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1.
Int J Mol Sci ; 22(17)2021 Sep 06.
Artículo en Inglés | MEDLINE | ID: mdl-34502535

RESUMEN

Gut microbiota are reported to be associated with many diseases, including cancers. Several bacterial taxa have been shown to be associated with cancer development or response to treatment. However, longitudinal microbiota alterations during the development of cancers are relatively unexplored. To better understand how microbiota changes, we profiled the gut microbiota composition from prostate cancer-bearing mice and control mice at five different time points. Distinct gut microbiota differences were found between cancer-bearing mice and control mice. Akkermansiaceae was found to be significantly higher in the first three weeks in cancer-bearing mice, which implies its role in the early stage of cancer colonization. We also found that Bifidobacteriaceae and Enterococcaceae were more abundant in the second and last sampling week, respectively. The increments of Akkermansiaceae, Bifidobacteriaceae and Enterococcaceae were previously found to be associated with responses to immunotherapy, which suggests links between these bacteria families and cancers. Additionally, our function analysis showed that the bacterial taxa carrying steroid biosynthesis and butirosin and neomycin biosynthesis were increased, whereas those carrying naphthalene degradation decreased in cancer-bearing mice. Our work identified the bacteria taxa altered during prostate cancer progression and provided a resource of longitudinal microbiota profiles during cancer development in a mouse model.


Asunto(s)
Microbioma Gastrointestinal/fisiología , Neoplasias de la Próstata/microbiología , Neoplasias de la Próstata/patología , Verrucomicrobia/fisiología , Animales , Bacterias/clasificación , Bacterias/genética , Bacterias/metabolismo , Heces/microbiología , Microbioma Gastrointestinal/genética , Humanos , Masculino , Ratones Endogámicos NOD , Ratones SCID , Estadificación de Neoplasias , ARN Ribosómico 16S/genética , Esteroides/biosíntesis , Factores de Tiempo , Verrucomicrobia/genética , Verrucomicrobia/metabolismo
2.
Microbiologyopen ; 10(1): e1175, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-33650794

RESUMEN

Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane- and iron-rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome-assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.


Asunto(s)
Bacteroidetes/metabolismo , Reactores Biológicos/microbiología , Sedimentos Geológicos/microbiología , Hierro/metabolismo , Metano/metabolismo , Verrucomicrobia/metabolismo , Anaerobiosis/fisiología , Bacteroidetes/crecimiento & desarrollo , Finlandia , Microbiota , Océanos y Mares , Oxidación-Reducción , Oxígeno/metabolismo , Suecia , Verrucomicrobia/crecimiento & desarrollo
3.
Int J Biol Macromol ; 172: 490-502, 2021 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-33472022

RESUMEN

Pea starches, in both native (NPS) and retrograded-autoclaved forms (RAPS), were subjected to simulated gastrointestinal (GI) digestion in vitro, their multi-scale structural characteristics, morphological features, molecular distribution and thermal properties were characterized. A gradual increase in the short-/long-range crystallinity, melting enthalpy of gelatinization on increasing digestion time was observed for both the native and retrograded-autoclaved pea starch samples based on the X-ray diffraction, Fourier-transform infrared spectra, solid-state 13CNMR and differential scanning calorimetry measurements. It was especially noticed that the growth rate of crystallinity and double helices, as well as the decrease in Mw values were evidently greater for RAPS than for NPS. To investigate how different molecular fine structure of pea starch substrate affects the gut microbiota shifts and dynamic short-chain fatty acid profile, their resistant starch residues obtained from both native and retrograded-autoclaved pea starch after 8 h of simulated GI tract digestion was used as the fermentation substrate. The levels of acetate, propionate and butyrate gradually increased with the increasing fermentation time for NPS and RAPS. In comparison to the blank control (i.e., the group without the addition of carbohydrate), the fermented NPS and RAPS obviously resulted in an increased abundance of Firmicutes and Bacteroidetes, accompanied by a decrease in Proteobacteria, Actinobacteria and Verrucomicrobia. Both NPS and RAPS promoted different shifts in the microbial community at the genus level, with an increase in the abundance of Bacteroides, Megamonas and Bifidobacterium, as well as a reduction in the abundance of Fusobacterium, Faecalibacterium and Lachnoclostridium in comparison to the blank control samples.


Asunto(s)
Ácidos Grasos Volátiles/biosíntesis , Microbioma Gastrointestinal/fisiología , Guisantes/química , Almidón Resistente/metabolismo , Actinobacteria/clasificación , Actinobacteria/aislamiento & purificación , Actinobacteria/metabolismo , Adulto , Bacteroidetes/clasificación , Bacteroidetes/aislamiento & purificación , Bacteroidetes/metabolismo , Materiales Biomiméticos/química , Conformación de Carbohidratos , Ácidos Grasos Volátiles/clasificación , Heces/microbiología , Femenino , Fermentación , Firmicutes/clasificación , Firmicutes/aislamiento & purificación , Firmicutes/metabolismo , Jugo Gástrico/química , Humanos , Hidrólisis , Masculino , Filogenia , Proteobacteria/clasificación , Proteobacteria/aislamiento & purificación , Proteobacteria/metabolismo , Almidón Resistente/análisis , Verrucomicrobia/clasificación , Verrucomicrobia/aislamiento & purificación , Verrucomicrobia/metabolismo
4.
Proc Natl Acad Sci U S A ; 117(39): 24459-24463, 2020 09 29.
Artículo en Inglés | MEDLINE | ID: mdl-32913059

RESUMEN

Aerobic and nitrite-dependent methanotrophs make a living from oxidizing methane via methanol to carbon dioxide. In addition, these microorganisms cometabolize ammonia due to its structural similarities to methane. The first step in both of these processes is catalyzed by methane monooxygenase, which converts methane or ammonia into methanol or hydroxylamine, respectively. Methanotrophs use methanol for energy conservation, whereas toxic hydroxylamine is a potent inhibitor that needs to be rapidly removed. It is suggested that many methanotrophs encode a hydroxylamine oxidoreductase (mHAO) in their genome to remove hydroxylamine, although biochemical evidence for this is lacking. HAOs also play a crucial role in the metabolism of aerobic and anaerobic ammonia oxidizers by converting hydroxylamine to nitric oxide (NO). Here, we purified an HAO from the thermophilic verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV and characterized its kinetic properties. This mHAO possesses the characteristic P460 chromophore and is active up to at least 80 °C. It catalyzes the rapid oxidation of hydroxylamine to NO. In methanotrophs, mHAO efficiently removes hydroxylamine, which severely inhibits calcium-dependent, and as we show here, lanthanide-dependent methanol dehydrogenases, which are more prevalent in the environment. Our results indicate that mHAO allows methanotrophs to thrive under high ammonia concentrations in natural and engineered ecosystems, such as those observed in rice paddy fields, landfills, or volcanic mud pots, by preventing the accumulation of inhibitory hydroxylamine. Under oxic conditions, methanotrophs mainly oxidize ammonia to nitrite, whereas in hypoxic and anoxic environments reduction of both ammonia-derived nitrite and NO could lead to nitrous oxide (N2O) production.


Asunto(s)
Amoníaco/metabolismo , Proteínas Bacterianas/metabolismo , Metano/metabolismo , Óxido Nítrico/metabolismo , Oxidorreductasas/metabolismo , Verrucomicrobia/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Oxidación-Reducción , Oxidorreductasas/química , Oxidorreductasas/genética , Verrucomicrobia/genética , Verrucomicrobia/metabolismo
5.
Nat Commun ; 11(1): 4822, 2020 09 24.
Artículo en Inglés | MEDLINE | ID: mdl-32973149

RESUMEN

Abiraterone acetate (AA) is an inhibitor of androgen biosynthesis, though this cannot fully explain its efficacy against androgen-independent prostate cancer. Here, we demonstrate that androgen deprivation therapy depletes androgen-utilizing Corynebacterium spp. in prostate cancer patients and that oral AA further enriches for the health-associated commensal, Akkermansia muciniphila. Functional inferencing elucidates a coinciding increase in bacterial biosynthesis of vitamin K2 (an inhibitor of androgen dependent and independent tumor growth). These results are highly reproducible in a host-free gut model, excluding the possibility of immune involvement. Further investigation reveals that AA is metabolized by bacteria in vitro and that breakdown components selectively impact growth. We conclude that A. muciniphila is a key regulator of AA-mediated restructuring of microbial communities, and that this species may affect treatment response in castrate-resistant cohorts. Ongoing initiatives aimed at modulating the colonic microbiota of cancer patients may consider targeted delivery of poorly absorbed selective bacterial growth agents.


Asunto(s)
Acetato de Abiraterona/farmacología , Microbioma Gastrointestinal/efectos de los fármacos , Neoplasias de la Próstata Resistentes a la Castración/tratamiento farmacológico , Neoplasias de la Próstata/tratamiento farmacológico , Verrucomicrobia/efectos de los fármacos , Acetato de Abiraterona/metabolismo , Acetato de Abiraterona/uso terapéutico , Akkermansia , Antagonistas de Andrógenos/farmacología , Andrógenos/metabolismo , Bacterias/metabolismo , Heces/microbiología , Humanos , Masculino , ARN Ribosómico 16S/genética , Verrucomicrobia/genética , Verrucomicrobia/metabolismo , Vitamina K 2/metabolismo , Vitamina K 2/farmacología
6.
Nat Commun ; 11(1): 4844, 2020 09 24.
Artículo en Inglés | MEDLINE | ID: mdl-32973204

RESUMEN

Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila, an O-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also contribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins.


Asunto(s)
Microbioma Gastrointestinal/fisiología , Mucinas/metabolismo , Péptido-N4-(N-acetil-beta-glucosaminil) Asparagina Amidasa/química , Péptido-N4-(N-acetil-beta-glucosaminil) Asparagina Amidasa/metabolismo , Verrucomicrobia/metabolismo , Akkermansia , Animales , Sitios de Unión , Cristalografía por Rayos X , Glicopéptidos/química , Humanos , Mamíferos , Simulación del Acoplamiento Molecular , Mucina-1/metabolismo , Polisacáridos/química , Conformación Proteica , Alineación de Secuencia , Verrucomicrobia/enzimología
7.
Environ Microbiol ; 22(11): 4669-4688, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-32840024

RESUMEN

Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free-living organisms or as symbionts of eukaryotic hosts. Little is known about host-associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto-Mediterranean sponge Petrosia ficiformis and three genomes from strains that we isolated from offshore seawater of the Eastern Mediterranean Sea. Phylogenomic analysis of these five strains indicated that they are all members of Verrucomicrobia subdivision 4, order Opitutales. We compared these novel sponge-associated and seawater-isolated genomes to closely related Verrucomicrobia. Genomic analysis revealed that Planctomycetes-Verrucomicrobia microcompartment gene clusters are enriched in the genomes of symbiotic Opitutales including sponge symbionts but not in free-living ones. We hypothesize that in sponge symbionts these microcompartments are used for degradation of l-fucose and l-rhamnose, which are components of algal and bacterial cell walls and therefore may be found at high concentrations in the sponge tissue. Furthermore, we observed an enrichment of toxin-antitoxin modules in symbiotic Opitutales. We suggest that, in sponges, verrucomicrobial symbionts utilize these modules as a defence mechanism against antimicrobial activity deriving from the abundant microbial community co-inhabiting the host.


Asunto(s)
Poríferos/microbiología , Azúcares/metabolismo , Simbiosis , Sistemas Toxina-Antitoxina/genética , Verrucomicrobia/fisiología , Animales , Mar Mediterráneo , Microbiota , Filogenia , Agua de Mar/microbiología , Verrucomicrobia/clasificación , Verrucomicrobia/genética , Verrucomicrobia/metabolismo
8.
Appl Environ Microbiol ; 86(18)2020 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-32631865

RESUMEN

Industrial methanol production converts methane from natural gas into methanol through a multistep chemical process. Biological methane-to-methanol conversion under moderate conditions and using biogas would be more environmentally friendly. Methanotrophs, bacteria that use methane as an energy source, convert methane into methanol in a single step catalyzed by the enzyme methane monooxygenase, but inhibition of methanol dehydrogenase, which catalyzes the subsequent conversion of methanol into formaldehyde, is a major challenge. In this study, we used the thermoacidophilic methanotroph "Methylacidiphilum fumariolicum" SolV for biological methanol production. This bacterium possesses a XoxF-type methanol dehydrogenase that is dependent on rare earth elements for activity. By using a cultivation medium nearly devoid of lanthanides, we reduced methanol dehydrogenase activity and obtained a continuous methanol-producing microbial culture. The methanol production rate and conversion efficiency were growth-rate dependent. A maximal conversion efficiency of 63% mol methanol produced per mol methane consumed was obtained at a relatively high growth rate, with a methanol production rate of 0.88 mmol/g (dry weight)/h. This study demonstrates that methanotrophs can be used for continuous methanol production. Full-scale application will require additional increases in the titer, production rate, and efficiency, which can be achieved by further decreasing the lanthanide concentration through the use of increased biomass concentrations and novel reactor designs to supply sufficient gases, including methane, oxygen, and hydrogen.IMPORTANCE The production of methanol, an important chemical, is completely dependent on natural gas. The current multistep chemical process uses high temperature and pressure to convert methane in natural gas to methanol. In this study, we used the methanotroph "Methylacidiphilum fumariolicum" SolV to achieve continuous methanol production from methane as the substrate. The production rate was highly dependent on the growth rate of this microorganism, and high conversion efficiencies were obtained. Using microorganisms for the production of methanol might enable the use of more sustainable sources of methane, such as biogas, rather than natural gas.


Asunto(s)
Metano/metabolismo , Metanol/metabolismo , Verrucomicrobia/metabolismo , Verrucomicrobia/crecimiento & desarrollo
9.
Nat Commun ; 11(1): 3285, 2020 07 03.
Artículo en Inglés | MEDLINE | ID: mdl-32620774

RESUMEN

The early life human gut microbiota exerts life-long health effects on the host, but the mechanisms underpinning its assembly remain elusive. Particularly, the early colonization of Clostridiales from the Roseburia-Eubacterium group, associated with protection from colorectal cancer, immune- and metabolic disorders is enigmatic. Here, we describe catabolic pathways that support the growth of Roseburia and Eubacterium members on distinct human milk oligosaccharides (HMOs). The HMO pathways, which include enzymes with a previously unknown structural fold and specificity, were upregulated together with additional glycan-utilization loci during growth on selected HMOs and in co-cultures with Akkermansia muciniphila on mucin, suggesting an additional role in enabling cross-feeding and access to mucin O-glycans. Analyses of 4599 Roseburia genomes underscored the preponderance and diversity of the HMO utilization loci within the genus. The catabolism of HMOs by butyrate-producing Clostridiales may contribute to the competitiveness of this group during the weaning-triggered maturation of the microbiota.


Asunto(s)
Butiratos/metabolismo , Clostridiales/metabolismo , Leche Humana/metabolismo , Mucinas/metabolismo , Oligosacáridos/metabolismo , Akkermansia , Bifidobacterium/metabolismo , Clostridiales/genética , Colon/microbiología , Eubacterium/metabolismo , Microbioma Gastrointestinal/fisiología , Humanos , Lactante , Recién Nacido , Metabolismo/fisiología , Leche Humana/química , Polisacáridos/metabolismo , Verrucomicrobia/metabolismo , Destete
10.
Nat Microbiol ; 5(8): 1026-1039, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32451471

RESUMEN

Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.


Asunto(s)
Phaeophyta/metabolismo , Polisacáridos/metabolismo , Verrucomicrobia/enzimología , Verrucomicrobia/metabolismo , Proteínas Bacterianas/metabolismo , Pared Celular/metabolismo , Esterasas , Genes Bacterianos/genética , Glicósido Hidrolasas , Redes y Vías Metabólicas , Metagenoma , Filogenia , Proteoma , Especificidad por Sustrato , Sulfatasas , Sulfatos/metabolismo , Transcriptoma , Estados Unidos , Verrucomicrobia/genética , Verrucomicrobia/aislamiento & purificación
11.
Gut Microbes ; 11(5): 1348-1361, 2020 09 02.
Artículo en Inglés | MEDLINE | ID: mdl-32372706

RESUMEN

The understanding of the effects of compounds on the gut microbiome is limited. In particular, it is unclear whether structurally similar compounds would have similar or distinct effects on the gut microbiome. Here, we selected berberine (BBR), an isoquinoline quaternary alkaloid, and 16 structural analogs and evaluated their effects on seven individual gut microbiomes cultured in vitro. The responses of the individual microbiomes were evaluated by metaproteomic profiles and by assessing butyrate production. We show that both interindividual differences and compound treatments significantly contributed to the variance of metaproteomic profiles. BBR and eight analogs led to changes in proteins involved in microbial defense and stress responses and enrichment of proteins from Verrucomicrobia, Proteobacteria, and Bacteroidetes phyla. It also led to a decrease in proteins from the Firmicutes phylum and its Clostridiales order which correlated to decrease proteins involved in the butyrate production pathway and butyrate concentration. Three of the compounds, sanguinarine, chelerythrine, and ethoxysanguinarine, activated bacterial protective mechanisms, enriched Proteobacteria, increased opacity proteins, and markedly reduced butyrate production. Dihydroberberine had a similar function to BBR in enriching the Akkermansia genus. In addition, it showed less overall adverse impacts on the functionality of the gut microbiome, including a better maintenance of the butyrate level. Our study shows that ex vivo microbiome assay can assess differential regulating effects of compounds with subtle differences and reveals that compound analogs can have distinct effects on the microbiome.


Asunto(s)
Bacteroidetes/efectos de los fármacos , Berberina/análogos & derivados , Berberina/farmacología , Firmicutes/efectos de los fármacos , Microbioma Gastrointestinal/efectos de los fármacos , Proteobacteria/efectos de los fármacos , Verrucomicrobia/efectos de los fármacos , Proteínas Bacterianas/metabolismo , Bacteroidetes/crecimiento & desarrollo , Bacteroidetes/metabolismo , Berberina/química , Variación Biológica Poblacional , Butiratos/metabolismo , Firmicutes/crecimiento & desarrollo , Firmicutes/metabolismo , Microbioma Gastrointestinal/fisiología , Humanos , Redes y Vías Metabólicas , Estructura Molecular , Proteobacteria/crecimiento & desarrollo , Proteobacteria/metabolismo , Proteómica , Verrucomicrobia/crecimiento & desarrollo , Verrucomicrobia/metabolismo
12.
ISME J ; 14(5): 1223-1232, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-32042101

RESUMEN

The trace amounts (0.53 ppmv) of atmospheric hydrogen gas (H2) can be utilized by microorganisms to persist during dormancy. This process is catalyzed by certain Actinobacteria, Acidobacteria, and Chloroflexi, and is estimated to convert 75 × 1012 g H2 annually, which is half of the total atmospheric H2. This rapid atmospheric H2 turnover is hypothesized to be catalyzed by high-affinity [NiFe] hydrogenases. However, apparent high-affinity H2 oxidation has only been shown in whole cells, rather than for the purified enzyme. Here, we show that the membrane-associated hydrogenase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV possesses a high apparent affinity (Km(app) = 140 nM) for H2 and that methanotrophs can oxidize subatmospheric H2. Our findings add to the evidence that the group 1h [NiFe] hydrogenase is accountable for atmospheric H2 oxidation and that it therefore could be a strong controlling factor in the global H2 cycle. We show that the isolated enzyme possesses a lower affinity (Km = 300 nM) for H2 than the membrane-associated enzyme. Hence, the membrane association seems essential for a high affinity for H2. The enzyme is extremely thermostable and remains folded up to 95 °C. Strain SolV is the only known organism in which the group 1h [NiFe] hydrogenase is responsible for rapid growth on H2 as sole energy source as well as oxidation of subatmospheric H2. The ability to conserve energy from H2 could increase fitness of verrucomicrobial methanotrophs in geothermal ecosystems with varying CH4 fluxes. We propose that H2 oxidation can enhance growth of methanotrophs in aerated methane-driven ecosystems. Group 1h [NiFe] hydrogenases could therefore contribute to mitigation of global warming, since CH4 is an important and extremely potent greenhouse gas.


Asunto(s)
Verrucomicrobia/fisiología , Ecosistema , Hidrógeno , Hidrogenasas/metabolismo , Metano , Oxidación-Reducción , Verrucomicrobia/metabolismo
13.
PLoS One ; 15(1): e0227373, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-31910227

RESUMEN

METHODS: Patients transplanted at our institution provided fecal samples before, and 3-9 months after KT. Fecal bacterial DNA was extracted and 9 bacteria or bacterial groups were quantified by qPCR. RESULTS: 50 patients (19 controls without diabetes, 15 who developed New Onset Diabetes After Transplantation, NODAT, and 16 with type 2 diabetes before KT) were included. Before KT, Lactobacillus sp. tended to be less frequently detected in controls than in those who would become diabetic following KT (NODAT) and in initially diabetic patients (60%, 87.5%, and 100%, respectively, p = 0.08). The relative abundance of Faecalibacterium prausnitzii was 30 times lower in initially diabetic patients than in controls (p = 0.002). The relative abundance of F. prausnitzii of NODAT patients was statistically indistinguishable from controls and from diabetic patients. The relative abundance of Lactobacillus sp. increased following KT in NODAT and in initially diabetic patients (20-fold, p = 0.06, and 25-fold, p = 0.02, respectively). In contrast, the proportion of Akkermansia muciniphila decreased following KT in NODAT and in initially diabetic patients (2,500-fold, p = 0.04, and 50,000-fold, p<0.0001, respectively). The proportion of Lactobacillus and A. muciniphila did not change in controls between before and after the transplantation. Consequently, after KT the relative abundance of Lactobacillus sp. was 25 times higher (p = 0.07) and the relative abundance of A. muciniphila was 2,000 times lower (p = 0.002) in diabetics than in controls. CONCLUSION: An alteration of the gut microbiota composition involving Lactobacillus sp., A. muciniphila and F. prausnitzii is associated with the glycemic status in KT recipients, raising the question of their role in the genesis of NODAT.


Asunto(s)
ADN Bacteriano/genética , Diabetes Mellitus Tipo 2/microbiología , Microbioma Gastrointestinal/genética , Trasplante de Riñón/efectos adversos , Akkermansia , Diabetes Mellitus Tipo 2/complicaciones , Diabetes Mellitus Tipo 2/metabolismo , Diabetes Mellitus Tipo 2/patología , Faecalibacterium prausnitzii/genética , Faecalibacterium prausnitzii/aislamiento & purificación , Faecalibacterium prausnitzii/metabolismo , Heces/microbiología , Femenino , Humanos , Lactobacillus/genética , Lactobacillus/aislamiento & purificación , Lactobacillus/metabolismo , Masculino , Persona de Mediana Edad , Factores de Riesgo , Verrucomicrobia/genética , Verrucomicrobia/aislamiento & purificación , Verrucomicrobia/metabolismo
14.
Am J Physiol Endocrinol Metab ; 318(4): E480-E491, 2020 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-31961709

RESUMEN

Probiotic bacteria can protect from ovariectomy (ovx)-induced bone loss in mice. Akkermansia muciniphila is considered to have probiotic potential due to its beneficial effect on obesity and insulin resistance. The purpose of the present study was to determine if treatment with pasteurized Akkermansia muciniphila (pAkk) could prevent ovx-induced bone loss. Mice were treated with vehicle or pAkk for 4 wk, starting 3 days before ovx or sham surgery. Treatment with pAkk reduced fat mass accumulation confirming earlier findings. However, treatment with pAkk decreased trabecular and cortical bone mass in femur and vertebra of gonadal intact mice and did not protect from ovx-induced bone loss. Treatment with pAkk increased serum parathyroid hormone (PTH) levels and increased expression of the calcium transporter Trpv5 in kidney suggesting increased reabsorption of calcium in the kidneys. Serum amyloid A 3 (SAA3) can suppress bone formation and mediate the effects of PTH on bone resorption and bone loss in mice and treatment with pAkk increased serum levels of SAA3 and gene expression of Saa3 in colon. Moreover, regulatory T cells can be protective of bone and pAkk-treated mice had decreased number of regulatory T cells in mesenteric lymph nodes and bone marrow. In conclusion, treatment with pAkk protected from ovx-induced fat mass gain but not from bone loss and reduced bone mass in gonadal intact mice. Our findings with pAkk differ from some probiotics that have been shown to protect bone mass, demonstrating that not all prebiotic and probiotic factors have the same effect on bone.


Asunto(s)
Tejido Adiposo/crecimiento & desarrollo , Microbioma Gastrointestinal/fisiología , Osteoporosis/metabolismo , Probióticos/farmacología , Verrucomicrobia/metabolismo , Tejido Adiposo/metabolismo , Akkermansia , Animales , Canales de Calcio/metabolismo , Colon/efectos de los fármacos , Colon/microbiología , Femenino , Fémur/efectos de los fármacos , Ganglios Linfáticos/citología , Ratones , Ratones Endogámicos C57BL , Ovariectomía , Hormona Paratiroidea/metabolismo , Pasteurización , Proteína Amiloide A Sérica/metabolismo , Columna Vertebral/efectos de los fármacos , Linfocitos T Reguladores , Canales Catiónicos TRPV/metabolismo
15.
Appl Environ Microbiol ; 86(3)2020 01 21.
Artículo en Inglés | MEDLINE | ID: mdl-31757822

RESUMEN

Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a "next-generation probiotic." However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B12) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B12 biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B12 was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B12 production by the AmII phylogroup. This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome.IMPORTANCE There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B12 The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health.


Asunto(s)
Genoma Bacteriano , Verrucomicrobia/genética , Vitamina B 12/biosíntesis , Vitaminas/biosíntesis , Niño , Preescolar , Genómica , Humanos , Verrucomicrobia/metabolismo , Vitamina B 12/genética , Vitaminas/genética
16.
Int J Mol Sci ; 21(1)2019 Dec 20.
Artículo en Inglés | MEDLINE | ID: mdl-31861919

RESUMEN

Akkermansia muciniphila can produce various mucin-degrading proteins. However, the functional characteristics of these proteins and their role in mucin degradation are unclear. Of the predicted protein-coding genes, Amuc_1434, which encodes for a hypothetical protein, is the focus in this study. A recombinant enzyme Amuc_1434 containing the 6× His-tag produced in Escherichia coli (hereinafter termed Amuc_1434*) was isolated to homogeneity and biochemically characterised. Results showed that the enzyme can hydrolyse hemoglobin with an activity of 17.21 U/µg. The optimal pH and temperature for hemoglobin hydrolysis of Amuc_1434* were found to be around 8.0 and 40 °C, respectively. Amuc_1434* is identified as a member of the aspartic protease family through the action of inhibitor pepstatin A. Amuc_1434* promotes the adhesion of colon cancer cell line LS174T, which can highly express Muc2. Significantly Amuc_1434* can degrade Muc2 of colon cancer cells. Amuc_1434 is mainly located in the colon of BALB/c mice. These results suggest that the presence of Amuc_1434 from Akkermansia muciniphila may be correlated with the restoration of gut barrier function by decreasing mucus layer thickness.


Asunto(s)
Proteasas de Ácido Aspártico/metabolismo , Proteínas Bacterianas/metabolismo , Mucina 2/metabolismo , Verrucomicrobia/metabolismo , Akkermansia , Animales , Proteasas de Ácido Aspártico/aislamiento & purificación , Línea Celular Tumoral , Células HeLa , Humanos , Ratones Endogámicos BALB C , Proteolisis
17.
Sci Rep ; 9(1): 19835, 2019 12 27.
Artículo en Inglés | MEDLINE | ID: mdl-31882618

RESUMEN

Interrelations between epiphytic bacteria and macroalgae are multifaceted and complicated, though little is known about the community structure, interaction and functions of those epiphytic bacteria. This study comprehensively characterized the epiphytic bacterial communities associated with eight different common seaweeds collected from a rocky intertidal zone on the Indian Ocean at Cape Vidal, South Africa. High-throughput sequencing analyses indicated that seaweed-associated bacterial communities were dominated by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Energy-dispersive X-ray (EDX) analysis showed the presence of elemental composition in the surface of examined seaweeds, in varying concentrations. Cluster analysis showed that bacterial communities of brown seaweeds (SW2 and SW4) were closely resembled those of green seaweeds (SW1) and red seaweeds (SW7) while those of brown seaweeds formed a separate branch. Predicted functional capabilities of epiphytic bacteria using PICRUSt analysis revealed abundance of genes related to metabolic and biosynthetic activities. Further important identified functional interactions included genes for bacterial chemotaxis, which could be responsible for the observed association and network of elemental-microbes interaction. The study concludes that the diversity of epiphytic bacteria on seaweed surfaces is greatly influenced by algal organic exudates as well as elemental deposits on their surfaces, which triggers chemotaxis responses from epiphytic bacteria with the requisite genes to metabolise those substrates.


Asunto(s)
Bacterias/genética , Biodiversidad , Ecosistema , Algas Marinas/microbiología , Actinobacteria/clasificación , Actinobacteria/genética , Actinobacteria/metabolismo , Bacterias/clasificación , Bacterias/metabolismo , Firmicutes/clasificación , Firmicutes/genética , Firmicutes/metabolismo , Variación Genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Interacciones Microbiota-Huesped , Océano Índico , Filogenia , Proteobacteria/clasificación , Proteobacteria/genética , Proteobacteria/metabolismo , Algas Marinas/clasificación , Sudáfrica , Verrucomicrobia/clasificación , Verrucomicrobia/genética , Verrucomicrobia/metabolismo
18.
Cell Host Microbe ; 26(6): 779-794.e8, 2019 12 11.
Artículo en Inglés | MEDLINE | ID: mdl-31784260

RESUMEN

Fecal transfer from healthy donors is being explored as a microbiome modality. MicroRNAs (miRNAs) have been found to affect the microbiome. Multiple sclerosis (MS) patients have been shown to have an altered gut microbiome. Here, we unexpectedly found that transfer of feces harvested at peak disease from the experimental autoimmune encephalomyelitis (EAE) model of MS ameliorates disease in recipients in a miRNA-dependent manner. Specifically, we show that miR-30d is enriched in the feces of peak EAE and untreated MS patients. Synthetic miR-30d given orally ameliorates EAE through expansion of regulatory T cells (Tregs). Mechanistically, miR-30d regulates the expression of a lactase in Akkermansia muciniphila, which increases Akkermansia abundance in the gut. The expanded Akkermansia in turn increases Tregs to suppress EAE symptoms. Our findings report the mechanistic underpinnings of a miRNA-microbiome axis and suggest that the feces of diseased subjects might be enriched with miRNAs with therapeutic properties.


Asunto(s)
Encefalomielitis Autoinmune Experimental , Trasplante de Microbiota Fecal , MicroARNs/uso terapéutico , Esclerosis Múltiple/tratamiento farmacológico , Verrucomicrobia , Administración Oral , Akkermansia , Animales , Encefalomielitis Autoinmune Experimental/tratamiento farmacológico , Encefalomielitis Autoinmune Experimental/inmunología , Heces , Microbioma Gastrointestinal/inmunología , Interacciones Microbiota-Huesped , Humanos , Lactasa/metabolismo , Ratones , Ratones Endogámicos C57BL , MicroARNs/metabolismo , Linfocitos T Reguladores/metabolismo , Verrucomicrobia/crecimiento & desarrollo , Verrucomicrobia/inmunología , Verrucomicrobia/metabolismo
19.
Sci Rep ; 9(1): 15683, 2019 10 30.
Artículo en Inglés | MEDLINE | ID: mdl-31666581

RESUMEN

Akkermansia muciniphila utilises colonic mucin as its substrate. Abundance is reduced in ulcerative colitis (UC), as is the relative proportion of sulphated mucin in the mucus gel layer (MGL). It is unknown if these phenomena are related, however reduced sulphated mucins could contribute to reduced abundance, owing to a lack of substrate. The aim of this study was to quantify A. muciniphila within the MGL and to relate these findings with markers of inflammation and the relative proportion of sulphomucin present. Colonic biopsies and mucus brushings were obtained from 20 patients with active UC (AC), 14 with quiescent UC (QUC) and 20 healthy controls (HC). A. muciniphila abundance was determined by RT-PCR. High iron diamine alcian-blue staining was performed for histological analysis. Patients with AC had reduced abundance of A. muciniphila compared to HC and QUC. A positive association was found between A. muciniphila abundance and higher percentage of sulphated mucin (ρ 0.546, p = 0.000). Lower abundances of A. muciniphila correlated with higher inflammatory scores (ρ = 0.294 (p = 0.001)). This study confirms an inverse relationship between A. muciniphila and inflammation and a positive association between A. muciniphila abundance and percentage of sulfated mucin in the MGL.


Asunto(s)
Colitis Ulcerosa/microbiología , Inflamación/genética , Mucinas/metabolismo , Verrucomicrobia/metabolismo , Adolescente , Adulto , Akkermansia , Biopsia , Colitis Ulcerosa/metabolismo , Colitis Ulcerosa/patología , Colon/metabolismo , Colon/microbiología , Femenino , Voluntarios Sanos , Humanos , Inflamación/metabolismo , Inflamación/microbiología , Mucosa Intestinal/metabolismo , Mucosa Intestinal/microbiología , Intestinos/microbiología , Masculino , Persona de Mediana Edad , Mucinas/aislamiento & purificación , Moco/metabolismo , Moco/microbiología , Verrucomicrobia/patogenicidad , Adulto Joven
20.
BMC Genomics ; 20(1): 642, 2019 Aug 09.
Artículo en Inglés | MEDLINE | ID: mdl-31399023

RESUMEN

BACKGROUND: The candidate genus "Methylacidiphilum" comprises thermoacidophilic aerobic methane oxidizers belonging to the Verrucomicrobia phylum. These are the first described non-proteobacterial aerobic methane oxidizers. The genes pmoCAB, encoding the particulate methane monooxygenase do not originate from horizontal gene transfer from proteobacteria. Instead, the "Ca. Methylacidiphilum" and the sister genus "Ca. Methylacidimicrobium" represent a novel and hitherto understudied evolutionary lineage of aerobic methane oxidizers. Obtaining and comparing the full genome sequences is an important step towards understanding the evolution and physiology of this novel group of organisms. RESULTS: Here we present the closed genome of "Ca. Methylacidiphilum kamchatkense" strain Kam1 and a comparison with the genomes of its two closest relatives "Ca. Methylacidiphilum fumariolicum" strain SolV and "Ca. Methylacidiphilum infernorum" strain V4. The genome consists of a single 2,2 Mbp chromosome with 2119 predicted protein coding sequences. Genome analysis showed that the majority of the genes connected with metabolic traits described for one member of "Ca. Methylacidiphilum" is conserved between all three genomes. All three strains encode class I CRISPR-cas systems. The average nucleotide identity between "Ca. M. kamchatkense" strain Kam1 and strains SolV and V4 is ≤95% showing that they should be regarded as separate species. Whole genome comparison revealed a high degree of synteny between the genomes of strains Kam1 and SolV. In contrast, comparison of the genomes of strains Kam1 and V4 revealed a number of rearrangements. There are large differences in the numbers of transposable elements found in the genomes of the three strains with 12, 37 and 80 transposable elements in the genomes of strains Kam1, V4 and SolV respectively. Genomic rearrangements and the activity of transposable elements explain much of the genomic differences between strains. For example, a type 1h uptake hydrogenase is conserved between strains Kam1 and SolV but seems to have been lost from strain V4 due to genomic rearrangements. CONCLUSIONS: Comparing three closed genomes of "Ca. Methylacidiphilum" spp. has given new insights into the evolution of these organisms and revealed large differences in numbers of transposable elements between strains, the activity of these explains much of the genomic differences between strains.


Asunto(s)
Genómica , Verrucomicrobia/genética , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Biomasa , Genoma Bacteriano/genética , Filogenia , Especificidad de la Especie , Verrucomicrobia/metabolismo
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