Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome

BACKGROUND

The gut microbiome is altered in several neurologic disorders, including Parkinson's disease (PD).

OBJECTIVES

The aim is to profile the fecal gut metagenome in PD for alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products, and their relationship with disease progression.

METHODS

Shotgun metagenomic sequencing was conducted on 244 stool donors from two independent cohorts in the United States, including individuals with PD (n = 48, n = 47, respectively), environmental household controls (HC, n = 29, n = 30), and community population controls (PC, n = 41, n = 49). Microbial features consistently altered in PD compared to HC and PC subjects were identified. Data were cross-referenced to public metagenomic data sets from two previous studies in Germany and China to determine generalizable microbiome features.

RESULTS

We find several significantly altered taxa between PD and controls within the two cohorts sequenced in this study. Analysis across global cohorts returns consistent changes only in Intestinimonas butyriciproducens. Pathway enrichment analysis reveals disruptions in microbial carbohydrate and lipid metabolism and increased amino acid and nucleotide metabolism in PD. Global gene-level signatures indicate an increased response to oxidative stress, decreased cellular growth and microbial motility, and disrupted intercommunity signaling.

CONCLUSIONS

A metagenomic meta-analysis of PD shows consistent and novel alterations in functional metabolic potential and microbial gene abundance across four independent studies from three continents. These data reveal that stereotypic changes in the functional potential of the gut microbiome are a consistent feature of PD, highlighting potential diagnostic and therapeutic avenues for future research. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Gut microbiota suppress feeding induced by palatable foods

Feeding behaviors depend on intrinsic and extrinsic factors including genetics, food palatability, and the environment.^1,2,3,4,5 The gut microbiota is a major environmental contributor to host physiology and impacts feeding behavior.^{6,7,8,9,10,11,12} Here, we explored the hypothesis that gut bacteria influence behavioral responses to palatable foods and reveal that antibiotic depletion (ABX) of the gut microbiota in mice results in overconsumption of several palatable foods with conserved effects on feeding dynamics. Gut microbiota restoration via fecal transplant into ABX mice is sufficient to rescue overconsumption of high-sucrose pellets. Operant conditioning tests found that ABX mice exhibit intensified motivation to pursue high-sucrose rewards. Accordingly, neuronal activity in mesolimbic brain regions, which have been linked with motivation and reward-seeking behavior,³ was elevated in ABX mice after consumption of high-sucrose pellets. Differential antibiotic treatment and functional microbiota transplants identified specific gut bacterial taxa from the family S24-7 and the genus Lactobacillus whose abundances associate with suppression of high-sucrose pellet consumption. Indeed, colonization of mice with S24-7 and Lactobacillus johnsonii was sufficient to reduce overconsumption of high-sucrose pellets in an antibiotic-induced model of binge eating. These results demonstrate that extrinsic influences from the gut microbiota can suppress the behavioral response toward palatable foods in mice.

Microbiota regulate social behaviour via stress response neurons in the brain

Social interactions among animals mediate essential behaviours, including mating, nurturing, and defence^1,2. The gut microbiota contribute to social activity in mice^3,4, but the gut-brain connections that regulate this complex behaviour and its underlying neural basis are unclear^5,6. Here we show that the microbiome modulates neuronal activity in specific brain regions of male mice to regulate canonical stress responses and social behaviours. Social deviation in germ-free and antibiotic-treated mice is associated with elevated levels of the stress hormone corticosterone, which is primarily produced by activation of the hypothalamus-pituitary-adrenal (HPA) axis. Adrenalectomy, antagonism of glucocorticoid receptors, or pharmacological inhibition of corticosterone synthesis effectively corrects social deficits following microbiome depletion. Genetic ablation of glucocorticoid receptors in specific brain regions or chemogenetic inactivation of neurons in the paraventricular nucleus of the hypothalamus that produce corticotrophin-releasing hormone (CRH) reverse social impairments in antibiotic-treated mice. Conversely, specific activation of CRH-expressing neurons in the paraventricular nucleus induces social deficits in mice with a normal microbiome. Via microbiome profiling and in vivo selection, we identify a bacterial species, Enterococcus faecalis, that promotes social activity and reduces corticosterone levels in mice following social stress. These studies suggest that specific gut bacteria can restrain the activation of the HPA axis, and show that the microbiome can affect social behaviours through discrete neuronal circuits that mediate stress responses in the brain.

CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity

Hexanucleotide repeat expansions in the C9orf72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9FTD/ALS). The nucleotide repeat expansions are translated into dipeptide repeat (DPR) proteins, which are aggregation-prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene knockout screens for suppressors and enhancers of C9orf72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA processing pathways, and in chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9orf72 DPRs in neurons, and improved survival of human induced motor neurons from C9orf72 ALS patients. Together, this work demonstrates the promise of CRISPR-Cas9 screens to define mechanisms of neurodegenerative diseases.

Influence of maternal size on placental, fetal and postnatal growth in the horse. I. Development in utero

The interacting influences of maternal size and fetal genotype on placental and fetal development in the mare were assessed by comparing conventional within-breed Thoroughbred (Tb-in-Tb, n = 7) and Pony (P-in-P, n = 7) control pregnancies established by artificial insemination (AI) with between-breed (Tb-in-P, n = 8; deprived in utero condition and P-in-Tb, n = 7; luxurious in utero condition) experimental pregnancies established by embryo transfer. All foals were born spontaneously and the mean (+/- SEM) duration of gestation in the two groups of control mares was significantly different (P < 0.001) at 325 +/- 3.0 days for the P-in-P pregnancies and 339 +/- 3.0 days for the Tb-in-Tb pregnancies, whereas the durations of gestation for the two experimental groups were very similar and midway between those of the control pregnancies at 332 +/- 2.8 days for the Tb-in-P and 331 +/- 2.7 days for the P-in-Tb. Mean (+/- SEM) foal birth weight and the mean (+/- SEM) values for the mass, gross area and volume of the allantochorion were all highest in the seven Tb-in-Tb pregnancies (53.1 +/- 2.6 kg, 3.8 +/- 0.3 kg, 12.9 +/- 0.3 x 10(3) cm(2), 3.5 +/- 0.2 l, respectively) and lowest in the seven P-in-P control pregnancies (24.0 +/- 1.3 kg, 1.7 +/- 0.1 kg, 8.3 +/- 0.3 x 10(3) cm(2), 1.8 +/- 0.1 l, respectively). These parameters were higher in the seven P-in-Tb pregnancies (37.9 +/- 2.1 kg, 2.7 +/- 0.1 kg, 10.1 +/- 0.5 x 10(3) cm(2), 2.5 +/- 0.1 l, respectively) than in the eight Tb-in-P (33.0 +/- 2.4 kg, 2.3 +/- 0.2 kg, 9.0 +/- 0.5 x 10(3) cm(2), 2.1 +/- 0.1 l) experimental pregnancies. Foal birth weight was positively correlated with the mass (r = 0.84, P < 0.001), gross area (r = 0.87, P < 0.001) and volume (r = 0.91, P < 0.001) of the allantochorion, and maternal weight was also positively correlated with both the mass and gross area of the allantochorion (r = 0.64 and 0.69, respectively; both P < 0.001). Application of stereology to multiple random biopsies recovered from each placenta produced mean values for the surface density of microcotyledons on the allantochorion (S(v)). Values were higher in Thoroughbred than in Pony mares regardless of the breed of fetus being carried. Multiplication of S(v) by the volume of the allantochorion to give the total microscopic area of fetomaternal contact at the placental interface was also positively correlated with foal birth weight (r = 0.84, P < 0.001). Foal birth weight was determined by the microscopic area of fetomaternal contact of the placenta and there were no differences in foal weight per m(2) of placenta regardless of fetal or maternal genomes. Thus, the results indicate that in equids, maternal size interacts with both the maternal and fetal genotypes to control the rate and extent of fetal growth by influencing the gross area of the diffuse allantochorion, and the density, complexity and depth of the microcotyledons on its surface.

Influence of maternal size on placental, fetal and postnatal growth in the horse. I. Development in utero

The interacting influences of maternal size and fetal genotype on placental and fetal development in the mare were assessed by comparing conventional within-breed Thoroughbred (Tb-in-Tb, n = 7) and Pony (P-in-P, n = 7) control pregnancies established by artificial insemination (AI) with between-breed (Tb-in-P, n = 8; deprived in utero condition and P-in-Tb, n = 7; luxurious in utero condition) experimental pregnancies established by embryo transfer. All foals were born spontaneously and the mean (+/- SEM) duration of gestation in the two groups of control mares was significantly different (P < 0.001) at 325 +/- 3.0 days for the P-in-P pregnancies and 339 +/- 3.0 days for the Tb-in-Tb pregnancies, whereas the durations of gestation for the two experimental groups were very similar and midway between those of the control pregnancies at 332 +/- 2.8 days for the Tb-in-P and 331 +/- 2.7 days for the P-in-Tb. Mean (+/- SEM) foal birth weight and the mean (+/- SEM) values for the mass, gross area and volume of the allantochorion were all highest in the seven Tb-in-Tb pregnancies (53.1 +/- 2.6 kg, 3.8 +/- 0.3 kg, 12.9 +/- 0.3 x 10(3) cm(2), 3.5 +/- 0.2 l, respectively) and lowest in the seven P-in-P control pregnancies (24.0 +/- 1.3 kg, 1.7 +/- 0.1 kg, 8.3 +/- 0.3 x 10(3) cm(2), 1.8 +/- 0.1 l, respectively). These parameters were higher in the seven P-in-Tb pregnancies (37.9 +/- 2.1 kg, 2.7 +/- 0.1 kg, 10.1 +/- 0.5 x 10(3) cm(2), 2.5 +/- 0.1 l, respectively) than in the eight Tb-in-P (33.0 +/- 2.4 kg, 2.3 +/- 0.2 kg, 9.0 +/- 0.5 x 10(3) cm(2), 2.1 +/- 0.1 l) experimental pregnancies. Foal birth weight was positively correlated with the mass (r = 0.84, P < 0.001), gross area (r = 0.87, P < 0.001) and volume (r = 0.91, P < 0.001) of the allantochorion, and maternal weight was also positively correlated with both the mass and gross area of the allantochorion (r = 0.64 and 0.69, respectively; both P < 0.001). Application of stereology to multiple random biopsies recovered from each placenta produced mean values for the surface density of microcotyledons on the allantochorion (S(v)). Values were higher in Thoroughbred than in Pony mares regardless of the breed of fetus being carried. Multiplication of S(v) by the volume of the allantochorion to give the total microscopic area of fetomaternal contact at the placental interface was also positively correlated with foal birth weight (r = 0.84, P < 0.001). Foal birth weight was determined by the microscopic area of fetomaternal contact of the placenta and there were no differences in foal weight per m(2) of placenta regardless of fetal or maternal genomes. Thus, the results indicate that in equids, maternal size interacts with both the maternal and fetal genotypes to control the rate and extent of fetal growth by influencing the gross area of the diffuse allantochorion, and the density, complexity and depth of the microcotyledons on its surface.

The influence of maternal size on placental, fetal and postnatal growth in the horse. II. Endocrinology of pregnancy

Within-breed artificial insemination and between-breed embryo transfer were carried out in small pony (P) and large Thoroughbred (Tb) mares to create 4 types of horse pregnancy in which the fetus experienced spatial and nutritional deprivation (Tb-in-P; n=8), luxury (P-in-Tb; n=7) or normality (Tb-in-Tb; n=7 and P-in-P; n=7) in utero. Measurement of equine chorionic gonadotrophin (eCG), total conjugated oestrogens and progestagen concentrations in serial peripheral serum samples recovered from all the mares throughout gestation showed that the amount of eCG produced during the first half of gestation was dependent upon the breed of the mare rather than the breed of the fetus being carried. In contrast, the mean total amounts of oestrogens produced, as measured by area under the curve, were significantly greater (P=0.003) in the two types of pregnancy in which a Thoroughbred fetus was being carried (Tb-in-Tb and Tb-in-P) than those in which a pony fetus was gestated (P-in-P and P-in-Tb); the evidence suggests that the Tb fetus may have larger gonads than the P fetus and thereby secrete more C-19 precursor steroids for aromatisation to oestrogens by the placenta. In the final weeks of pregnancy mean plasma progestagen concentrations rose much earlier, and to significantly higher levels (P<0.001), in the Tb-in-P than in the P-in-Tb pregnancies, thereby reflecting the increased fetal stress in the former causing premature maturation of the fetal adrenal gland. This, in turn, resulted in increased secretion of pregnenolone by the adrenal cortex for conversion to progestagens by the placenta.

The relationship between the concentration of ionised calcium and parathyroid hormone-related protein (PTHrP[1-34]) in the milk of mares

Once lactation is established in mares, there is little change in the ionised calcium concentration in their milk. In contrast, the concentration of PTHrP(1-34) in the milk increases to a maximum level by the end of the second week of lactation, near which it remains for the rest of the lactation. As found in other species, the concentration of PTHrP(1-34) in mare's milk is considerably higher than that in plasma, sampled at the same time. No significant correlation could be demonstrated between the concentrations of PTHrP(1-34) and ionised calcium in the milk except during the last 10 weeks of lactation.

Localisation of 15-hydroxy prostaglandin dehydrogenase (PGDH) and steroidogenic enzymes in the equine placenta

15-hydroxy prostaglandin dehydrogenase (PGDH) is the critical enzyme that determines metabolism of primary prostaglandins. Its expression is determined in part by steroid hormones, particularly progesterone, formed from delta(5) steroids through 3beta-hydroxysteroid dehydrogenase (3beta-HSD) activity. To assess whether the regulation of PGDH might occur in a paracrine, autocrine or intracrine fashion, we used immunohistochemistry (IHC) to determine the localisation of key steroidogenic enzymes in the equine placenta and compared these patterns to the distribution of immunoreactive (IR-) PGDH. Placental tissue was obtained from pony or Thoroughbred mares at about Days 150, 250-280 and >300 of pregnancy (term 320 to 360 days; n=5-8 each group). IR-PGDH, 3beta-HSD, cholesterol side chain cleavage enzyme (P450(scc)) and 17-hydroxylase/lyase (P450(C17)) were localised using specific antibodies and the avidin-biotin peroxidase technique and visualised using diaminobenzidine as substrate. IR-P450(scc) was present in trophoblast cells, but not in maternal tissues of the microcotyledons. In contrast, at Days 150 and 280, IR-PGDH was present in maternal epithelial and interstitial cells in the microcotyledons, but was not detected in trophoblast epithelium, chorioallantois or endometrial glands. After Day 300, IR-PGDH was present in the maternal epithelium and interstitial cells of the placenta and it was also present in trophoblast cells in some specimens.

Release of lipid from the equine placenta during in vitro incubation

An in vitro incubation technique was used to examine release of lipids from the equine placenta. Placental tissue was obtained at term (n = 5, term = 320-365 days) and earlier in gestation (n = 8, mean = 266 days). Term placentae were incubated at two temperatures, 4 degrees C (control) and 37 degrees C for 2 h. Pre-term placentae were incubated at 37 degrees C with two different concentrations of fatty acid in the medium. Tissues and media were analysed for their lipid concentrations. Term and pre-term placentae released free fatty acid (FFA) and phospholipid into the incubation medium during incubation at 37 degrees C. Long chain polyunsaturated fatty acids derived from the essential fatty acids were released into the media. The fatty acid profiles of the lipids released during incubation more closely resembled those of fetal plasma than maternal plasma lipids as measured in previous studies. These data are consistent with the view that the equine placenta is a source of both FFA and phospholipid for the fetus and that the placenta may provide long chain polyunsaturated fatty acids for the fetal foal.

The IHR-McCormick Automated Toy Discrimination test--description and initial evaluation

McCormick's Toy Discrimination test allows a skilled audiologist to obtain word discrimination thresholds in quiet from children with mental ages of 2 years and above. A semi-automatic version of the test has been developed and evaluated by testing the hearing of 46 children and five adults. The equipment for the new version of the test both produces the stimuli and scores the responses, thereby reducing the burden on the tester. It is reliable and allows greater sensitivity than the manual test as well as solving problems of standardization and calibration.

Serum amyloid A protein (SAA) in horses: objective measurement of the acute phase response

A sensitive and precise immunoassay for equine serum amyloid A protein (SAA) was established and used to determine, for the first time, the circulating concentration of this protein in health and disease. As in other species, equine SAA was present only at trace levels in healthy animals but behaved as an extremely sensitive and rapidly responding acute phase reactant following most forms of tissue injury, infection and inflammation, objectively reflecting the extent and activity of disease. Measurements of SAA should make a significant contribution to diagnosis and management of viral and bacterial infection in horses, and routine serial assays could provide an objective criterion for monitoring prospectively the general health of horses in training and racing.

The foramen ovale of the foetal and neonatal foal

Hearts from 24 foals were studied; 10 were from foetuses ranging in gestational age from 230 to 322 days and 14 were from newborn and young foals aged between birth and 17 days. The foramen ovale and associated vena caval and atrial structures were examined by scanning electron microscopy. Additional observations were made by light and transmission electron microscopy. A tube-like flap of tissue was observed, extending from the aperture in the caudal vena cava to the lumen of the left atrium. In the younger foetuses, the distal end of this tube was covered with a thread-like network of tissue. In animals nearer to term, the network was replaced by distal fenestrations. Protrusions were seen on the rim of the opening of the tube as it entered the atrium. The role that these may play, together with the significance of cardiac muscle and non-elastic connective tissue in the wall of the tube, were discussed with respect to possible mechanisms of closure of the foramen ovale.

Studies on equine prematurity 3: Insulin secretion in the foal during the perinatal period

The factors influencing beta cell function in the foetal and neonatal foal have been investigated in chronically catheterised foetal foals and in newborn foals delivered either spontaneously at term or by induction at different gestational ages. Insulin was detected in the foetal plasma from as early as 150 days of gestation (term = 340 days) and during the last third of gestation the foetal beta cells responded to exogenous administration of glucose and arginine and to endogenous variations in the glucose level. Insulin secretion by the foetal beta cells was depressed by anaesthesia and surgery. At birth, there was a significant positive correlation between the plasma concentrations of insulin and glucose irrespective of the maturity at birth or type of delivery (r = 0.86, n = 39, P less than 0.01). The slope of this relationship was significantly less than that relating the postoperative foetal concentration but only when delivery was difficult or prolonged was the beta cell sensitivity to glucose completely abolished. At birth, there were no significant differences in the plasma concentrations of insulin or glucose between full term foals delivered spontaneously or by induction. However, the spontaneously delivered foals showed a transient increase in the insulin concentration 15 mins after birth which was not observed in the full term foals delivered by induction. Plasma glucose concentrations were maintained during the 2 h after birth in the absence of sucking in both the induced and the spontaneously delivered full term foals. Premature foals had significantly lower plasma glucose concentrations at birth than full term foals.(ABSTRACT TRUNCATED AT 250 WORDS)