The Structure and Function of the Human Small Intestinal Microbiota: Current Understanding and Future Directions

Name: Work Video:
Duration: 3 min 30 s
Arthur Kastl; Natalie A. Terry; Gary D. Wu; Lindsey Albenberg
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3192, 3979, 4048, 4138, 4206], 'Arumugam': [555, 1645, 2527, 3043, 3272, 3397, 3518, 3597, 3731], 'Sunagawa': [557, 1011], 'Mitreva': [559], 'Tap': [561, 869], 'J.': [562, 572, 622, 624, 857, 870, 908, 910, 922, 933, 974, 982, 1000, 1004, 1026, 1239, 1287, 1289, 1565, 1608, 1640, 1675, 2490, 2522, 2557, 3038, 3073, 3111, 3235, 3267, 3302, 3392, 3427, 3513, 3548, 3592, 3627, 3661, 3726, 3761, 4010, 4056, 4146, 4214], 'Zhu': [563], 'Waller': [565], 'Mende': [567, 865], 'D.R.': [568, 866, 2648], 'Kultima': [569], 'J.R.': [570], 'Martin': [571], 'Kota': [573], 'K.': [574, 894, 989, 1016, 2640, 4042, 4046, 4132, 4136, 4200, 4204], 'Sunyaev': [575], 'S.R.': [576, 3840], 'Weinstock': [577], 'G.M.': [578], 'Bork': [579, 1029, 1651, 2533, 3049, 3278, 3403, 3524, 3603, 3737], 'P.': [580, 1006, 1030, 1200, 1334, 1652, 2266, 2415, 2534, 3050, 3279, 3404, 3525, 3604, 3738, 3815, 3985, 4052, 4142, 4210], 'Genomic': [581], 'variation': [582, 1544, 2868, 2950, 3008, 3172, 3212, 3674], 'landscape': [583], 'microbiome.Nature.': [588, 1036], '2013;': [589, 1594, 1629, 2511, 3132, 3256], '493:': [590], '45-50Crossref': [591], '(374)': [594], '3Yatsunenko': [597], 'Rey': [599], 'F.E.': [600], 'Manary': [601], 'M.J.': [602, 2605, 3850], 'Trehan': [603], 'I.': [604], 'Dominguez-Bello': [605], 'M.G.': [606], 'Contreras': [607], 'Magris': [609], 'Hidalgo': [611], 'G.': [612, 955, 980, 1018, 1024, 1190, 1255, 1293, 2228, 2377, 2703, 2705, 2711, 3848], 'Baldassano': [613], 'R.N.': [614], 'Anokhin': [615], 'A.P.': [616], 'Warner': [619], 'Reeder': [621], 'Kuczynski': [623], 'Caporaso': [625], 'J.G.': [626], 'Lozupone': [627], 'C.A.': [628, 4062, 4152, 4220], 'Lauber': [629], 'C.': [630, 900, 945, 947, 949, 953, 961, 978, 998, 1297, 2701, 3651], 'Clemente': [631], 'J.C.': [632, 2607], 'Knights': [633], 'D.': [634, 862, 916, 1204, 2736], 'Human': [639, 1374, 1725], 'viewed': [642], 'across': [643, 2340, 2825, 3487], 'age': [644], 'geography.Nature.': [646], '2012;': [647, 1676, 2558, 3074, 3303, 3428, 3549, 3628, 3762], '486:': [648], '222-227Crossref': [649], '(2985)': [652], 'Scholar': [654, 724, 776, 829, 1044, 1138, 1440, 1683, 1749, 1788, 1857, 1899, 2047, 2144, 2204, 2333, 2763, 2883, 2965, 3023, 3081, 3139, 3335, 3435, 3556, 3635, 3697, 3769, 3876, 3924, 3965, 4018, 4095, 4185], 'properties': [656], 'less': [666, 1967, 2835], 'characterized,': [668], 'because': [670, 736], 'challenges': [672, 1095], 'sampling': [674, 1097, 1158, 1483], 'segment': [676], 'tract.4Booijink': [680], 'C.C.': [681, 802, 1522, 1648, 2342, 2530, 2846, 2928, 2986, 3046, 3190, 3275, 3400, 3521, 3600, 3734], 'Zoetendal': [682, 803, 919, 1538, 1570, 1614, 2343, 2496, 2862, 2944, 3002, 3117, 3206, 3241, 3387], 'E.G.': [683, 804, 920, 1539, 1571, 1615, 1638, 2344, 2497, 2520, 2863, 2945, 3003, 3036, 3118, 3207, 3242, 3265, 3312, 3390, 3511, 3590, 3724], 'Kleerebezem': [684, 805, 891, 1533, 1572, 1616, 1658, 2345, 2498, 2540, 2857, 2939, 2997, 3056, 3119, 3201, 3243, 3285, 3410, 3531, 3610, 3744], 'de': [686, 807, 927, 963, 1609, 1655, 1834, 2347, 2491, 2537, 3053, 3112, 3236, 3282, 3315, 3407, 3528, 3607, 3741], 'Vos': [687, 808, 928, 1536, 1656, 1835, 2348, 2538, 2860, 2942, 3000, 3054, 3204, 3283, 3316, 3408, 3529, 3608, 3742], 'W.M.': [688, 809, 929, 1537, 1657, 1836, 2349, 2539, 2861, 2943, 3001, 3055, 3205, 3284, 3317, 3409, 3530, 3609, 3743], 'Microbial': [689, 810, 2350], 'intestine:': [695, 816, 2356], 'coupling': [696, 817, 2357], 'diversity': [697, 818, 1259, 1339, 2232, 2271, 2358, 2381, 2420, 3319], 'metagenomics.Future': [699, 820, 2360], 'Microbiol.': [700, 821, 1351, 1432, 1551, 2039, 2109, 2196, 2283, 2325, 2361, 2432, 2474, 2875, 2957, 3015, 3219], '2007;': [701, 822, 1240, 1352, 2284, 2362, 2433], '2:': [702, 823, 2363], '285-295Crossref': [703, 824, 2364], '(83)': [706, 827, 2367], '5Cotter': [709], 'P.D.': [710, 1124], 'Small': [711, 1125, 2743, 4067, 4157, 4225], 'microbiota.Curr': [714, 1128], 'Opin': [715, 1129], 'Gastroenterol.': [716, 1130, 2623, 2757], '2011;': [717, 1037, 1131], '27:': [718, 767, 1132, 3956], '99-105Crossref': [719, 1133], '(29)': [722, 1136], 'principally': [731], 'health,': [735], 'duodenum': [738, 1994, 3938], 'jejunum': [740], 'tasked': [742], 'facilitating': [744], 'majority': [746], 'nutrient': [748, 3578], 'assimilation': [749], 'absorption.6Volk': [751], 'N.': [752, 878, 906, 1010, 2638, 3941, 4044, 4134, 4202], 'Lacy': [753, 3942], 'Anatomy': [755, 3944], 'physiology': [757, 3946], 'bowel.Gastrointest': [761, 3950], 'Endosc': [762, 3951], 'Clin': [763, 3952], 'N': [764, 3953], 'Am.': [765, 3954], '2017;': [766, 1781, 1893, 3955], '1-13Abstract': [768, 3957], 'Full': [769, 771, 1515, 2139, 2587, 2670, 2672, 3958, 3960, 4086, 4088, 4176, 4178], 'Text': [770, 772, 1516, 2140, 2588, 2671, 2673, 3959, 3961, 4087, 4089, 4177, 4179], 'PDF': [773, 1517, 2141, 2589, 2674, 3962, 4090, 4180], 'In': [777, 2048], 'addition,': [778, 2049], 'there': [779, 3096], 'significant': [781, 2968], 'contact': [782], 'between': [783, 2794, 2975], 'food': [784, 1946, 3718], 'substrate': [785, 1947], 'commensal': [787], 'bacteria': [788, 2777], 'creating': [793, 4109], 'environment': [795, 1928, 3351], 'rich': [796], 'microbe–microbe': [798], 'host–microbe': [800, 2806], 'interactions.4Booijink': [801], 'concepts': [832], 'analysis.7Arumugam': [854], 'Raes': [856, 1639, 2521, 3037, 3266, 3391, 3512, 3591, 3725], 'Pelletier': [858], 'E.': [859, 918, 967, 991, 1020, 1208, 2707], 'Le': [860, 987], 'Paslier': [861], 'Yamada': [863], 'Fernandes': [867], 'G.R.': [868], 'Bruls': [871], 'Batto': [873], 'J.M.': [874], 'Bertalan': [875], 'Borruel': [877], 'Casellas': [879], 'F.': [880, 898, 924, 939, 969, 1833, 2713, 3659, 3813, 3846, 3991], 'Fernandez': [881], 'L.': [882, 884, 1295, 1491, 1493, 2602, 2636, 3817], 'Gautier': [883], 'Hansen': [885], 'Hattori': [887], 'Hayashi': [889], 'Kurokawa': [893], 'Leclerc': [895], 'Levenez': [897], 'Manichanh': [899], 'Nielsen': [901, 903], 'H.B.': [902], 'Pons': [905], 'Poulain': [907], 'Qin': [909], 'Sicheritz-Ponten': [911], 'Tims': [913], 'Torrents': [915], 'Ugarte': [917], 'Wang': [921], 'Guarner': [923], 'Pedersen': [925], 'O.': [926, 984, 1367, 1606, 1718, 2488, 3109, 3233], 'Brunak': [930], 'Dore': [932], 'Meta': [934], 'H.I.T.C.': [935], 'Antolin': [936], 'Artiguenave': [938], 'Blottiere': [940], 'H.M.': [941], 'Almeida': [942], 'Brechot': [944], 'Cara': [946], 'Chervaux': [948], 'Cultrone': [950], 'Delorme': [952], 'Denariaz': [954], 'Dervyn': [956], 'Foerstner': [958], 'K.U.': [959], 'Friss': [960], 'van': [962, 972, 1641, 2523, 3039, 3268, 3393, 3514, 3593, 3727], 'Guchte': [964], 'Guedon': [966], 'Haimet': [968], 'Huber': [970], 'W.': [971], 'Hylckama-Vlieg': [973], 'Jamet': [975], 'Juste': [977], 'Kaci': [979], 'Knol': [981], 'Lakhdari': [983], 'Layec': [985], 'Roux': [988], 'Maguin': [990], 'Merieux': [992], 'Melo': [994], 'Minardi': [995], "M'Rini": [997], 'Muller': [999], 'Oozeer': [1001], 'Parkhill': [1003], 'Renault': [1005], 'Rescigno': [1007], 'Sanchez': [1009], 'Torrejon': [1013], 'Turner': [1015], 'Vandemeulebrouck': [1017], 'Varela': [1019], 'Winogradsky': [1021], 'Y.': [1022, 1206, 1408, 2015, 2085, 2172, 2301, 2450, 2594], 'Zeller': [1023], 'Weissenbach': [1025], 'Ehrlich': [1027], 'S.D.': [1028], 'Enterotypes': [1031], '473:': [1038], '174-180Crossref': [1039], '(2958)': [1042], 'properties,': [1064], 'methodologic': [1065, 1752], 'challenges,': [1066], 'roles': [1069], 'conditions.': [1077, 1982], 'distinguishing': [1079], 'feature': [1080], 'compared': [1085, 3447, 3973], 'colon': [1088, 3639], 'inaccessibility,': [1092], 'poses': [1094], 'experimental': [1099], 'design.': [1100], 'Although': [1101, 1684], 'samples': [1103, 1697, 3439], 'most': [1104], 'commonly': [1105, 2207], 'collected': [1107, 3436], 'stool': [1114], 'accurately': [1116], 'represents': [1117], 'distal': [1119, 2000, 2069], 'portions': [1120], 'gut,5Cotter': [1123], 'leaving': [1139], 'hidden': [1145], 'from': [1146, 1180, 1447, 1485, 1580, 1988, 2066, 3092, 3490], 'view.': [1147], 'Studies': [1148, 1498], 'involved': [1156, 4121], 'invasive': [1157, 1222], 'procedures': [1159], 'esophagoduodenogastroscopy': [1161], 'nasoduodenal': [1163], 'catheters,': [1164], 'while': [1165, 4104], 'other': [1166], 'sampled': [1169], 'ileal': [1170, 1215, 1312, 1549, 2873, 2905, 2955, 3013, 3217, 3491], 'mucosa': [1171, 1216, 2660], 'obtained': [1172], 'during': [1173], 'colonoscopy,': [1174], 'resection,': [1176], 'small-bowel': [1177], 'transplantation,': [1178], 'or': [1179, 1451, 1467], 'sudden': [1181], 'death': [1182], 'victims.8Baumgart': [1183], 'Dogan': [1185], 'Rishniw': [1187], 'Weitzman': [1189], 'Bosworth': [1191], 'Yantiss': [1193], 'Orsi': [1195], 'R.H.': [1196], 'Wiedmann': [1197], 'McDonough': [1199], 'Kim': [1201], 'S.G.': [1202], 'Berg': [1203], 'Schukken': [1205], 'Scherl': [1207], 'Simpson': [1209], 'K.W.': [1210], 'Culture': [1211], 'independent': [1212], 'analysis': [1213, 1410, 1576, 2017, 2087, 2174, 2303, 2452, 3322, 3558, 3819, 3854], 'reveals': [1217, 1585], 'selective': [1219], 'increase': [1220, 1987], 'Escherichia': [1223], 'coli': [1224], 'novel': [1226], 'phylogeny': [1227], 'depletion': [1230], 'Clostridiales': [1232, 2798], "Crohn's": [1234, 1313], 'involving': [1236], 'ileum.ISME': [1238], '1:': [1241], '403-418Crossref': [1242], '(359)': [1245], '9Wang': [1248, 2370], 'Ahrne': [1250, 2223, 2372], 'Jeppsson': [1252, 2225, 2374], 'Molin': [1254, 2227, 2376], 'Comparison': [1256, 2229, 2378], 'along': [1260, 2233, 2382], 'direct': [1266, 2239, 2388, 2651], 'cloning': [1267, 2240, 2389], 'sequencing': [1269, 2242, 2391, 3145], '16S': [1271, 1421, 2028, 2098, 2185, 2244, 2314, 2393, 2463, 3141], 'rRNA': [1272, 1422, 2029, 2099, 2186, 2245, 2315, 2394, 2464], 'genes.FEMS': [1273, 2246, 2395], 'Microbiol': [1274, 1627, 2247, 2396, 2509, 3130, 3254], 'Ecol.': [1275, 1628, 2248, 2397, 2510, 3131, 3255], '2005;': [1276, 1433, 2040, 2110, 2197, 2249, 2326, 2398, 2475], '54:': [1277, 1434, 2041, 2111, 2198, 2250, 2327, 2399, 2476], '219-231Crossref': [1278, 2251, 2400], '(208)': [1281, 2254, 2403], '10Willing': [1284], 'Halfvarson': [1286], 'Dicksved': [1288], 'Rosenquist': [1290], 'Jarnerot': [1292], 'Engstrand': [1294, 3816], 'Tysk': [1296], 'Jansson': [1298], 'J.K.': [1299], 'Twin': [1300], 'reveal': [1302], 'specific': [1303, 2791], 'imbalances': [1304], 'mucosa-associated': [1307], 'patients': [1310, 2615, 2892], 'disease.Inflamm': [1314], 'Bowel': [1315], 'Dis.': [1316], '15:': [1318], '653-660Crossref': [1319], '(306)': [1322], '11Ahmed': [1325, 2257, 2406], 'Macfarlane': [1327, 1335, 2259, 2267, 2408, 2416], 'G.T.': [1328, 2260, 2409], 'Fite': [1329, 2261, 2410], 'McBain': [1331, 2263, 2412], 'A.J.': [1332, 2264, 2413], 'Gilbert': [1333, 2265, 2414], 'Mucosa-associated': [1337, 2269, 2418], 'relation': [1341, 2273, 2422], 'terminal': [1344, 1426, 2033, 2103, 2190, 2276, 2319, 2425, 2468], 'ileum': [1345, 2277, 2426], 'colonic': [1347, 1418, 2025, 2095, 2182, 2279, 2311, 2428, 2460], 'biopsy': [1348, 2280, 2429], 'samples.Appl': [1349, 2281, 2430], 'Environ': [1350, 2282, 2431], '73:': [1353, 2285, 2434], '7435-7442Crossref': [1354, 2286, 2435], '(137)': [1357, 2289, 2438], '12Hartman': [1360], 'A.L.': [1361, 1712], 'Lough': [1362, 1713], 'D.M.': [1363, 1714], 'Barupal': [1364, 1715], 'D.K.': [1365, 1716], 'Fiehn': [1366, 1717], 'Fishbein': [1368, 1719], 'Zasloff': [1370, 1721], 'Eisen': [1372, 1723], 'J.A.': [1373, 1724], 'adopts': [1377, 1728], 'alternative': [1379, 1730], 'state': [1380, 1731, 1915], 'following': [1381, 1732], 'transplantation.Proc': [1384, 1735], 'Natl': [1385, 1736, 3684, 3863, 3911], 'Acad': [1386, 1737, 3685, 3864, 3912], 'Sci': [1387, 1738, 3686, 3865, 3913], 'U': [1388, 1739, 3687, 3866, 3914], 'S': [1389, 1740, 3688, 3867, 3915], '106:': [1392, 1743], '17187-17192Crossref': [1393, 1744], '(182)': [1396, 1747], '13Hayashi': [1399, 2292, 2441], 'H.': [1400, 1532, 2007, 2077, 2119, 2164, 2293, 2442, 2567, 2856, 2938, 2996, 3200, 3811], 'Takahashi': [1401, 2008, 2078, 2165, 2294, 2443], 'Nishi': [1403, 2010, 2080, 2167, 2296, 2445], 'Sakamoto': [1405, 2012, 2082, 2169, 2298, 2447], 'Benno': [1407, 2014, 2084, 2171, 2300, 2449], 'Molecular': [1409, 2016, 2086, 2173, 2302, 2451, 3853], 'jejunal,': [1412, 2019, 2089, 2176, 2305, 2454], 'ileal,': [1413, 2020, 2090, 2177, 2306, 2455], 'caecal': [1414, 2021, 2091, 2178, 2307, 2456], 'recto-sigmoidal': [1416, 2023, 2093, 2180, 2309, 2458], 'using': [1420, 2027, 2097, 2184, 2313, 2462], 'gene': [1423, 2030, 2100, 2187, 2316, 2465, 3144], 'libraries': [1424, 2031, 2101, 2188, 2317, 2466], 'restriction': [1427, 2034, 2104, 2191, 2320, 2469], 'fragment': [1428, 2035, 2105, 2192, 2321, 2470], 'length': [1429, 2036, 2106, 2193, 2322, 2471], 'polymorphism.J': [1430, 2037, 2107, 2194, 2323, 2472], 'Med': [1431, 2038, 2108, 2195, 2324, 2473], '1093-1101Crossref': [1435, 2042, 2112, 2199, 2328, 2477], '(196)': [1438, 2045, 2115, 2202, 2331, 2480], 'These': [1441, 2145], 'methodologies': [1442, 2772], 'subject': [1444], 'contamination': [1446], 'oropharyngeal': [1449], 'cavity': [1450], 'colon,': [1452, 2839], 'limit': [1455], 'ability': [1457], 'study': [1459, 2889, 3034, 3084], 'function': [1464, 3382, 3504], 'time': [1466, 3166], 'change': [1469], '(eg,': [1470, 3780], 'diet).': [1471], 'Some': [1472], 'enrolled': [1475], 'participants': [1476], 'ileostomies,': [1478], 'affords': [1480], 'longitudinal': [1481], 'effluent': [1482, 2906, 3438], 'directly': [1484], 'intestine.14Gorbach': [1488], 'S.L.': [1489, 2687], 'Nahas': [1490], 'Weinstein': [1492], 'Levitan': [1494], 'Patterson': [1496], 'J.F.': [1497, 4054, 4144, 4212], 'microflora.': [1501], 'IV.': [1502], 'microflora': [1504, 2689], 'ileostomy': [1506, 3437], 'effluent:': [1507], 'ecology.Gastroenterology.': [1511], '1967;': [1512], '53:': [1513], '874-880Abstract': [1514], '15Booijink': [1521], 'El-Aidy': [1523, 2847, 2929, 2987, 3191], 'Rajilic-Stojanovic': [1525, 2849, 2931, 2989, 3193, 3313], 'Heilig': [1527, 2851, 2933, 2991, 3195], 'H.G.': [1528, 2852, 2934, 2992, 3196], 'Troost': [1529, 1649, 2531, 2853, 2935, 2993, 3047, 3197, 3276, 3401, 3522, 3601, 3735], 'F.J.': [1530, 1650, 2532, 2854, 2936, 2994, 3048, 3198, 3277, 3402, 3523, 3602, 3736], 'Smidt': [1531, 2855, 2937, 2995, 3199], 'De': [1535, 2859, 2941, 2999, 3203], 'High': [1540, 2864, 2946, 3004, 3208], 'inter-individual': [1543, 2867, 2949, 3007, 3211], 'detected': [1545, 2869, 2951, 3009, 3213], 'microbiota.Environ': [1550, 2874, 2956, 3014, 3218], '2010;': [1552, 2876, 2958, 3016, 3220, 3690, 4011], '12:': [1553, 2877, 2959, 3017, 3221], '3213-3227Crossref': [1554, 2878, 2960, 3018, 3222], '(121)': [1557, 2881, 2963, 3021, 3225], '16Van': [1560], 'den': [1561, 1602, 1642, 2484, 2524, 3040, 3105, 3229, 3269, 3394, 3515, 3594, 3728], 'Bogert': [1562, 1603, 1643, 2485, 2525, 3041, 3106, 3230, 3270, 3395, 3516, 3595, 3729], 'Boekhorst': [1564, 1607, 2489, 3110, 3234], 'Herrmann': [1566], 'Smid': [1568, 1612, 2494, 3115, 3239], 'E.J.': [1569, 1613, 2495, 3116, 3240], 'Comparative': [1574, 3818], 'genomics': [1575], 'Streptococcus': [1578, 1623, 2505, 2921, 3088, 3126, 3151, 3250, 3788, 3901], 'isolates': [1579, 3162], 'their': [1586, 2888, 3882], 'adaptation': [1587], 'highly': [1590, 3566], 'dynamic': [1591], 'ecosystem.PLoS': [1592], 'One.': [1593, 3827], '8e83418Crossref': [1595], '(31)': [1598], '17van': [1601, 2483, 3228], 'Erkus': [1605, 2487, 3108, 3232], 'Goffau': [1610, 2492, 3113, 3237], 'Diversity': [1618, 2500, 3121, 3245], 'Veillonella': [1625, 2507, 2926, 3090, 3128, 3154, 3252, 3790], 'populations.FEMS': [1626, 2508, 3129, 3253], '85:': [1630, 2512, 3133, 3257], '376-388Crossref': [1631, 2513, 3134, 3258], '(67)': [1634, 2516, 3137, 3261], '18Zoetendal': [1637, 2519, 3264], 'Booijink': [1647, 2529, 2843, 3045, 3274, 3399, 3520, 3599, 3733], 'Wels': [1653, 2535, 3051, 3280, 3405, 3526, 3605, 3739], 'driven': [1666, 2548, 3064, 3293, 3418, 3539, 3618, 3752], 'rapid': [1668, 2550, 3066, 3295, 3420, 3541, 3620, 3754], 'uptake': [1669, 2551, 3067, 3296, 3421, 3542, 3621, 3755], 'conversion': [1671, 2553, 3069, 3298, 3423, 3544, 3623, 3757], 'simple': [1673, 2555, 3071, 3300, 3425, 3546, 3585, 3625, 3759], 'carbohydrates.ISME': [1674, 2556, 3072, 3301, 3426, 3547, 3626, 3760], '6:': [1677, 2559, 3075, 3304, 3429, 3550, 3629, 3763], '1415-1426Crossref': [1678, 2560, 3076, 3305, 3430, 3551, 3630, 3764], '(250)': [1681, 2563, 3079, 3308, 3433, 3554, 3633, 3767], 'may': [1686, 1707, 3339], 'methodologically': [1688], 'advantageous,': [1689], 'it': [1690], 'recognize': [1694], 'ostomy': [1696], 'exposed': [1699], 'skin': [1702], 'external': [1704], 'environment,': [1705], 'impact': [1708], 'community.12Hartman': [1711], 'An': [1750], 'additional': [1751], 'challenge': [1753, 1901], 'investigations': [1756], 'moving': [1758, 1902], 'beyond': [1759, 1774], 'correlations': [1760], 'associations,': [1762], 'toward': [1763], 'pinpointing': [1765], 'microbe–phenotype': [1766], 'relationships': [1767], 'causality.19Surana': [1769], 'N.K.': [1770], 'Kasper': [1771], 'D.L.': [1772], 'Moving': [1773], 'microbiome-wide': [1775], 'associations': [1776], 'causal': [1778], 'microbe': [1779], 'identification.Nature.': [1780], '552:': [1782], '244-247Crossref': [1783], '(60)': [1786, 1855], 'Thus,': [1789], 'models': [1791, 1838], 'germ-free': [1793], '(GF),': [1794], 'gnotobiotic,': [1795], 'conventionalized': [1797], 'mice': [1798, 3967, 3975, 3998, 4035], 'continue': [1799], 'valuable': [1802], 'mechanistic': [1804], 'exploration,': [1805], 'although': [1806], 'major': [1807, 2819, 3346], 'differences': [1808, 2766], 'beings': [1811], 'size,': [1816], 'metabolic': [1817, 2792, 3375, 3563, 3883], 'rate,': [1818], 'habits,': [1820], 'spatiotemporal': [1822], 'structures': [1824], 'need': [1825, 1975], 'considered': [1828], 'carefully': [1829], 'when': [1830, 1907, 4033, 4187], 'extrapolating': [1831], 'data.20Hugenholtz': [1832], 'Mouse': [1837], 'research:': [1843], 'critical': [1845], 'evaluation.Cell': [1846], 'Mol': [1847], 'Life': [1848], 'Sci.': [1849], '2018;': [1850, 4082, 4172], '75:': [1851], '149-160Crossref': [1852], 'term': [1859], 'used': [1862], 'pervasively': [1863], 'refer': [1868], 'imbalance,': [1871], 'serves': [1873], 'communication': [1877, 3899], 'tool': [1878], 'without': [1879], 'establishment': [1881], 'cause': [1883], 'effect.21Hooks': [1885], 'K.B.': [1886], "O'Malley": [1887], 'M.A.': [1888, 2121, 2569], 'Dysbiosis': [1889], 'discontents.MBio.': [1892], '8Crossref': [1894], '(15)': [1897], 'forward': [1903], 'establish': [1906], 'how': [1909], 'contributes': [1911], 'opposed': [1917], 'presence': [1920], 'alone.': [1921], 'harsh': [1927], 'life': [1931], 'owing': [1932, 2764], 'short': [1934], 'transit': [1935, 2003], 'time,': [1936], 'influx': [1938], 'enzymes': [1941], 'bile,': [1943], 'intermittent': [1945], 'delivery.': [1948], 'As': [1949], 'result,': [1951], 'region': [1957], 'lower': [1964], 'biomass,': [1965], 'diverse,': [1968], 'but': [1969, 2334, 2840, 3797], 'dynamic,': [1972], 'given': [1973], 'respond': [1977], 'changing': [1980], 'luminal': [1981, 2750, 3350], 'Generally': [1983], 'speaking,': [1984], '104–5': [1990], 'CFU/mL': [1991, 1997], '107–8': [1996], 'ileum,': [2001], 'where': [2002], 'slows': [2004], '(Figure': [2005, 2773, 3783], '1).13Hayashi': [2006], 'proportion': [2051], 'gram-positive': [2053], 'gram-negative,': [2055], 'facultative': [2059, 2161], 'anaerobic': [2060, 2162], 'strict': [2062], 'anaerobic,': [2063], 'increases': [2065], 'proximal': [2067, 2158], 'segments': [2070], 'colon.13Hayashi': [2076], '22Thadepalli': [2118, 2566], 'Lou': [2120, 2568], 'Bach': [2122, 2570], 'V.T.': [2123, 2571], 'Matsui': [2124, 2572], 'T.K.': [2125, 2573], 'Mandal': [2126, 2574], 'A.K.': [2127, 2575], 'Microflora': [2128, 2576], 'intestine.Am': [2133, 2581], 'J': [2134, 2582, 2622, 2756], 'Surg.': [2135, 2583], '1979;': [2136, 2584], '138:': [2137, 2585], '845-850Abstract': [2138, 2586], 'changes': [2146], 'thought': [2148], 'secondary,': [2151], 'part,': [2153], 'oxygen': [2155], 'use': [2156], 'aerobic': [2159], 'communities.13Hayashi': [2163], 'Bacterial': [2205, 2608], 'genera': [2206, 2778], 'found': [2208, 2776], 'include': [2213], 'Lactobacillus,': [2214], 'Clostridium,': [2215], 'Staphylococcus,': [2216], 'Streptococcus,': [2217, 2795, 3496], 'Bacteroides,': [2219, 4108], 'among': [2220], 'others,9Wang': [2221], 'taxonomic': [2335], 'classification': [2336], 'has': [2337, 2822, 3027], 'inconsistent': [2339], 'studies4Booijink': [2341], '23Bouhnik': [2593], 'Alain': [2595], 'Attar': [2597], 'Flourie': [2599], 'Raskine': [2601], 'Sanson-Le': [2603], 'Pors': [2604], 'Rambaud': [2606], 'contaminating': [2610], 'upper': [2612], 'overgrowth': [2620, 2716, 2751], 'syndrome.Am': [2621], '1999;': [2624], '94:': [2625], '1327-1331Crossref': [2626], '(125)': [2629], '24Ivanov': [2632], 'II,': [2633], 'Frutos': [2634], 'Rde': [2635], 'Manel': [2637], 'Yoshinaga': [2639], 'Rifkin': [2641], 'D.B.': [2642], 'Sartor': [2643], 'R.B.': [2644], 'Finlay': [2645], 'B.B.': [2646], 'Littman': [2647], 'Specific': [2649], 'differentiation': [2653], 'IL-17-producing': [2655], 'T-helper': [2656], 'cells': [2657], 'intestine.Cell': [2664], 'Host': [2665, 4080, 4170], 'Microbe.': [2666, 4081, 4171], '2008;': [2667, 3328, 3828], '4:': [2668], '337-349Abstract': [2669], '(970)': [2677], '25Nichols': [2680], 'R.L.': [2681], 'Condon': [2682], 'Bentley': [2684], 'D.W.': [2685], 'Gorbach': [2686], 'Ileal': [2688], 'surgical': [2691], 'patients.J': [2692], 'Urol.': [2693], '1971;': [2694], '105:': [2695], '351-353Crossref': [2696], '26Pignata': [2700], 'Budillon': [2702], 'Monaco': [2704], 'Nani': [2706], 'Cuomo': [2708], 'Parrilli': [2710], 'Ciccimarra': [2712], 'Jejunal': [2714], 'permeability': [2719], 'children': [2721], 'immunodeficiency': [2723], 'syndromes.Gut.': [2724], '1990;': [2725], '31:': [2726], '879-882Crossref': [2727], '27Riordan': [2731], 'S.M.': [2732], 'McIver': [2733], 'C.J.': [2734, 3995], 'Wakefield': [2735], 'Duncombe': [2737], 'V.M.': [2738], 'Thomas': [2739], 'M.C.': [2740], 'Bolin': [2741], 'T.D.': [2742], 'mucosal': [2745], 'immunity': [2746], 'morphometry': [2748], 'indigenous': [2753], 'flora.Am': [2755], '2001;': [2758], '96:': [2759], '494-500Crossref': [2760], 'analytic': [2771], '2).Figure': [2774], '2Commonly': [2775], 'brief': [2785], 'overview': [2786], 'interaction': [2793, 3884], 'Veillonella,': [2796, 3781], 'highlighted': [2800, 2884, 3094], 'show': [2802, 3441], 'example': [2804], 'interactions.View': [2809], 'Large': [2810], 'Image': [2811], 'Figure': [2812], 'ViewerDownload': [2813], 'Hi-res': [2814], 'image': [2815], 'Download': [2816], '(PPT)': [2817], 'concept': [2820, 2886], 'shown': [2824], 'phylogenetically': [2834], 'diverse': [2836], 'dynamic.': [2842], 'et': [2844, 3388], 'al15Booijink': [2845], '7': [2891, 3160], 'inflammatory': [2894], '(IBD),': [2897], 'whom': [2900], 'had': [2901, 2907], 'ileostomies.': [2902], 'There,': [2903, 3140], 'higher': [2909], 'abundance': [2911, 4101], 'within': [2914, 3163], 'orders': [2916], 'Lactobacillales': [2917], 'Clostridiales,': [2919], 'mainly': [2920], 'bovis–related': [2922], 'species,': [2923], 'group.15Booijink': [2927], 'were': [2967, 3485], 'interindividual': [2969], 'differences,': [2970], 'intraindividual': [2972], 'fluxes,': [2974], 'morning': [2976], 'afternoon': [2978], 'profiles': [2979], 'over': [2980, 3030], 'period': [2982], '9–28': [2984], 'days,15Booijink': [2985], 'notion': [3025], 'corroborated': [3029], 'much': [3032], 'longer': [3033], 'period.18Zoetendal': [3035], 'separate': [3083], 'looking': [3085], 'specifically': [3086], 'at': [3087], 'ileostomies': [3093], 'incredible': [3098], 'strain-level': [3099], 'richness': [3100], 'intestine.17van': [3104], 'ribosomal': [3142], 'RNA': [3143], 'showed': [3146, 3559], 'total': [3148], '160': [3150], '37': [3153], 'isolates,': [3155], 'variance': [3158], 'predominant': [3161], '72-hour': [3165], 'frame.': [3167], 'theme': [3169], 'stark': [3180], 'contrast': [3181], 'relatively': [3184], 'stable': [3185], 'colon,15Booijink': [3189], '28Zoetendal': [3311], 'High-throughput': [3318], 'gastrointestinal': [3325], 'microbiota.Gut.': [3327], '57:': [3329], '1605-1615Crossref': [3330], '(422)': [3333], 'influences': [3338], 'drive': [3340], 'some': [3341], 'findings.': [3344], 'contributor': [3347], 'host': [3354, 4071, 4161], 'diet,': [3355], 'examined': [3359], 'isolated': [3363], 'macronutrients': [3364], 'resulting': [3374], 'profiles.': [3376], 'Carbohydrate': [3377], 'fermentation': [3378, 3771], 'microbiota.': [3386], 'al18Zoetendal': [3389], 'metagenome,': [3446, 3451], 'significantly': [3453], 'enriched': [3455, 3700], 'genes': [3457, 3702, 4120], 'related': [3458], 'carbohydrate': [3460, 3499], 'metabolism.': [3461], 'Processes': [3462], 'such': [3463, 3480], 'sugar': [3465], 'phosphotransferase': [3466], 'systems,': [3467], 'pentose': [3469], 'phosphate': [3470], 'pathway,': [3471], 'lactate': [3472], 'propionate': [3474], 'fermentation,': [3475], 'cofactors': [3479], 'cobalamin': [3482], 'biotin,': [3484], 'encoded': [3486], 'taxa': [3489], 'effluent,': [3492], 'particular': [3495], 'arguing': [3497], 'metabolism': [3500], 'central': [3503, 3935], 'collective': [3507], 'microbiota.18Zoetendal': [3510], 'Metatranscriptomic': [3557], 'earlier-mentioned': [3562], 'processes': [3564, 3932], 'active,': [3567], 'adapt': [3574], 'availability': [3579], 'lumen,': [3582], 'metabolizing': [3584], 'maintenance.18Zoetendal': [3589], 'This': [3636], 'contrasts': [3637], 'communities,': [3640], 'equipped': [3644], 'degrade': [3646], 'carbohydrates.29Turnbaugh': [3648], 'Quince': [3650], 'Faith': [3652], 'J.J.': [3653], 'McHardy': [3654], 'Niazi': [3658], 'Organismal,': [3670], 'genetic,': [3671], 'transcriptional': [3673], 'deeply': [3677], 'sequenced': [3678], 'microbiomes': [3680], 'identical': [3682], 'twins.Proc': [3683], '107:': [3691], '7503-7508Crossref': [3692], '(282)': [3695], 'Streptococci': [3698], 'energy': [3704], 'generation,': [3705], 'suggested': [3708], 'make': [3710], 'considerable': [3712], 'contribution': [3713], 'primary': [3715], 'digestion': [3716, 3926], 'components': [3719], 'bowel,18Zoetendal': [3723], 'products': [3772], 'support': [3774], 'growth': [3776], 'secondary': [3778], 'fermenters': [3779], 'Clostridium)': [3782], '2).': [3784], 'Indeed,': [3785, 4186], 'cohabitation': [3786], 'occurs': [3791], 'not': [3792], 'only': [3793], 'stomach,': [3801], 'esophagus,': [3802], 'throat,': [3803], 'oral': [3805], 'cavity,30Andersson': [3806], 'A.F.': [3807], 'Lindberg': [3808], 'Jakobsson': [3810], 'Backhed': [3812], 'Nyren': [3814], 'barcoded': [3825], 'pyrosequencing.PLoS': [3826], '3e2836Crossref': [3829], '(621)': [3832], '31Bik': [3835], 'E.M.': [3836], 'Eckburg': [3837], 'P.B.': [3838], 'Gill': [3839], 'Nelson': [3841], 'K.E.': [3842], 'Purdom': [3843], 'E.A.': [3844], 'Francois': [3845], 'Perez-Perez': [3847], 'Blaser': [3849], 'Relman': [3851], 'D.A.': [3852], 'stomach.Proc': [3862], '2006;': [3869], '103:': [3870], '732-737Crossref': [3871], '(562)': [3874], 'likely': [3879], 'attributed': [3880], 'surrounding': [3885], 'lactic': [3886], 'acid': [3887], 'production': [3888], 'utilization,': [3890], 'respectively.32Egland': [3891], 'P.G.': [3892], 'Palmer': [3893], 'Jr.,': [3894], 'R.J.': [3895], 'Kolenbrander': [3896], 'P.E.': [3897], 'Interspecies': [3898], 'gordonii-Veillonella': [3902], 'atypica': [3903], 'biofilms:': [3904], 'signaling': [3905], 'flow': [3907], 'requires': [3909], 'juxtaposition.Proc': [3910], '2004;': [3917], '101': [3918], '(16917–1622)Crossref': [3919], '(139)': [3922], 'Lipid': [3925], 'absorption': [3928, 4198], 'jejunum.6Volk': [3940], 'GF': [3966, 4195], 'increased': [3969], 'lipid': [3971, 4024, 4126, 4197], 'levels': [3972], 'conventional': [3977], 'housing,33Rabot': [3978], 'Membrez': [3980], 'Bruneau': [3982], 'Gerard': [3984], 'Harach': [3986], 'Moser': [3988], 'Raymond': [3990], 'Mansourian': [3992], 'Chou': [3994], 'Germ-free': [3996], 'C57BL/6J': [3997], 'resistant': [4000], 'high-fat-diet-induced': [4002], 'insulin': [4003], 'resistance': [4004], 'altered': [4007], 'cholesterol': [4008], 'metabolism.FASEB': [4009], '24:': [4012], '4948-4959Crossref': [4013], '(299)': [4016], 'positing': [4019], 'modulates': [4023], 'physiology.': [4026], 'Furthermore,': [4027], 'differ': [4032], 'comparing': [4034], 'low-fat': [4037], 'high-fat': [4039], '(HF)': [4040], 'diets.34Martinez-Guryn': [4041], 'Hubert': [4043, 4133, 4201], 'Frazier': [4045, 4135, 4203], 'Urlass': [4047, 4137, 4205], 'Musch': [4049, 4139, 4207], 'M.W.': [4050, 4140, 4208], 'Ojeda': [4051, 4141, 4209], 'Pierre': [4053, 4143, 4211], 'Miyoshi': [4055, 4145, 4213], 'Sontag': [4057, 4147, 4215], 'T.J.': [4058, 4148, 4216], 'Cham': [4059, 4149, 4217], 'C.M.': [4060, 4150, 4218], 'Reardon': [4061, 4151, 4219], 'Leone': [4063, 4153, 4221], 'V.': [4064, 4154, 4222], 'Chang': [4065, 4155, 4223], 'E.B.': [4066, 4156, 4224], 'regulate': [4070, 4160], 'absorptive': [4074, 4164], 'adaptive': [4075, 4165], 'responses': [4076, 4166], 'lipids.Cell': [4079, 4169], '23:': [4083, 4173], '458-469': [4084, 4174], 'e5Abstract': [4085, 4175], '(54)': [4093, 4183], 'HF': [4097, 4189], 'diet': [4098, 4190], 'induces': [4099], 'Clostridia,': [4103], 'decreasing': [4105], 'Bifidobacteria': [4106], 'genetic': [4112], 'profile': [4113], 'enhanced': [4116], 'capacity': [4117], 'inducing': [4119], 'epithelial': [4125], 'transport': [4127], 'pancreatic': [4129], 'cholecystokinin': [4130], 'signaling.34Martinez-Guryn': [4131], 'was': [4192], 'transplanted': [4193], 'into': [4194], 'mice,': [4196], 'improved.34Martinez-Guryn': [4199]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2963848324', 'counts_by_year': [{'year': 2024, 'cited_by_count': 55}, {'year': 2023, 'cited_by_count': 74}, {'year': 2022, 'cited_by_count': 50}, {'year': 2021, 'cited_by_count': 57}, {'year': 2020, 'cited_by_count': 23}, {'year': 2019, 'cited_by_count': 1}], 'updated_date': '2024-12-31T00:53:11.085423', 'created_date': '2019-07-30'}
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