stability of soil microbiomes in reforestation ecosystems. Specifically, the core taxa within one cluster of soil network, which had similar ecological preferences, had major contributions to functional stability. Reforestation significantly decreased the functional stability of soil microbiomes, which exhibited significant variations along the vertical soil profile in the reforested soils. Overall, the findings enhance our understanding of the factors driving functional stability in soil microbiomes, and suggests that core microbiota should be considered a key factor and integrated in policy and management activities targeting the enhancement and maintenance of functional stability and ecosystem sustainability in ecological restoration programs.}, }
@article {pmid34856283, year = {2022}, author = {Marcoleta, AE and Arros, P and Varas, MA and Costa, J and Rojas-Salgado, J and Berríos-Pastén, C and Tapia-Fuentes, S and Silva, D and Fierro, J and Canales, N and Chávez, FP and Gaete, A and González, M and Allende, ML and Lagos, R}, title = {The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {152003}, doi = {10.1016/j.scitotenv.2021.152003}, pmid = {34856283}, issn = {1879-1026}, mesh = {Antarctic Regions ; Anti-Bacterial Agents ; Genes, Bacterial ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Soil ; }, abstract = {The rise of multiresistant bacterial pathogens is currently one of the most critical threats to global health, encouraging a better understanding of the evolution and spread of antimicrobial resistance. In this regard, the role of the environment as a source of resistance mechanisms remains poorly understood. Moreover, we still know a minimal part of the microbial diversity and resistome present in remote and extreme environments, hosting microbes that evolved to resist harsh conditions and thus a potentially rich source of novel resistance genes. This work demonstrated that the Antarctic Peninsula soils host a remarkable microbial diversity and a widespread presence of autochthonous antibiotic-resistant bacteria and resistance genes. We observed resistance to a wide array of antibiotics among isolates, including Pseudomonas resisting ten or more different compounds, with an overall increased resistance in bacteria from non-intervened areas. In addition, genome analysis of selected isolates showed several genes encoding efflux pumps, as well as a lack of known resistance genes for some of the resisted antibiotics, including colistin, suggesting novel uncharacterized mechanisms. By combining metagenomic approaches based on analyzing raw reads, assembled contigs, and metagenome-assembled genomes, we found hundreds of widely distributed genes potentially conferring resistance to different antibiotics (including an outstanding variety of inactivation enzymes), metals, and biocides, hosted mainly by Polaromonas, Pseudomonas, Streptomyces, Variovorax, and Burkholderia. Furthermore, a proportion of these genes were found inside predicted plasmids and other mobile elements, including a putative OXA-like carbapenemase from Polaromonas harboring conserved key residues and predicted structural features. All this evidence indicates that the Antarctic Peninsula soil microbiota has a broad natural resistome, part of which could be transferred horizontally to pathogenic bacteria, acting as a potential source of novel resistance genes.}, }
@article {pmid34855234, year = {2022}, author = {Zarei, A and Javid, H and Sanjarian, S and Senemar, S and Zarei, H}, title = {Metagenomics studies for the diagnosis and treatment of prostate cancer.}, journal = {The Prostate}, volume = {82}, number = {3}, pages = {289-297}, doi = {10.1002/pros.24276}, pmid = {34855234}, issn = {1097-0045}, mesh = {Genitalia, Male/*microbiology ; Humans ; Male ; Metagenomics/*methods ; Microbiota/*genetics ; Precision Medicine ; *Prostatic Neoplasms/genetics/metabolism/therapy ; }, abstract = {AIM: Mutation occurs in the prostate cell genes, leading to abnormal prostate proliferation and ultimately cancer. Prostate cancer (PC) is one of the most common cancers amongst men, and its prevalence worldwide increases relative to men's age. About 16% of the world's cancers are the result of microbes in the human body. Impaired population balance of symbiosis microbes in the human reproductive system is linked to PC development.<br><br>DISCUSSION: With the advent of metagenomics science, the genome sequence of the microbiota of the human body has been unveiled. Therefore, it is now possible to identify a higher range of microbiome changes in PC tissue via the Next Generation Technique, which will have positive consequences in personalized medicine. In this review, we intend to question the role of metagenomics studies in the diagnosis and treatment of PC.<br><br>CONCLUSION: The microbial imbalance in the men's genital tract might have an effect on prostate health. Based on next-generation sequencing-generated data, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodetes are the nine frequent phyla detected in a PC sample, which might be involved in inducing mutation in the prostate cells that cause cancer.}, }
@article {pmid34851181, year = {2021}, author = {Wu, K and Xu, Y and Zhang, W and Mao, H and Chen, B and Zheng, Y and Hu, X}, title = {Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0191821}, pmid = {34851181}, issn = {2165-0497}, mesh = {Animal Husbandry/*methods ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Deer/*microbiology/physiology ; *Drug Resistance, Bacterial ; Ecosystem ; Feces/*microbiology ; *Gastrointestinal Microbiome ; }, abstract = {This study aimed to compare the fecal microbiome and antimicrobial resistance between captive and free-range sika deer with the same exposure to antibiotic anthelmintics. The taxonomic differences mainly involved significant changes in the dominant phyla, genera, and species. Linear discriminant analysis effect size (LEfSe) analysis revealed that 22 taxa were significantly different between the two groups. The KEGG analysis showed that the fecal microbiome metabolic function, and all level 2 categories in metabolism had higher abundance in the free-range deer. Based on the carbohydrate-active enzyme (CAZy) database analysis, glycoside hydrolases and carbohydrate-binding modules showed remarkable differences between the two groups. Regarding antibiotic resistance, tetQ and lnuC dominated the antibiotic resistance ontology (ARO) terms, and tetracycline and lincosamide resistance dominated the antimicrobial resistance patterns. Furthermore, the lnuC, ErmF, and tetW/N/W AROs and lincosamide resistance showed higher abundance in the captive deer, suggesting that captivity may yield more serious resistance issues because of the differences in greenfeed diet, breeding density, and/or housing environment. The results also revealed important associations between the phylum Proteobacteria, genus Prevotella, and major antibiotic resistance genes. Although the present study was a pilot study with a limited sample size that was insufficient control for some potential factors, it serves as the metagenomic study on the microbial communities and antimicrobial resistance in sika deer. IMPORTANCE We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.}, }
@article {pmid34847216, year = {2021}, author = {Sirven, MA and Venancio, VP and Shankar, S and Klemashevich, C and Castellón-Chicas, MJ and Fang, C and Mertens-Talcott, SU and Talcott, ST}, title = {Ulcerative colitis results in differential metabolism of cranberry polyphenols by the colon microbiome in vitro.}, journal = {Food &amp; function}, volume = {12}, number = {24}, pages = {12751-12764}, doi = {10.1039/d1fo03047g}, pmid = {34847216}, issn = {2042-650X}, mesh = {Adolescent ; Adult ; Aged ; Colitis, Ulcerative/*metabolism ; Colon/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; In Vitro Techniques ; Male ; Middle Aged ; Plant Extracts/metabolism ; Polyphenols/*metabolism ; Vaccinium macrocarpon/*metabolism ; Young Adult ; }, abstract = {The microbiome plays a major role in polyphenol metabolism, producing metabolites that are bioavailable and potentially more bioactive than the compounds from which they are derived. However, the microbiome can vary among individuals, and especially for those with co-morbidities, such as ulcerative colitis. In subjects with ulcerative colitis, the consequence of a 'dysbiotic' microbiome is characterized by decreased diversity of microbiota that may impact their capability to metabolize polyphenols into bioavailable metabolites. On this premise, the microbiome metabolism of cranberry polyphenols between healthy individuals and those with ulcerative colitis was compared in vitro. Fecal samples from volunteers, with or without diagnosed ulcerative colitis, were cultured anaerobically in the presence of cranberry polyphenols. The resulting metabolites were then quantified via LC-ESI-MS/MS. 16S rRNA metagenomics analysis was also utilized to assess differences in microbiota composition between healthy and ulcerative colitis microbiomes and the modulatory effects of cranberry polyphenols on microbiota composition. Healthy microbiomes produced higher (p < 0.05) concentrations of 5-(3',4'-dihydroxyphenyl)-gamma-valerolactone and 3-hydroxyphenylacetic acid in comparison to ulcerative colitis microbiomes. Additionally, healthy microbiomes contained a higher (p < 0.05) abundance of Ruminococcaceae, which could explain their ability to produce higher concentrations of cranberry polyphenol metabolites. Health status and the presence of cranberry polyphenols also significantly impacted the production of several short-chain and branched-chain fatty acids. These results suggest that efficiency of polyphenol metabolism is dependent on microbiota composition and future works should include metabolite data to account for inter-individual differences in polyphenol metabolism.}, }
@article {pmid34844317, year = {2022}, author = {Chen, S and Holyoak, M and Liu, H and Bao, H and Ma, Y and Dou, H and Jiang, G}, title = {Effects of spatially heterogeneous warming on gut microbiota, nutrition and gene flow of a heat-sensitive ungulate population.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 1}, pages = {150537}, doi = {10.1016/j.scitotenv.2021.150537}, pmid = {34844317}, issn = {1879-1026}, mesh = {Animals ; *Deer ; Ecosystem ; *Gastrointestinal Microbiome ; Gene Flow ; Hot Temperature ; }, abstract = {Effects of climate warming on trophic cascades are increasingly reported for large herbivores occupying northern latitudes. During the last 40 years, moose (Alces alces) in northeast China have lost nearly half of their historical distribution through their habitat shifting northwards. There are many possible causes of bottom-up and top-down effects of temperature and for moose in northeast China they are poorly understood. Of particular relevance are the effects of extrinsic environmental factors on gene flow, nutritional adaptions, and gut microbiota that occur as moose populations retreat northwards. We combined molecular biology, nutritional ecology and metagenomics to gain deeper mechanistic insights into the effects of temperature on moose populations. In this study, we revealed that the direction and intensity of gene flow is consistent with global warming driving retreats of moose populations. We interpret this as evidence for the northward movement of moose populations, with cooler northern populations receiving more immigrants and warmer southern populations supplying emigrants. Comparison across latitudes showed that warmer late spring temperatures were associated with plant community composition and facilitated related changes in moose protein and carbohydrate intake through altering forage availability, forage quality and diet composition. Furthermore, these nutrient shifts were accompanied by changes in gut microbial composition and functional pathways related to nutrient metabolism. This study provided insights into mechanisms driving effects of spatial heterogeneous warming on genetic, nutritional and physiological adaptions related to key demographic rates and patterns of survival of heat-sensitive ungulates along a latitude gradient. Understanding such changes helps to identify key habitat areas and plant species to ensure accurate assessment of population status and targeted management of moose populations.}, }
@article {pmid34843867, year = {2021}, author = {Novak, B and Lopes Hasuda, A and Ghanbari, M and Mayumi Maruo, V and Bracarense, APFRL and Neves, M and Emsenhuber, C and Wein, S and Oswald, IP and Pinton, P and Schatzmayr, D}, title = {Effects of Fusarium metabolites beauvericin and enniatins alone or in mixture with deoxynivalenol on weaning piglets.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {158}, number = {}, pages = {112719}, doi = {10.1016/j.fct.2021.112719}, pmid = {34843867}, issn = {1873-6351}, mesh = {Animals ; Depsipeptides/*toxicity ; Eating/drug effects ; Fusarium/metabolism ; Gastrointestinal Microbiome/drug effects/*genetics ; Intestines/drug effects/pathology ; Liver/drug effects/enzymology/pathology ; Swine ; Trichothecenes/*toxicity ; Weaning ; Weight Gain/*drug effects ; }, abstract = {The impact of the Fusarium-derived metabolites beauvericin, enniatin B and B1 (EB) alone or in combination with deoxynivalenol (DON) was investigated in 28-29 days old weaning piglets over a time period of 14 days. The co-application of EB and DON (EB + DON) led to a significant decrease in the weight gain of the animals. Liver enzyme activities in plasma were significantly decreased at day 14 in piglets receiving the EB + DON-containing diet compared to piglets receiving the control diet. All mycotoxin-contaminated diets led to moderate to severe histological lesions in the jejunum, the liver and lymph nodes. Shotgun metagenomics revealed a significant effect of EB-application on the gut microbiota. Our results provide novel insights into the harmful impact of emerging mycotoxins alone or with DON on the performance, gut health and immunological parameters in pigs.}, }
@article {pmid34838907, year = {2022}, author = {Zhang, T and Li, J and Wang, N and Wang, H and Yu, L}, title = {Metagenomic analysis reveals microbiome and resistome in the seawater and sediments of Kongsfjorden (Svalbard, High Arctic).}, journal = {The Science of the total environment}, volume = {809}, number = {}, pages = {151937}, doi = {10.1016/j.scitotenv.2021.151937}, pmid = {34838907}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Genes, Bacterial ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Seawater ; Svalbard ; }, abstract = {Kongsfjorden in the high Arctic, a typical Arctic fjord, experienced long-time input of nutrients and pollutants from the remote and local resources, providing a platform for characterizing the diversity and distribution of antibiotic resistance genes (ARGs). However, the microbiome and antibiotic resistome in this pristine marine system have not been well documented. The present study aimed to characterize the diversity and distribution of bacterial communities and associated ARGs in seawater (12 samples) and sediments (13 samples) of Kongsfjorden via metagenomic analysis. In terms of both bacterial community compositions and ARG profiles, the seawater was significantly distinct from sediment. Only 29 ARG subtypes were detected in the Arctic seawater and sediments. Furthermore, three geochemical factors (i.e., longitude, depth, and PO43-) greatly influenced the bacterial communities in sediment samples, while longitude, depth, and latitude were crucial geochemical factors influencing the ARG profiles in sediment samples. Procrustes analysis revealed a significant correlation between bacterial community compositions and ARG profiles in seawater and sediment samples. Further analysis revealed the metagenome-assembled genomes (MAGs) with ARG subtypes. Overall, our study provides insights into the microbiome and resistome in a pristine Arctic fjord, thereby providing vital information for environmental management.}, }
@article {pmid34838108, year = {2021}, author = {Lin, D and Zheng, X and Sanogo, B and Ding, T and Sun, X and Wu, Z}, title = {Bacterial composition of midgut and entire body of laboratory colonies of Aedes aegypti and Aedes albopictus from Southern China.}, journal = {Parasites &amp; vectors}, volume = {14}, number = {1}, pages = {586}, pmid = {34838108}, issn = {1756-3305}, support = {2020YFC1200100//the National Key R&amp;D Program of China/ ; 2016YFC1200500//the National Key R&amp;D Program of China/ ; 2019A1515012068//Natural Science Foundation of Guangdong Province/ ; 2020A1515010896//Natural Science Foundation of Guangdong Province/ ; 2021A1515010976//Natural Science Foundation of Guangdong Province/ ; 82072308//the National Natural Science Foundation of China/ ; 82002168//the National Natural Science Foundation of China/ ; 20201192//the 6th Nuclear Energy R&amp;D Project/ ; B12003//The 111 Project/ ; }, mesh = {Aedes/*microbiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Laboratories ; Metagenomics ; Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are invasive mosquito species and significantly impact human health in southern China. Microbiota are confirmed to affect the development and immunity of mosquitoes. However, scientists have focused more on midgut microbiota of female mosquitoes and bacterial differences between female and male Aedes mosquitoes. The relationship between the midgut and entire body microbiota of Aedes is unclear. In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.<br><br>METHODS: In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.<br><br>RESULTS: A total of 341 OTUs were identified, showing that Proteobacteria was the dominant phylum and Methylobacterium the dominant genus in both Aedes aegypti and Aedes albopictus. The bacterial diversity and community structures of the entire bodies were similar between males and females in both Aedes aegypti and Aedes albopictus. Conversely, the bacterial compositions of male and female Aedes aegypti and Aedes albopictus were significantly different. NMDS analysis, UPGMA analysis, diversity indices and OTU distribution demonstrated that compositions and structures in midgut microbiota were similar but significantly different in the entire bodies of Aedes aegypti and Aedes albopictus. Functional prediction analysis showed that metabolism and environmental information processing were the dominant KEGG pathways at level 1. Our study showed that there were significantly different level 2 and 3 KEGG pathways in the midgut microbiota (16 level 2 and 24 level 3) and the entire bodies (33 level 2 and 248 level 3) between female Aedes albopictus and Aedes Aegypti.<br><br>CONCLUSIONS: Our findings that Aedes aegypti and Aedes albopictus reared in the same laboratory harbor a similar gut bacterial microbiome but different entire body microbiota imply that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype, but the entire body microbiota is more genetically determined. Our findings improved the understanding of the microbiota in the entire and partial tissues of Aedes mosquitoes.}, }
@article {pmid34838016, year = {2021}, author = {He, J and He, X and Ma, Y and Yang, L and Fang, H and Shang, S and Xia, H and Lian, G and Tang, H and Wang, Q and Wang, J and Lin, Z and Wen, J and Liu, Y and Zhai, C and Wang, W and Jiang, X and Xuan, J and Liu, M and Lu, S and Li, X and Wang, H and Ouyang, C and Cao, M and Lin, A and Zhang, B and Wu, D and Chen, Y and Xiao, C}, title = {A comprehensive approach to stool donor screening for faecal microbiota transplantation in China.}, journal = {Microbial cell factories}, volume = {20}, number = {1}, pages = {216}, pmid = {34838016}, issn = {1475-2859}, support = {81730003//national natural science foundation of china/ ; 82004433//national natural science foundation of china/ ; 2017ZX09304021//national major science and technology projects of china/ ; 16CZX064//national office for philosophy and social sciences/ ; }, mesh = {Adolescent ; Adult ; China ; Clostridium Infections/therapy ; Computational Biology/methods ; Donor Selection/*methods ; Fecal Microbiota Transplantation/*methods ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenomics/*methods ; Retrospective Studies ; *Tissue Donors ; Young Adult ; }, abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridium difficile infections and chronic gastrointestional infections. However, the risks of FMT and the selection process of suitable donors remain insufficiently characterized. The eligibility rate for screening, underlying microbial basis, and core ethical issues of stool donors for FMT are yet to be elucidated in China.<br><br>RESULTS: The potential stool donors were screened from December 2017 to December 2019 with the help of an online survey, clinical assessments, and stool and blood testing. Bioinformatics analyses were performed, and the composition and stability of gut microbiota in stool obtained from eligible donors were dynamically observed using metagenomics. Meanwhile, we build a donor microbial evaluation index (DoMEI) for stool donor screening. In the screening process, we also focused on ethical principles and requirements. Of the 2071 participants, 66 donors were selected via the screening process (3.19% success rate). Although there were significant differences in gut microbiota among donors, we found that the changes in the gut microbiota of the same donor were typically more stable than those between donors over time.<br><br>CONCLUSIONS: DoMEI provides a potential reference index for regular stool donor re-evaluation. In this retrospective study, we summarised the donor recruitment and screening procedure ensuring the safety and tolerability for FMT in China. Based on the latest advances in this field, we carried out rigorous recommendation and method which can assist stool bank and clinicians to screen eligible stool donor for FMT.}, }
@article {pmid34837955, year = {2021}, author = {Yan, Y and Yi, X and Duan, Y and Jiang, B and Huang, T and Inglis, BM and Zheng, B and Si, W}, title = {Alteration of the gut microbiota in rhesus monkey with spontaneous osteoarthritis.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {328}, pmid = {34837955}, issn = {1471-2180}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Biomarkers ; Disease Models, Animal ; Female ; *Gastrointestinal Microbiome ; Humans ; Knee Joint/pathology ; Macaca mulatta ; Osteoarthritis/*microbiology/pathology ; }, abstract = {BACKGROUND: The spontaneous osteoarthritis (OA) in rhesus macaque is similar to OA in human, which maintains an upright body posture and shows very similar biomechanical properties of bones to humans. At present, there is no good treatment for OA. This study aims to explore relationship between OA and intestinal microbiota, and provide a reference for the treatment of clinical OA.<br><br>RESULTS: We collected colonic contents of the 20 rhesus macaque (6-15 years old, female) for intestinal microbiota analysis by metagenomics sequencing, of which 10 were spontaneous OA monkeys and 10 were normal monkeys. Our results showed the diversity of gut microbiota in monkeys with OA was decreased compared to the normal monkeys (p = 0.16). Mollicutes, Tenericutes, Coprobacillus and Faecalitalea may be biomarkers for the monkeys of OA. Lactobacillus found significantly increased in OA monkeys. Prevotella and Ruminococcus were higher in the normal group than OA group. Zinc/manganese transport system permease protein (p = 0.0011) and Cyclopropane-fatty-acyl-phospholipid synthase (p = 0.0012) are a microbiota metabolic pathway related to cartilage production.<br><br>CONCLUSIONS: Our results indicate that the diversity and composition of intestinal microbiota in monkeys with OA are different compared to the normal monkeys. we have found microbes that may be a biomarker for the diagnosis of osteoarthritis. Functional analysis of the microbiota also predicts cartilage damage in the monkeys with osteoarthritis. Non-human primates are closely related to humans, so this study can provide a reference for the development of drugs for the treatment of OA.}, }
@article {pmid34836555, year = {2021}, author = {Hwang, Y and Schulze-Makuch, D and Arens, FL and Saenz, JS and Adam, PS and Sager, C and Bornemann, TLV and Zhao, W and Zhang, Y and Airo, A and Schloter, M and Probst, AJ}, title = {Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {234}, pmid = {34836555}, issn = {2049-2618}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Desert Climate ; *Microbiota ; Soil Microbiology ; }, abstract = {BACKGROUND: The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core.<br><br>RESULTS: Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins.<br><br>CONCLUSION: We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract.}, }
@article {pmid34836550, year = {2021}, author = {Ter Horst, AM and Santos-Medellín, C and Sorensen, JW and Zinke, LA and Wilson, RM and Johnston, ER and Trubl, G and Pett-Ridge, J and Blazewicz, SJ and Hanson, PJ and Chanton, JP and Schadt, CW and Kostka, JE and Emerson, JB}, title = {Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {233}, pmid = {34836550}, issn = {2049-2618}, mesh = {*Ecosystem ; Minnesota ; *Soil/chemistry ; Soil Microbiology ; Virome ; }, abstract = {BACKGROUND: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems.<br><br>RESULTS: Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes.<br><br>CONCLUSIONS: Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.}, }
@article {pmid34836316, year = {2021}, author = {Enaud, R and Cambos, S and Viaud, E and Guichoux, E and Chancerel, E and Marighetto, A and Etchamendy, N and Clark, S and Mohammedi, K and Cota, D and Delhaes, L and Gatta-Cherifi, B}, title = {Gut Microbiota and Mycobiota Evolution Is Linked to Memory Improvement after Bariatric Surgery in Obese Patients: A Pilot Study.}, journal = {Nutrients}, volume = {13}, number = {11}, pages = {}, pmid = {34836316}, issn = {2072-6643}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/growth &amp; development ; *Bariatric Surgery ; Feces/microbiology ; Female ; Fungi/growth &amp; development ; *Gastrointestinal Microbiome ; Humans ; Male ; *Memory ; Middle Aged ; *Mycobiome ; Obesity, Morbid/microbiology/psychology/*surgery ; Pilot Projects ; Prospective Studies ; Young Adult ; }, abstract = {Patients with obesity are known to exhibit gut microbiota dysbiosis and memory deficits. Bariatric surgery (BS) is currently the most efficient anti-obesity treatment and may improve both gut dysbiosis and cognition. However, no study has investigated association between changes of gut microbiota and cognitive function after BS. We prospectively evaluated 13 obese patients on anthropometric data, memory functions, and gut microbiota-mycobiota before and six months after BS. The Rey Auditory Verbal Learning Test (AVLT) and the symbol span (SS) of the Weschler Memory Scale were used to assess verbal and working memory, respectively. Fecal microbiota and mycobiota were longitudinally analyzed by 16S and ITS2 rRNA sequencing respectively. AVLT and SS scores were significantly improved after BS (AVLT scores: 9.7 ± 1.7 vs. 11.2 ± 1.9, p = 0.02, and SS scores: 9.7 ± 23.0 vs. 11.6 ± 2.9, p = 0.05). An increase in bacterial alpha-diversity, and Ruminococcaceae, Prevotella, Agaricus, Rhodotorula, Dipodascus, Malassezia, and Mucor were significantly associated with AVLT score improvement after BS, while an increase in Prevotella and a decrease in Clostridium, Akkermansia,&amp;nbsp;Dipodascus and Candida were linked to SS scores improvement. We identified several changes in the microbial communities that differ according to the improvement of either the verbal or working memories, suggesting a complex gut-brain-axis that evolves after BS.}, }
@article {pmid34835128, year = {2021}, author = {Cebriá-Mendoza, M and Bracho, MA and Arbona, C and Larrea, L and Díaz, W and Sanjuán, R and Cuevas, JM}, title = {Exploring the Diversity of the Human Blood Virome.}, journal = {Viruses}, volume = {13}, number = {11}, pages = {}, pmid = {34835128}, issn = {1999-4915}, mesh = {*Genome, Viral ; Healthy Volunteers ; Humans ; Spain ; *Virome ; Viruses/*isolation &amp; purification ; }, abstract = {Metagenomics is greatly improving our ability to discover new viruses, as well as their possible associations with disease. However, metagenomics has also changed our understanding of viruses in general. The vast expansion of currently known viral diversity has revealed a large fraction of non-pathogenic viruses, and offers a new perspective in which viruses function as important components of many ecosystems. In this vein, studies of the human blood virome are often motivated by the search for new viral diseases, especially those associated with blood transfusions. However, these studies have revealed the common presence of apparently non-pathogenic viruses in blood, particularly human anelloviruses and, to a lower extent, human pegiviruses (HPgV). To shed light on the diversity of the human blood virome, we subjected pooled plasma samples from 587 healthy donors in Spain to a viral enrichment protocol, followed by massive parallel sequencing. This showed that anelloviruses were clearly the major component of the blood virome and showed remarkable diversity. In total, we assembled 332 complete or near-complete anellovirus genomes, 50 of which could be considered new species. HPgV was much less frequent, but we, nevertheless, recovered 17 different isolates that we subsequently used for characterizing the diversity of this virus. In-depth investigation of the human blood virome should help to elucidate the ecology of these viruses, and to unveil potentially associated diseases.}, }
@article {pmid34834933, year = {2021}, author = {Turzynski, V and Monsees, I and Moraru, C and Probst, AJ}, title = {Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples.}, journal = {Viruses}, volume = {13}, number = {11}, pages = {}, pmid = {34834933}, issn = {1999-4915}, mesh = {Genome, Viral ; Metagenomics ; Microscopy/*methods ; Microscopy, Electron/*methods ; Virome ; Viruses/classification/*genetics/isolation &amp; purification/ultrastructure ; }, abstract = {Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.}, }
@article {pmid34831411, year = {2021}, author = {Schierova, D and Roubalova, R and Kolar, M and Stehlikova, Z and Rob, F and Jackova, Z and Coufal, S and Thon, T and Mihula, M and Modrak, M and Kverka, M and Bajer, L and Kostovcikova, K and Drastich, P and Hercogova, J and Novakova, M and Vasatko, M and Lukas, M and Tlaskalova-Hogenova, H and Jiraskova Zakostelska, Z}, title = {Fecal Microbiome Changes and Specific Anti-Bacterial Response in Patients with IBD during Anti-TNF Therapy.}, journal = {Cells}, volume = {10}, number = {11}, pages = {}, pmid = {34831411}, issn = {2073-4409}, support = {grant number NV18-09-00493.//Ministry of Health of the Czech Republic/ ; }, mesh = {Adult ; Antibodies/blood ; Biodiversity ; Case-Control Studies ; Feces/*microbiology ; Female ; Fungi/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Inflammatory Bowel Diseases/blood/*drug therapy/*microbiology/surgery ; Interleukin-17/metabolism ; Leukocytes, Mononuclear/metabolism ; Male ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Tumor Necrosis Factor Inhibitors/*therapeutic use ; }, abstract = {Inflammatory bowel diseases (IBD) are chronic disorders of the gastrointestinal tract that have been linked to microbiome dysbiosis and immune system dysregulation. We investigated the longitudinal effect of anti-TNF therapy on gut microbiota composition and specific immune response to commensals in IBD patients. The study included 52 patients tracked over 38 weeks of therapy and 37 healthy controls (HC). To characterize the diversity and composition of the gut microbiota, we used amplicon sequencing of the V3V4 region of 16S rRNA for the bacterial community and of the ITS1 region for the fungal community. We measured total antibody levels as well as specific antibodies against assorted gut commensals by ELISA. We found diversity differences between HC, Crohn's disease, and ulcerative colitis patients. The bacterial community of patients with IBD was more similar to HC at the study endpoint, suggesting a beneficial shift in the microbiome in response to treatment. We identified factors such as disease severity, localization, and surgical intervention that significantly contribute to the observed changes in the gut bacteriome. Furthermore, we revealed increased IgM levels against specific gut commensals after anti-TNF treatment. In summary, this study, with its longitudinal design, brings insights into the course of anti-TNF therapy in patients with IBD and correlates the bacterial diversity with disease severity in patients with ulcerative colitis (UC).}, }
@article {pmid34828970, year = {2021}, author = {Barbieri, F and Tabanelli, G and Montanari, C and Dall'Osso, N and Šimat, V and Smole Možina, S and Baños, A and Özogul, F and Bassi, D and Fontana, C and Gardini, F}, title = {Mediterranean Spontaneously Fermented Sausages: Spotlight on Microbiological and Quality Features to Exploit Their Bacterial Biodiversity.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {34828970}, issn = {2304-8158}, support = {Project ID 1467//PRIMA programme (supported by the European Union H2020 programme)/ ; }, abstract = {The wide array of spontaneously fermented sausages of the Mediterranean area can represent a reservoir of microbial biodiversity and can be an important source of new technological and functional strains able to preserve product properties, counteracting the impoverishment of their organoleptic typical features due to the introduction of commercial starter cultures. We analysed 15 artisanal salamis from Italy, Spain, Croatia and Slovenia to evaluate the microbiota composition, through culture-dependent and culture-independent techniques (i.e., metagenomic analysis), chemical-physical features, biogenic amines and aroma profile. The final pH varied according to origin and procedures (e.g., higher pH in Italian samples due to long ripening and mold growth). Lactic acid bacteria (LAB) and coagulase-negative cocci (CNC) were the dominant population, with highest LAB counts in Croatian and Italian samples. Metagenomic analysis showed high variability in qualitative and quantitative microbial composition: among LAB, Latilactobacillus sakei was the dominant species, but Companilactobacillus spp. was present in high amounts (45-55% of the total ASVs) in some Spanish sausages. Among staphylococci, S. epidermidis, S. equorum, S. saprophyticus, S. succinus and S. xylosus were detected. As far as biogenic amines, tyramine was always present, while histamine was found only in two Spanish samples. These results can valorize the bacterial genetic heritage present in Mediterranean products, to find new candidates of autochthonous starter cultures or bioprotective agents.}, }
@article {pmid34828362, year = {2021}, author = {Lach, J and Jęcz, P and Strapagiel, D and Matera-Witkiewicz, A and Stączek, P}, title = {The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools.}, journal = {Genes}, volume = {12}, number = {11}, pages = {}, pmid = {34828362}, issn = {2073-4425}, mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Biological Products/*analysis ; Computational Biology ; Data Mining ; Genome, Archaeal ; Genome, Bacterial ; Salt Tolerance ; Sequence Analysis, DNA/*methods ; }, abstract = {Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile's genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.}, }
@article {pmid34827957, year = {2021}, author = {Benmazouz, I and Jokimäki, J and Lengyel, S and Juhász, L and Kaisanlahti-Jokimäki, ML and Kardos, G and Paládi, P and Kövér, L}, title = {Corvids in Urban Environments: A Systematic Global Literature Review.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {11}, pages = {}, pmid = {34827957}, issn = {2076-2615}, support = {SH-00355-004/2019//Stipendium Hungaricum program/ ; NKFIH-OTKA K134391//National Research, Development, and Innovation Office of Hungary/ ; }, abstract = {Urbanization is one of the most prevalent drivers of biodiversity loss, yet few taxonomic groups are remarkably successful at adapting to urban environments. We systematically surveyed the global literature on the effects of urbanization on species of family Corvidae (crows, choughs, jackdaws, jays, magpies, nutcrackers, ravens, rooks, treepies) to assess the occurrence of corvids in urban environments and the factors affecting their success. We found a total of 424 primary research articles, and the number of articles has increased exponentially since the 1970s. Most studies were carried out in cities of Europe and North America (45.5% and 31.4%, respectively) and were directed on a single species (75.2). We found that 30 corvid species (23% of 133 total) regularly occur in urban environments. The majority (72%) of the studies reported positive effects of urbanization on corvids, with 85% of studies detecting population increases and 64% of studies detecting higher breeding success with urbanization. Of the factors proposed to explain corvids' success (availability of nesting sites and food sources, low predation and persecution), food availability coupled with diet shifts emerged as the most important factors promoting Corvidae to live in urban settings. The breeding of corvids in urban environments was further associated with earlier nesting, similar or larger clutches, lower hatching but higher fledging success, reduced home range size and limited territoriality, increased tolerance towards humans and increasing frequency of conflicts with humans. Despite geographic and taxonomic biases in our literature sample, our review indicates that corvids show both flexibility in resource use and behavioral plasticity that enable them to exploit novel resources for nesting and feeding. Corvids can thus be urban exploiters of the large-scale modifications of ecosystems caused by urbanization.}, }
@article {pmid34826491, year = {2022}, author = {Nóbrega, MS and Silva, BS and Tschoeke, DA and Appolinario, LR and Calegario, G and Venas, TM and Macedo, L and Asp, N and Cherene, B and Marques, JSJ and Seidel, M and Dittmar, T and Santos, IR and de Rezende, CE and Thompson, CC and Thompson, FL}, title = {Mangrove microbiome reveals importance of sulfur metabolism in tropical coastal waters.}, journal = {The Science of the total environment}, volume = {813}, number = {}, pages = {151889}, doi = {10.1016/j.scitotenv.2021.151889}, pmid = {34826491}, issn = {1879-1026}, mesh = {Carbon ; Estuaries ; *Microbiota ; Nitrogen ; Sulfur ; Wetlands ; }, abstract = {Mangroves under macro-tidal regimes are global carbon sequestration hotspots but the microbial drivers of biogeochemical cycles remain poorly understood. Here, we investigate the drivers of mangrove microbial community composition across a porewater-creek-estuary-ocean continuum. Observations were performed on the Amazon region in one of the largest mangrove systems worldwide with effective sequestration of organic carbon buried in soils and dissolved carbon via outwelling to the ocean. The potential export to the adjacent oceanic region ranged from 57 to 380 kg of dissolved and particulate organic carbon per second (up to 33 thousand tons C per day). Macro tides modulated microbial communities and their metabolic processes, e.g., anoxygenic phototrophy, sulfur, and nitrogen cycling. Respiration, sulfur metabolism and dissolved organic carbon (DOC) levels were linked to functional groups and microbial cell counts. Total microbial counts decreased and cyanobacteria counts peaked in the spring tide. The microbial groups driving carbon, nitrogen, sulfur and methane cycles were consistent across all spatial scales. Taxonomic groups engaged in sulfur cycling (Allochromatium, Desulfovibrio, and Thibacillus) within mangroves were abundant at all scales. Tidally-driven porewater exchange within mangroves drove a progressive increase of sulfur cycle taxonomic groups and their functional genes both temporally (tidal cycles) and spatially (from mangrove porewater to continental shelf). Overall, we revealed a unified and consistent response of microbiomes at different spatial and temporal scales to tidally-driven mangrove porewater exchange.}, }
@article {pmid34826164, year = {2022}, author = {Ma, Y and Liu, D and Wariss, HM and Zhang, R and Tao, L and Milne, RI and Sun, W}, title = {Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple.}, journal = {Molecular ecology}, volume = {31}, number = {3}, pages = {767-779}, doi = {10.1111/mec.16289}, pmid = {34826164}, issn = {1365-294X}, support = {2017FY100100//Survey and Germplasm Conservation of Plant Species with Extremely Small Populations in Southwest China/ ; 2019QZKK0502//Second Tibetan Plateau Scientific Expedition and Research Program/ ; U1302262//NSFC (National Natural Science Foundation of China) Yunnan Joint Fund/ ; 2019HC015//Yunnan Science and Technology Innovation Team Program for PSESP Conservation and Utilization/ ; }, mesh = {*Acer/genetics ; Animals ; Anthropogenic Effects ; China ; Endangered Species ; Genetic Variation ; Genomics ; Humans ; Metagenomics ; Population Density ; }, abstract = {Recent advancements in whole genome sequencing techniques capable of covering nearly all the nucleotide variations of a genome would make it possible to set up a conservation framework for threatened plants at the genomic level. Here we applied a whole genome resequencing approach to obtain genome-wide data from 105 individuals sampled from the 10 currently known extant populations of Acer yangbiense, an endangered species with fragmented habitats and restricted distribution in Yunnan, China. To inform meaningful conservation action, we investigated what factors might have contributed to the formation of its extremely small population sizes and what threats it currently suffers at a genomic level. Our results revealed that A. yangbiense has low genetic diversity and comprises different numbers of genetic groups based on neutral (seven) and selected loci (13), with frequent gene flow between populations. Repeated bottleneck events, particularly the most recent one occurring within ~10,000 years before present, which decreased its effective population size (Ne) < 200, and severe habitat fragmentation resulting from anthropogenic activities as well as a biased gender ratio of mature individuals in its natural habitat, might have together contributed to the currently fragmented and endangered status of A. yangbiense. The species has suffered from inbreeding and deleterious mutation load, both of which varied among populations but had similar patterns; that is, populations with higher FROH (frequency of runs of homozygosity) always carried a larger number of deleterious mutations in the homozygous state than in populations with lower FROH. In addition, based on our genetic differentiation results, and the distribution patterns of homozygous deleterious mutations in individuals, we recommend certain conservation actions regarding the genetic rescue of A. yangbiense. Overall, our study provides meaningful insights into the conservation genetics and a framework for the further conservation for the endangered A. yangbiense.}, }
@article {pmid34824318, year = {2021}, author = {Chen, YF and Hsieh, AH and Wang, LC and Huang, YJ and Yun-Chen Tsai,  and Tseng, WY and Kuo, YL and Luo, SF and Yu, KH and Kuo, CF}, title = {Fecal microbiota changes in NZB/W F1 mice after induction of lupus disease.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22953}, pmid = {34824318}, issn = {2045-2322}, support = {108-2314-B-182A-064//Ministry of Science and Technology, Taiwan/ ; CMRPG3G0851//Chang Gung Memorial Hospital, Linkou/ ; CMRPG3F1703//Chang Gung Memorial Hospital, Linkou/ ; CMRPG3H1393//Chang Gung Memorial Hospital, Linkou/ ; }, mesh = {Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial ; Disease Models, Animal ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Lupus Erythematosus, Systemic/*microbiology ; Metagenomics ; Mice ; Mice, Inbred NZB ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The association between the gut microbiota and the development of lupus is unclear. We investigated alterations in the gut microbiota after induction of lupus in a murine model using viral peptide of human cytomegalovirus (HCMV). Three treatment arms for the animals were prepared: intraperitoneal injection of HCMVpp65 peptide, adjuvant alone, and PBS injection. Feces were collected before and after lupus induction biweekly for 16S rRNA sequencing. HCMVpp65 peptide immunization induced lupus-like effects, with higher levels of anti-dsDNA antibodies, creatinine, proteinuria, and glomerular damage, compared with mice treated with nothing or adjuvant only. The Simpson diversity value was higher in mice injected with HCMVpp65 peptide, but there was no difference in ACE or Chao1 among the three groups. Statistical analysis of metagenomic profiles showed a higher abundance of various families (Saccharimonadaceae, Marinifiaceae, and Desulfovibrionaceae) and genera (Candidatus Saccharimonas, Roseburia, Odoribacter, and Desulfovibrio) in HCMVpp65 peptide-treated mice. Significant correlations between increased abundances of related genera (Candidatus Saccharimonas, Roseburia, Odoribacter, and Desulfovibrio) and HCMVpp65 peptide immunization-induced lupus-like effects were observed. This study provides insight into the changes in the gut microbiota after lupus onset in a murine model.}, }
@article {pmid34824209, year = {2021}, author = {Kandathil, AJ and Cox, AL and Page, K and Mohr, D and Razaghi, R and Ghanem, KG and Tuddenham, SA and Hsieh, YH and Evans, JL and Coller, KE and Timp, W and Celentano, DD and Ray, SC and Thomas, DL}, title = {Plasma virome and the risk of blood-borne infection in persons with substance use disorder.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6909}, pmid = {34824209}, issn = {2041-1723}, support = {U19 AI159822/AI/NIAID NIH HHS/United States ; R01 DA016017/DA/NIDA NIH HHS/United States ; R21 DA053145/DA/NIDA NIH HHS/United States ; }, mesh = {Adult ; Amino Acid Sequence ; Anelloviridae ; *Blood-Borne Infections ; Blood-Borne Pathogens ; Female ; Hepatitis C/epidemiology ; Humans ; Knowledge ; Male ; Metagenomics ; Phylogeny ; *Plasma ; Public Health ; *Substance-Related Disorders ; *Virome ; Young Adult ; }, abstract = {There is an urgent need for innovative methods to reduce transmission of bloodborne pathogens like HIV and HCV among people who inject drugs (PWID). We investigate if PWID who acquire non-pathogenic bloodborne viruses like anelloviruses and pegiviruses might be at greater risk of acquiring a bloodborne pathogen. PWID who later acquire HCV accumulate more non-pathogenic viruses in plasma than matched controls who do not acquire HCV infection. Additionally, phylogenetic analysis of those non-pathogenic virus sequences reveals drug use networks. Here we find first in Baltimore and confirm in San Francisco that the accumulation of non-pathogenic viruses in PWID is a harbinger for subsequent acquisition of pathogenic viruses, knowledge that may guide the prioritization of the public health resources to combat HIV and HCV.}, }
@article {pmid34824201, year = {2021}, author = {Li, L and Solvi, C and Zhang, F and Qi, Z and Chittka, L and Zhao, W}, title = {Gut microbiome drives individual memory variation in bumblebees.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6588}, pmid = {34824201}, issn = {2041-1723}, mesh = {Animals ; Bacteria/genetics/metabolism ; Bees/*microbiology/*physiology ; Gastrointestinal Microbiome/genetics/*physiology ; Glycerophospholipids/metabolism ; Individuality ; Lactobacillus/genetics/metabolism ; Memory, Long-Term/*physiology ; Metabolomics ; Metagenome ; *Metagenomics ; }, abstract = {The potential of the gut microbiome as a driver of individual cognitive differences in natural populations of animals remains unexplored. Here, using metagenomic sequencing of individual bumblebee hindguts, we find a positive correlation between the abundance of Lactobacillus Firm-5 cluster and memory retention on a visual discrimination task. Supplementation with the Firm-5 species Lactobacillus apis, but not other non-Firm-5 bacterial species, enhances bees' memory. Untargeted metabolomics after L. apis supplementation show increased LPA (14:0) glycerophospholipid in the haemolymph. Oral administration of the LPA increases long-term memory significantly. Based on our findings and metagenomic/metabolomic analyses, we propose a molecular pathway for this gut-brain interaction. Our results provide insights into proximate and ultimate causes of cognitive differences in natural bumblebee populations.}, }
@article {pmid34821235, year = {2021}, author = {Robinson, SL and Piel, J and Sunagawa, S}, title = {A roadmap for metagenomic enzyme discovery.}, journal = {Natural product reports}, volume = {38}, number = {11}, pages = {1994-2023}, pmid = {34821235}, issn = {1460-4752}, mesh = {Amino Acid Sequence ; Biological Products/metabolism ; Catalytic Domain ; Cytochrome P-450 Enzyme System/chemistry/physiology ; Enzymes/chemistry/*isolation &amp; purification ; Machine Learning ; Metagenomics/*methods ; Microbiota ; Phylogeny ; }, abstract = {Covering: up to 2021Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a 'needle in a haystack' without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, genomic context, 3D structure-based approaches, and machine learning techniques. We also discuss various experimental strategies to test computational predictions including heterologous expression and screening. Finally, we provide an outlook for future directions in the field with an emphasis on meta-omics, single-cell genomics, cell-free expression systems, and sequence-independent methods.}, }
@article {pmid34819672, year = {2021}, author = {Balaich, J and Estrella, M and Wu, G and Jeffrey, PD and Biswas, A and Zhao, L and Korennykh, A and Donia, MS}, title = {The human microbiome encodes resistance to the antidiabetic drug acarbose.}, journal = {Nature}, volume = {600}, number = {7887}, pages = {110-115}, pmid = {34819672}, issn = {1476-4687}, support = {R01 GM110161/GM/NIGMS NIH HHS/United States ; T32 GM007388/GM/NIGMS NIH HHS/United States ; 1013579/WT_/Wellcome Trust/United Kingdom ; DP2 AI124441/AI/NIAID NIH HHS/United States ; P41 GM111244/GM/NIGMS NIH HHS/United States ; }, mesh = {Acarbose/metabolism/*pharmacology ; Amylases/metabolism ; Animals ; Drug Resistance, Bacterial/*drug effects ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hypoglycemic Agents/metabolism/*pharmacology ; *Inactivation, Metabolic ; Metagenome/drug effects/*genetics ; Models, Molecular ; Mouth/drug effects/*microbiology ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/*genetics/metabolism ; }, abstract = {The human microbiome encodes a large repertoire of biochemical enzymes and pathways, most of which remain uncharacterized. Here, using a metagenomics-based search strategy, we discovered that bacterial members of the human gut and oral microbiome encode enzymes that selectively phosphorylate a clinically used antidiabetic drug, acarbose1,2, resulting in its inactivation. Acarbose is an inhibitor of both human and bacterial α-glucosidases3, limiting the ability of the target organism to metabolize complex carbohydrates. Using biochemical assays, X-ray crystallography and metagenomic analyses, we show that microbiome-derived acarbose kinases are specific for acarbose, provide their harbouring organism with a protective advantage against the activity of acarbose, and are widespread in the microbiomes of western and non-western human populations. These results provide an example of widespread microbiome resistance to a non-antibiotic drug, and suggest that acarbose resistance has disseminated in the human microbiome as a defensive strategy against a potential endogenous producer of a closely related molecule.}, }
@article {pmid34819600, year = {2021}, author = {Tozzi, AE and Del Chierico, F and Pandolfi, E and Reddel, S and Gesualdo, F and Gardini, S and Guarrasi, V and Russo, L and Croci, I and Campagna, I and Linardos, G and Concato, C and Villani, A and Putignani, L}, title = {Nasopharyngeal microbiota in hospitalized children with Bordetella pertussis and Rhinovirus infection.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22858}, pmid = {34819600}, issn = {2045-2322}, mesh = {Bordetella Infections/diagnosis/*microbiology ; Bordetella pertussis/*isolation &amp; purification ; *Coinfection ; Dysbiosis ; Female ; *Hospitalization ; Host-Pathogen Interactions ; Humans ; Infant ; Male ; Metagenome ; Metagenomics ; Microbiota ; Nasopharynx/*microbiology/*virology ; Picornaviridae Infections/diagnosis/*virology ; Rhinovirus/*isolation &amp; purification ; Ribotyping ; }, abstract = {Despite great advances in describing Bordetella pertussis infection, the role of the host microbiota in pertussis pathogenesis remains unexplored. Indeed, the microbiota plays important role in defending against bacterial and viral respiratory infections. We investigated the nasopharyngeal microbiota in infants infected by B. pertussis (Bp), Rhinovirus (Rv) and simultaneously by both infectious agents (Bp + Rv). We demonstrated a specific nasopharyngeal microbiome profiles for Bp group, compared to Rv and Bp + Rv groups, and a reduction of microbial richness during coinfection compared to the single infections. The comparison amongst the three groups showed the increase of Alcaligenaceae and Achromobacter in Bp and Moraxellaceae and Moraxella in Rv group. Furthermore, correlation analysis between patients' features and nasopharyngeal microbiota profile highlighted a link between delivery and feeding modality, antibiotic administration and B. pertussis infection. A model classification demonstrated a microbiota fingerprinting specific of Bp and Rv infections. In conclusion, external factors since the first moments of life contribute to the alteration of nasopharyngeal microbiota, indeed increasing the susceptibility of the host to the pathogens' infections. When the infection is triggered, the presence of infectious agents modifies the microbiota favoring the overgrowth of commensal bacteria that turn in pathobionts, hence contributing to the disease severity.}, }
@article {pmid34819495, year = {2021}, author = {Hafner, L and Pichon, M and Burucoa, C and Nusser, SHA and Moura, A and Garcia-Garcera, M and Lecuit, M}, title = {Listeria monocytogenes faecal carriage is common and depends on the gut microbiota.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6826}, pmid = {34819495}, issn = {2041-1723}, mesh = {Animals ; Carrier State/diagnosis/*epidemiology/microbiology ; DNA, Bacterial/isolation &amp; purification ; Datasets as Topic ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Listeria monocytogenes/genetics/*isolation &amp; purification/pathogenicity ; Male ; Metagenomics/statistics &amp; numerical data ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Virulence ; }, abstract = {Listeria genus comprises two pathogenic species, L. monocytogenes (Lm) and L. ivanovii, and non-pathogenic species. All can thrive as saprophytes, whereas only pathogenic species cause systemic infections. Identifying Listeria species' respective biotopes is critical to understand the ecological contribution of Listeria virulence. In order to investigate the prevalence and abundance of Listeria species in various sources, we retrieved and analyzed 16S rRNA datasets from MG-RAST metagenomic database. 26% of datasets contain Listeria sensu stricto sequences, and Lm is the most prevalent species, most abundant in soil and host-associated environments, including 5% of human stools. Lm is also detected in 10% of human stool samples from an independent cohort of 900 healthy asymptomatic donors. A specific microbiota signature is associated with Lm faecal carriage, both in humans and experimentally inoculated mice, in which it precedes Lm faecal carriage. These results indicate that Lm faecal carriage is common and depends on the gut microbiota, and suggest that Lm faecal carriage is a crucial yet overlooked consequence of its virulence.}, }
@article {pmid34818799, year = {2022}, author = {Hernández-Álvarez, C and García-Oliva, F and Cruz-Ortega, R and Romero, MF and Barajas, HR and Piñero, D and Alcaraz, LD}, title = {Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150136}, doi = {10.1016/j.scitotenv.2021.150136}, pmid = {34818799}, issn = {1879-1026}, mesh = {*Cucurbita ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S ; *Rhizobiaceae ; Rhizosphere ; Soil Microbiology ; Streptomyces ; }, abstract = {Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.}, }
@article {pmid34818790, year = {2022}, author = {Soto, DF and Franzetti, A and Gómez, I and Huovinen, P}, title = {Functional filtering and random processes affect the assembly of microbial communities of snow algae blooms at Maritime Antarctic.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150305}, doi = {10.1016/j.scitotenv.2021.150305}, pmid = {34818790}, issn = {1879-1026}, mesh = {Antarctic Regions ; Bacteria/genetics ; Eutrophication ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The increasing temperatures at the West Antarctic Peninsula (Maritime Antarctic) could lead to a higher occurrence of snow algal blooms which are ubiquitous events that change the snow coloration, reducing albedo and in turn exacerbating melting. However, there is a limited understanding of snow algae blooms biodiversity, composition, and their functional profiles, especially in one of the world's areas most affected by climate change. In this study we used 16S rRNA and 18S rRNA metabarcoding, and shotgun metagenomics to assess the diversity, composition, and functional potential of the snow algae blooms bacterial and eukaryotic communities at three different sites of Maritime Antarctic, between different colors of the algae blooms and between seasonal and semi-permanent snowfields. We tested the hypothesis that the functional potential of snow algae blooms is conserved despite a changing taxonomic composition. Furthermore, we determined taxonomic co-occurrence patterns of bacteria and eukaryotes and assessed the potential for the exchange of metabolites among bacterial taxa. Here, we tested the prediction that there are co-occurring taxa within snow algae whose biotic interactions are marked by the exchange of metabolites. Our results show that the composition of snow algae blooms vary significantly among sites. For instance, a higher abundance of fungi and protists were detected in Fildes Peninsula compared with Doumer Island and O'Higgins. Likewise, the composition varied between snow colors and snow types. However, the functional potential varied only among sampling sites with a higher abundance of genes involved in tolerance to environmental stress at O'Higgins. Co-occurrence patterns of dominant bacterial genera such as Pedobacter, Polaromonas, Flavobacterium and Hymenobacter were recorded, contrasting the absence of co-occurring patterns displayed by Chlamydomonadales algae with other eukaryotes. Finally, genome-scale metabolic models revealed that bacteria within snow algae blooms likely compete for resources instead of forming cooperative communities.}, }
@article {pmid34818103, year = {2022}, author = {Huang, T and Lu, ZM and Peng, MY and Chai, LJ and Zhang, XJ and Shi, JS and Li, Q and Xu, ZH}, title = {Constructing a Defined Starter for Multispecies Vinegar Fermentation via Evaluation of the Vitality and Dominance of Functional Microbes in an Autochthonous Starter.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {3}, pages = {e0217521}, pmid = {34818103}, issn = {1098-5336}, mesh = {*Acetic Acid/metabolism ; Fermentation ; Food Microbiology ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Mature vinegar culture has usually been used as a type of autochthonous starter to rapidly initiate the next batch of acetic acid fermentation (AAF) and maintain the batch-to-batch uniformity of AAF in the production of traditional cereal vinegar. However, the vitality and dominance of functional microbes in autochthonous starters remain unclear, which hinders further improvement of fermentation yield and production. Here, based on metagenomic (MG), metatranscriptomic (MT), and 16S rRNA gene sequencings, 11 bacterial operational taxonomic units (OTUs) with significant metabolic activity (MT/MG ratio >1) and dominance (relative abundance >1%) were targeted in the autochthonous vinegar starter, all of which were assigned to 4 species (Acetobacter pasteurianus, Lactobacillus acetotolerans, L. helveticus, Acetilactobacillus jinshanensis). Then, we evaluated the successions and interactions of these 11 bacterial OTUs at different AAF stages. Last, a defined starter was constructed with 4 core species isolated from the autochthonous starter (A. pasteurianus, L. acetotolerans, L. helveticus, Ac. jinshanensis). The defined starter culture could rapidly initiate the AAF in a sterile or unsterilized environment, and similar dynamics of metabolites (ethanol, titratable acidity, acetic acid, lactic acid, and volatile compounds) and environmental indexes (temperature, pH) of fermentation were observed as compared with that of autochthonous starter (P > 0.05). This work provides a method to construct a defined microbiota from a complex system while preserving its metabolic function. IMPORTANCE Complex microorganisms are beneficial to the flavor formation in natural food fermentation, but they also pose challenges to the mass production of standardized products. It is attractive to construct a defined starter to rapidly initiate fermentation process and significantly improve fermentation yield. This study provides a comprehensive understanding of vital and dominant species in the autochthonous vinegar starter via multi-omics, and designs a defined microbial community for the efficient fermentation of cereal vinegar.}, }
@article {pmid34817234, year = {2021}, author = {Garber, AI and Zehnpfennig, JR and Sheik, CS and Henson, MW and Ramírez, GA and Mahon, AR and Halanych, KM and Learman, DR}, title = {Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0077021}, pmid = {34817234}, issn = {2379-5042}, mesh = {Antarctic Regions ; Carbon/metabolism ; Carbon Cycle ; Chemoautotrophic Growth/*physiology ; Climate Change ; Geologic Sediments/*microbiology ; Metagenome/physiology ; *Metagenomics ; Microbiota/*physiology ; Nitrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; }, abstract = {The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.}, }
@article {pmid34814938, year = {2021}, author = {Neves, ALA and Yu, J and Suzuki, Y and Baez-Magana, M and Arutyunova, E and O'Hara, E and McAllister, T and Ominski, KH and Lemieux, MJ and Guan, LL}, title = {Accelerated discovery of novel glycoside hydrolases using targeted functional profiling and selective pressure on the rumen microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {229}, pmid = {34814938}, issn = {2049-2618}, mesh = {Animals ; Cattle ; Glycoside Hydrolases/genetics/metabolism ; Metagenome ; Metagenomics ; *Microbiota ; *Rumen/microbiology ; }, abstract = {BACKGROUND: Carbohydrate-active enzymes (CAZymes) form the most widespread and structurally diverse set of enzymes involved in the breakdown, biosynthesis, or modification of lignocellulose that can be found in living organisms. However, the structural diversity of CAZymes has rendered the targeted discovery of novel enzymes extremely challenging, as these proteins catalyze many different chemical reactions and are sourced by a vast array of microbes. Consequently, many uncharacterized members of CAZyme families of interest have been overlooked by current methodologies (e.g., metagenomic screening) used to discover lignocellulolytic enzymes.<br><br>RESULTS: In the present study, we combined phenotype-based selective pressure on the rumen microbiota with targeted functional profiling to guide the discovery of unknown CAZymes. In this study, we found 61 families of glycoside hydrolases (GH) (out of 182 CAZymes) from protein sequences deposited in the CAZy database-currently associated with more than 20,324 microbial genomes. Phenotype-based selective pressure on the rumen microbiome showed that lignocellulolytic bacteria (e.g., Fibrobacter succinogenes, Butyrivibrio proteoclasticus) and three GH families (e.g., GH11, GH13, GH45) exhibited an increased relative abundance in the rumen of feed efficient cattle when compared to their inefficient counterparts. These results paved the way for the application of targeted functional profiling to screen members of the GH11 and GH45 families against a de novo protein reference database comprised of 1184 uncharacterized enzymes, which led to the identification of 18 putative xylanases (GH11) and three putative endoglucanases (GH45). The biochemical proof of the xylanolytic activity of the newly discovered enzyme validated the computational simulations and demonstrated the stability of the most abundant xylanase.<br><br>CONCLUSIONS: These findings contribute to the discovery of novel enzymes for the breakdown, biosynthesis, or modification of lignocellulose and demonstrate that the rumen microbiome is a source of promising enzyme candidates for the biotechnology industry. The combined approaches conceptualized in this study can be adapted to any microbial environment, provided that the targeted microbiome is easy to manipulate and facilitates enrichment for the microbes of interest. Video Abstract.}, }
@article {pmid34812271, year = {2021}, author = {Wang, Y and Sun, M and Duan, Y}, title = {Metagenomic Sequencing Analysis for Acne Using Machine Learning Methods Adapted to Single or Multiple Data.}, journal = {Computational and mathematical methods in medicine}, volume = {2021}, number = {}, pages = {8008731}, pmid = {34812271}, issn = {1748-6718}, mesh = {Acne Vulgaris/*genetics/metabolism/*microbiology ; Canonical Correlation Analysis ; Case-Control Studies ; Computational Biology ; Face/microbiology ; Humans ; Lipids/analysis/genetics ; *Machine Learning ; *Metagenome ; Metagenomics/statistics &amp; numerical data ; Microbiota/genetics ; Principal Component Analysis ; Skin/chemistry/microbiology ; }, abstract = {The human health status can be assessed by the means of research and analysis of the human microbiome. Acne is a common skin disease whose morbidity increases year by year. The lipids which influence acne to a large extent are studied by metagenomic methods in recent years. In this paper, machine learning methods are used to analyze metagenomic sequencing data of acne, i.e., all kinds of lipids in the face skin. Firstly, lipids data of the diseased skin (DS) samples and the healthy skin (HS) samples of acne patients and the normal control (NC) samples of healthy person are, respectively, analyzed by using principal component analysis (PCA) and kernel principal component analysis (KPCA). Then, the lipids which have main influence on each kind of sample are obtained. In addition, a multiset canonical correlation analysis (MCCA) is utilized to get lipids which can differentiate the face skins of the above three samples. The experimental results show the machine learning methods can effectively analyze metagenomic sequencing data of acne. According to the results, lipids which only influence one of the three samples or the lipids which simultaneously have different degree of influence on these three samples can be used as indicators to judge skin statuses.}, }
@article {pmid34807727, year = {2022}, author = {Wang, Y and Wu, M and Wang, Y and Wang, X and Yu, M and Liu, G and Tang, H}, title = {Diversity and function of microbial communities in the sand sheath of Agropyron cristatum by metagenomic analysis.}, journal = {Canadian journal of microbiology}, volume = {68}, number = {3}, pages = {177-189}, doi = {10.1139/cjm-2021-0129}, pmid = {34807727}, issn = {1480-3275}, mesh = {*Agropyron/genetics ; Metagenomics ; *Microbiota/genetics ; Sand ; Soil ; Soil Microbiology ; }, abstract = {The roots of most gramineous plants are surrounded by a variety of microorganisms; however, few studies have focused on the rhizosheath of psammophytes. Therefore, in this study, we used Illumina HiSeq high-throughput sequencing technology to analyse the composition and functional diversity of microbial communities in the rhizosheath of sand-grown Agropyron cristatum (L.) Gaertn. We found that the number of species and functions of microbial communities gradually decreased from the rhizosheath to the bulk soil. Thus, the microbial composition of the rhizosheath was richer and more diverse, and the abundance of bacteria, including Sphingosinicella, Rhizorhabdus, Friedmanniella, Geodermatophilus, Blastococcus, and Oscillatoria, was higher, and the abundance of fungi, such as Mycothermus, was higher. The abundance of CO2 fixation-related genes (acsA, Pcc, and cbbL) in the carbon cycle; NO3-, NO2-, NH2OH, and N2 transformation genes (nrtP, nirS, hao, and nifK) in the nitrogen cycle; soxB/A/C, Sat, and dsrB genes in the sulphur cycle; and 1-phosphate mannitol dehydrogenase (MtlD) gene and polyketide synthase gene (pks) were higher in the rhizosheath than in the bulk soil, as well as genes related to phosphorus uptake in the phosphorus cycle. Our findings showed that the rhizosheath may host the predominant microbial species related to the formation of a rhizosheath.}, }
@article {pmid34795375, year = {2021}, author = {Van Goethem, MW and Osborn, AR and Bowen, BP and Andeer, PF and Swenson, TL and Clum, A and Riley, R and He, G and Koriabine, M and Sandor, L and Yan, M and Daum, CG and Yoshinaga, Y and Makhalanyane, TP and Garcia-Pichel, F and Visel, A and Pennacchio, LA and O'Malley, RC and Northen, TR}, title = {Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {1302}, pmid = {34795375}, issn = {2399-3642}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; }, mesh = {Bacteria/genetics/*metabolism ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; *Secondary Metabolism ; *Soil Microbiology ; Utah ; }, abstract = {Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.}, }
@article {pmid34795298, year = {2021}, author = {Armstrong, AJS and Parmar, V and Blaser, MJ}, title = {Assessing saliva microbiome collection and processing methods.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {81}, pmid = {34795298}, issn = {2055-5008}, support = {R01 AI158911/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics ; COVID-19/genetics ; DNA/genetics ; DNA, Bacterial/genetics ; Female ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2/pathogenicity ; Saliva/*microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {The oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.}, }
@article {pmid34795236, year = {2021}, author = {Darnaud, M and De Vadder, F and Bogeat, P and Boucinha, L and Bulteau, AL and Bunescu, A and Couturier, C and Delgado, A and Dugua, H and Elie, C and Mathieu, A and Novotná, T and Ouattara, DA and Planel, S and Saliou, A and Šrůtková, D and Yansouni, J and Stecher, B and Schwarzer, M and Leulier, F and Tamellini, A}, title = {A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6686}, pmid = {34795236}, issn = {2041-1723}, support = {U2C DK119886/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Body Weight/genetics/physiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; *Germ-Free Life ; Male ; Metagenomics/methods ; Mice, Inbred C57BL ; Phenotype ; Species Specificity ; *Specific Pathogen-Free Organisms ; Whole Genome Sequencing/*methods ; }, abstract = {Mus musculus is the classic mammalian model for biomedical research. Despite global efforts to standardize breeding and experimental procedures, the undefined composition and interindividual diversity of the microbiota of laboratory mice remains a limitation. In an attempt to standardize the gut microbiome in preclinical mouse studies, here we report the development of a simplified mouse microbiota composed of 15 strains from 7 of the 20 most prevalent bacterial families representative of the fecal microbiota of C57BL/6J Specific (and Opportunistic) Pathogen-Free (SPF/SOPF) animals and the derivation of a standardized gnotobiotic mouse model called GM15. GM15 recapitulates extensively the functionalities found in the C57BL/6J SOPF microbiota metagenome, and GM15 animals are phenotypically similar to SOPF or SPF animals in two different facilities. They are also less sensitive to the deleterious effects of post-weaning malnutrition. In this work, we show that the GM15 model provides increased reproducibility and robustness of preclinical studies by limiting the confounding effect of fluctuation in microbiota composition, and offers opportunities for research focused on how the microbiota shapes host physiology in health and disease.}, }
@article {pmid34793277, year = {2021}, author = {Marfil-Sánchez, A and Zhang, L and Alonso-Pernas, P and Mirhakkak, M and Mueller, M and Seelbinder, B and Ni, Y and Santhanam, R and Busch, A and Beemelmanns, C and Ermolaeva, M and Bauer, M and Panagiotou, G}, title = {An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1993598}, pmid = {34793277}, issn = {1949-0984}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Bacteria/classification/drug effects/metabolism/pathogenicity ; Bile Acids and Salts/metabolism ; Candida/classification/drug effects/metabolism/pathogenicity ; *Critical Illness ; Drug Resistance, Fungal/drug effects ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infections/microbiology ; Intensive Care Units ; Metabolome/*drug effects ; Moths ; }, abstract = {Antibiotics are commonly used in the Intensive Care Unit (ICU); however, several studies showed that the impact of antibiotics to prevent infection, multi-organ failure, and death in the ICU is less clear than their benefit on course of infection in the absence of organ dysfunction. We characterized here the compositional and metabolic changes of the gut microbiome induced by critical illness and antibiotics in a cohort of 75 individuals in conjunction with 2,180 gut microbiome samples representing 16 different diseases. We revealed an "infection-vulnerable" gut microbiome environment present only in critically ill treated with antibiotics (ICU+). Feeding of Caenorhabditis elegans with Bifidobacterium animalis and Lactobacillus crispatus, species that expanded in ICU+ patients, revealed a significant negative impact of these microbes on host viability and developmental homeostasis. These results suggest that antibiotic administration can dramatically impact essential functional activities in the gut related to immune responses more than critical illness itself, which might explain in part untoward effects of antibiotics in the critically ill.}, }
@article {pmid34793112, year = {2021}, author = {Mitchell, AB and Li, CX and Oliver, BGG and Holmes, EC and Glanville, AR}, title = {High-resolution Metatranscriptomic Characterization of the Pulmonary RNA Virome After Lung Transplantation.}, journal = {Transplantation}, volume = {105}, number = {12}, pages = {2546-2553}, doi = {10.1097/TP.0000000000003713}, pmid = {34793112}, issn = {1534-6080}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Longitudinal Studies ; Lung ; *Lung Transplantation/adverse effects ; *RNA ; Virome/genetics ; }, abstract = {BACKGROUND: Lung transplantation provides a unique opportunity to investigate the constituents and temporal dynamics of the human pulmonary microbiome after lung transplantation. For methodological reasons, prior studies using metagenomics have detected DNA viruses but not demonstrated the presence of RNA viruses, including those that are common community acquired. In this proof-of-concept study, we aimed to further characterize the pulmonary microbiome after lung transplantation by using metagenomic next-generation sequencing (mNGS), with a particular focus on the RNA virome.<br><br>METHODS: We performed a single-center longitudinal study of lower respiratory tract RNA viruses and bacteria using bronchoalveolar lavage at postoperative day 1 and week 6 analyzed with total RNA sequencing (metatranscriptomics). Five primary and 5 repeat transplant recipients were recruited.<br><br>RESULTS: mNGS identified 5 RNA viruses (nil in the normal saline control), including 4 species of human rhinovirus not previously reported in Australia: A7 (HRV-A7), C22 (HRV-C22), B52 (HRV-B52), and B72 (HRV-B72). Overall, 12/20 specimens were virus positive in 7/10 cases. Human parainfluenza virus 3 was the most frequent virus in 7/20 specimens in 5/10 cases. In this small study, we did not detect a significant difference in abundance and diversity of RNA viruses and bacteria at postoperative day 1 and 6 wk, nor differences between retransplant recipients and primary lung transplant recipients.<br><br>CONCLUSIONS: Our study demonstrates how mNGS can also identify RNA viruses within the human pulmonary virome, including novel RNA viruses, and paves the way for a greater understanding of the complex relationships among the constituents of the pulmonary infectome.}, }
@article {pmid34792102, year = {2021}, author = {He, Q and Huang, J and Zheng, T and Lin, D and Zhang, H and Li, J and Sun, Z}, title = {Treatment with mixed probiotics induced, enhanced and diversified modulation of the gut microbiome of healthy rats.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {12}, pages = {}, doi = {10.1093/femsec/fiab151}, pmid = {34792102}, issn = {1574-6941}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Microbiota ; *Probiotics ; Rats ; Rats, Wistar ; }, abstract = {Previous studies demonstrated that multi-strain probitics could more strongly regulate intestinal cytokines and the mucosal barrier than the individual ingredient strains. Nevertheless, the potentially different gut microbiome modulation effects between multi-strain and single-strain probiotics treatments remain unexplored. Here, we administered three different Lactiplantibacillus plantarum strains or their mixture to healthy Wistar rats and compared the shift of gut microbiome among the treatment groups. A 4-week intervention with mixed probiotics induced more drastic and diversified gut microbiome modulation than single-strain probiotics administration (alpha diversity increased 8% and beta diversity increased 18.7%). The three single-strain probiotics treatments all converged the gut microbiota, decreasing between-individual beta diversity by 12.7% on average after the treatment, while multi-strain probiotics treatment diversified the gut microbiome and increased between-individual beta diversity by 37.2% on average. Covariation analysis of the gut microbes suggests that multi-strain probiotics could exert synergistic, modified and enhanced modulation effects on the gut microbiome based on strain-specific modulation effects of probiotics. The more heterogeneous responses to the multi-strain probiotics treatment suggest that future precision microbiome modulation should consider the potential interactions of the probiotic strains, and personalized response to probiotic formulas due to heterogenous gut microbial compositions.}, }
@article {pmid34788838, year = {2022}, author = {Dai, D and Zhu, J and Sun, C and Li, M and Liu, J and Wu, S and Ning, K and He, LJ and Zhao, XM and Chen, WH}, title = {GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison.}, journal = {Nucleic acids research}, volume = {50}, number = {D1}, pages = {D777-D784}, pmid = {34788838}, issn = {1362-4962}, mesh = {Biomarkers/blood ; *Databases, Genetic ; Datasets as Topic ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Intestinal Neoplasms/blood/genetics/*microbiology/pathology ; *Metagenome ; *Microbiota ; Molecular Sequence Annotation ; Phenotype ; RNA, Ribosomal, 16S ; Software ; }, abstract = {GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purposes are to increase the reusability and accessibility of human gut metagenomic data, and enable cross-project and phenotype comparisons. To achieve these goals, we performed manual curation on the meta-data and organized the datasets in a phenotype-centric manner. GMrepo v2 contains 353 projects and 71,642 runs/samples, which are significantly increased from the previous version. Among these runs/samples, 45,111 and 26,531 were obtained by 16S rRNA amplicon and whole-genome metagenomics sequencing, respectively. We also increased the number of phenotypes from 92 to 133. In addition, we introduced disease-marker identification and cross-project/phenotype comparison. We first identified disease markers between two phenotypes (e.g. health versus diseases) on a per-project basis for selected projects. We then compared the identified markers for each phenotype pair across datasets to facilitate the identification of consistent microbial markers across datasets. Finally, we provided a marker-centric view to allow users to check if a marker has different trends in different diseases. So far, GMrepo includes 592 marker taxa (350 species and 242 genera) for 47 phenotype pairs, identified from 83 selected projects. GMrepo v2 is freely available at: https://gmrepo.humangut.info.}, }
@article {pmid34787447, year = {2021}, author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H}, title = {Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0078521}, pmid = {34787447}, issn = {2379-5042}, mesh = {Ecosystem ; Metagenome ; *Metagenomics ; Microbiota/*genetics/physiology ; Nitrogen/metabolism ; *Nitrogen Fixation ; Oxidoreductases/*genetics ; Phylogeny ; }, abstract = {Nitrogen fixation, a distinct process incorporating the inactive atmospheric nitrogen into the active biological processes, has been a major topic in biological and geochemical studies. Currently, insights into diversity and distribution of nitrogen-fixing microbes are dependent upon homology-based analyses of nitrogenase genes, especially the nifH gene, which are broadly conserved in nitrogen-fixing microbes. Here, we report the pitfall of using nifH as a marker of microbial nitrogen fixation. We exhaustively analyzed genomes in RefSeq (231,908 genomes) and KEGG (6,509 genomes) and cooccurrence and gene order patterns of nitrogenase genes (including nifH) therein. Up to 20% of nifH-harboring genomes lacked nifD and nifK, which encode essential subunits of nitrogenase, within 10 coding sequences upstream or downstream of nifH or on the same genome. According to a phenotypic database of prokaryotes, no species and strains harboring only nifH possess nitrogen-fixing activities, which shows that these nifH genes are "pseudo"-nifH genes. Pseudo-nifH sequences mainly belong to anaerobic microbes, including members of the class Clostridia and methanogens. We also detected many pseudo-nifH reads from metagenomic sequences of anaerobic environments such as animal guts, wastewater, paddy soils, and sediments. In some samples, pseudo-nifH overwhelmed the number of "true" nifH reads by 50% or 10 times. Because of the high sequence similarity between pseudo- and true-nifH, pronounced amounts of nifH-like reads were not confidently classified. Overall, our results encourage reconsideration of the conventional use of nifH for detecting nitrogen-fixing microbes, while suggesting that nifD or nifK would be a more reliable marker. IMPORTANCE Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases. Here, we report that public databases include a significant amount of incorrectly annotated nifH sequences (pseudo-nifH). We exhaustively investigated the genomic structures of nifH-harboring genomes and found hundreds of pseudo-nifH sequences in RefSeq and KEGG. Over half of these pseudo-nifH sequences belonged to members of the class Clostridia, which is supposed to be a prominent nitrogen-fixing clade. We also found that the abundance of nitrogen fixers in metagenomes could be overestimated by 1.5 to >10 times due to pseudo-nifH recorded in public databases. Our results encourage reconsideration of the prevalent use of nifH as a marker of nitrogen-fixing microbes.}, }
@article {pmid34787442, year = {2021}, author = {Guajardo-Leiva, S and Santos, F and Salgado, O and Regeard, C and Quillet, L and Díez, B}, title = {Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0069421}, pmid = {34787442}, issn = {2165-0497}, mesh = {Bacteria/classification/genetics/radiation effects/*virology ; Biodiversity ; Genetic Variation ; Hot Springs/*virology ; *Lysogeny ; Metagenome ; Phototrophic Processes ; Phylogeny ; Virus Physiological Phenomena ; Viruses/classification/*genetics/isolation &amp; purification ; }, abstract = {Viruses exert diverse ecosystem impacts by controlling their host community through lytic predator-prey dynamics. However, the mechanisms by which lysogenic viruses influence their host-microbial community are less clear. In hot springs, lysogeny is considered an active lifestyle, yet it has not been systematically studied in all habitats, with phototrophic microbial mats (PMMs) being particularly not studied. We carried out viral metagenomics following in situ mitomycin C induction experiments in PMMs from Porcelana hot spring (Northern Patagonia, Chile). The compositional changes of viral communities at two different sites were analyzed at the genomic and gene levels. Furthermore, the presence of integrated prophage sequences in environmental metagenome-assembled genomes from published Porcelana PMM metagenomes was analyzed. Our results suggest that virus-specific replicative cycles (lytic and lysogenic) were associated with specific host taxa with different metabolic capacities. One of the most abundant lytic viral groups corresponded to cyanophages, which would infect the cyanobacteria Fischerella, the most active and dominant primary producer in thermophilic PMMs. Likewise, lysogenic viruses were related exclusively to chemoheterotrophic bacteria from the phyla Proteobacteria, Firmicutes, and Actinobacteria. These temperate viruses possess accessory genes to sense or control stress-related processes in their hosts, such as sporulation and biofilm formation. Taken together, these observations suggest a nexus between the ecological role of the host (metabolism) and the type of viral lifestyle in thermophilic PMMs. This has direct implications in viral ecology, where the lysogenic-lytic switch is determined by nutrient abundance and microbial density but also by the metabolism type that prevails in the host community. IMPORTANCE Hot springs harbor microbial communities dominated by a limited variety of microorganisms and, as such, have become a model for studying community ecology and understanding how biotic and abiotic interactions shape their structure. Viruses in hot springs are shown to be ubiquitous, numerous, and active components of these communities. However, lytic and lysogenic viral communities of thermophilic phototrophic microbial mats (PMMs) remain largely unexplored. In this work, we use the power of viral metagenomics to reveal changes in the viral community following a mitomycin C induction experiment in PMMs. The importance of our research is that it will improve our understanding of viral lifestyles in PMMs via exploring the differences in the composition of natural and induced viral communities at the genome and gene levels. This novel information will contribute to deciphering which biotic and abiotic factors may control the transitions between lytic and lysogenic cycles in these extreme environments.}, }
@article {pmid34784973, year = {2021}, author = {Wu, J and Lang, H and Mu, X and Zhang, Z and Su, Q and Hu, X and Zheng, H}, title = {Honey bee genetics shape the strain-level structure of gut microbiota in social transmission.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {225}, pmid = {34784973}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; Bees ; Bifidobacterium/genetics ; *Gastrointestinal Microbiome/genetics ; Genome-Wide Association Study ; *Microbiota ; }, abstract = {BACKGROUND: Honey bee gut microbiota transmitted via social interactions are beneficial to the host health. Although the microbial community is relatively stable, individual variations and high strain-level diversity have been detected across honey bees. Although the bee gut microbiota structure is influenced by environmental factors, the heritability of the gut members and the contribution of the host genetics remains elusive. Considering bees within a colony are not readily genetically identical due to the polyandry of the queen, we hypothesize that the microbiota structure can be shaped by host genetics.<br><br>RESULTS: We used shotgun metagenomics to simultaneously profile the microbiota and host genotypes of bees from hives of four different subspecies. Gut composition is more distant between genetically different bees at both phylotype- and "sequence-discrete population" levels. We then performed a successive passaging experiment within colonies of hybrid bees generated by artificial insemination, which revealed that the microbial composition dramatically shifts across batches of bees during the social transmission. Specifically, different strains from the phylotype of Snodgrassella alvi are preferentially selected by genetically varied hosts, and strains from different hosts show a remarkably biased distribution of single-nucleotide polymorphism in the Type IV pili loci. Genome-wide association analysis identified that the relative abundance of a cluster of Bifidobacterium strains is associated with the host glutamate receptor gene specifically expressed in the bee brain. Finally, mono-colonization of Bifidobacterium with a specific polysaccharide utilization locus impacts the alternative splicing of the gluR-B gene, which is associated with an increased GABA level in the brain.<br><br>CONCLUSIONS: Our results indicated that host genetics influence the bee gut composition and suggest a gut-brain connection implicated in the gut bacterial strain preference. Honey bees have been used extensively as a model organism for social behaviors, genetics, and the gut microbiome. Further identification of host genetic function as a shaping force of microbial structure will advance our understanding of the host-microbe interactions. Video abstract.}, }
@article {pmid34784754, year = {2022}, author = {Mahlanza, T and Makwarela, L and Roberts, R and van der Merwe, M}, title = {Occurrence of the Iflavirus-like Tomato Matilda Virus in Solanum Species in South Africa.}, journal = {Plant disease}, volume = {}, number = {}, pages = {PDIS03210613PDN}, doi = {10.1094/PDIS-03-21-0613-PDN}, pmid = {34784754}, issn = {0191-2917}, }
@article {pmid34782034, year = {2021}, author = {Thurman, CE and Klores, MM and Wolfe, AE and Poueymirou, WT and Levee, EM and Ericsson, AC and Franklin, CL and Reddyjarugu, B}, title = {Effect of Housing Condition and Diet on the Gut Microbiota of Weanling Immunocompromised Mice.}, journal = {Comparative medicine}, volume = {71}, number = {6}, pages = {485-491}, pmid = {34782034}, issn = {1532-0820}, support = {U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Diet ; *Gastrointestinal Microbiome ; Housing Quality ; Mice ; *Microbiota ; }, abstract = {Gastrointestinal microbiota are affected by a wide variety of extrinsic and intrinsic factors. In the husbandry of laboratory mice and design of experiments, controlling these factors where possible provides more reproducible results. However, the microbiome is dynamic, particularly in the weeks immediately after weaning. In this study, we characterized the baseline gastrointestinal microbiota of immunocompromised mice housed under standard conditions for our facility for 6 weeks after weaning, with housing either in an isolator or in individually ventilated cages and a common antibiotic diet (trimethoprim sulfamethoxazole). We compared these conditions to a group fed a standard diet and a group that was weaned to a standard diet then switched to antibiotic diet after 2 weeks. We found no clear effect of diet on richness and α diversity of the gastrointestinal microbiota. However, diet did affect which taxa were enriched at the end of the experiment. The change to antibiotic diet during the experiment did not convert the gastrointestinal microbiome to a state similar to mice consistently fed antibiotic diet, which may highlight the importance of the initial post-weaning period in the establishment of the gastrointestinal microbiome. We also observed a strong effect of housing type (isolator compared with individually ventilated cage) on the richness, α diversity, β diversity, and taxa enriched over the course of the experiment. Investigating whether the diet or microbiome affects a certain strain's phenotype is warranted in some cases. However, our findings do not suggest that maintaining immunocompromised mice on antibiotic feed has a clinical benefit when potential pathogens are operationally excluded, nor does it result in a more consistent or controlled microbiome in the post-weaning period.}, }
@article {pmid34781411, year = {2022}, author = {Sivaraj, S and Copeland, JK and Malik, A and Pasini, E and Angeli, M and Azhie, A and Husain, S and Kumar, D and Allard, J and Guttman, DS and Humar, A and Bhat, M}, title = {Characterization and predictive functional profiles on metagenomic 16S rRNA data of liver transplant recipients: A longitudinal study.}, journal = {Clinical transplantation}, volume = {36}, number = {2}, pages = {e14534}, doi = {10.1111/ctr.14534}, pmid = {34781411}, issn = {1399-0012}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; *Liver Transplantation ; Longitudinal Studies ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Long-term survival after Liver Transplantation (LT) is often compromised by infectious and metabolic complications. We aimed to delineate alterations in intestinal microbiome (IM) over time that could contribute to medical complications compromising long-term survival following LT. Fecal samples from LT recipients were collected at 3 months (3 M) and 6 months (6 M) post-LT. The bacterial DNA was extracted using E.Z.N.A. Stool DNA Kit and 16S rRNA gene sequencing at V4 hypervariable region was performed. DADA2 and Phyloseq was implemented to analyze the taxonomic composition. Differentially abundant taxa were identified by metagenomeSeq and LEfSe. Piphillin, an Inferred functional metagenomic analysis tool was used to study the bacterial functional content. For comparison, healthy samples were extracted from NCBI and analyzed similarly. The taxonomic &amp; functional profiles of LT recipients were validated with metagenomic sequencing data from animals exposed to immunosuppressants using Venny. Our findings provide a new perspective on longitudinal increase in specific IM communities post-LT along with an increase in bacterial genes associated with metabolic and infectious disease.}, }
@article {pmid34780902, year = {2022}, author = {Innard, N and Chong, JPJ}, title = {The challenges of monitoring and manipulating anaerobic microbial communities.}, journal = {Bioresource technology}, volume = {344}, number = {Pt B}, pages = {126326}, doi = {10.1016/j.biortech.2021.126326}, pmid = {34780902}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; Biomass ; *Bioreactors ; *Microbiota ; }, abstract = {Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.}, }
@article {pmid34779841, year = {2021}, author = {Curry, KD and Nute, MG and Treangen, TJ}, title = {It takes guts to learn: machine learning techniques for disease detection from the gut microbiome.}, journal = {Emerging topics in life sciences}, volume = {5}, number = {6}, pages = {815-827}, pmid = {34779841}, issn = {2397-8554}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Machine Learning ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {Associations between the human gut microbiome and expression of host illness have been noted in a variety of conditions ranging from gastrointestinal dysfunctions to neurological deficits. Machine learning (ML) methods have generated promising results for disease prediction from gut metagenomic information for diseases including liver cirrhosis and irritable bowel disease, but have lacked efficacy when predicting other illnesses. Here, we review current ML methods designed for disease classification from microbiome data. We highlight the computational challenges these methods have effectively overcome and discuss the biological components that have been overlooked to offer perspectives on future work in this area.}, }
@article {pmid34778105, year = {2021}, author = {Pang, L and Wang, Y and Ye, Y and Zhou, Y and Zhi, Q and Lin, H}, title = {Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {740981}, pmid = {34778105}, issn = {2235-2988}, mesh = {Adolescent ; Biofilms ; *Dental Caries ; Dental Caries Susceptibility ; *Dental Plaque ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Caries is one of the most prevalent infectious diseases worldwide and is driven by the dysbiosis of dental biofilms adhering to tooth surfaces. The pits and fissured surfaces are the most susceptible sites of caries. However, in