Deciphering microbial interactions in synthetic human gut microbiome communities

Name: Work Video:
Duration: 3 min 30 s
Ophelia S. Venturelli; Alex Carr; Garth Fisher; Ryan H. Hsu; Rebecca Lau; Benjamin P. Bowen; Susan Hromada; Trent R. Northen; Adam P. Arkin
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'multi-species': [737, 875, 1847], 'community': [738, 865, 876, 946, 1069, 1134, 1264, 1391, 1492, 1515, 1530, 1546, 1553, 1599, 1666, 1673, 1718, 1831, 1879, 1887, 2502, 2506, 2693, 2926, 2973, 3026, 3343, 3388, 3509, 3728, 3774, 3805, 3889, 3931, 3962, 4106], 'dynamics,': [739], 'as': [740, 967, 1064, 1214, 1303, 1447, 2477, 2517, 2578, 3113, 3132, 3394], 'opposed': [741], 'higher-order': [743, 1511], 'interactions.': [744, 758, 833, 1709, 1745, 1794, 1819, 3997], 'inferred': [746, 3621, 4029, 4067], 'network': [748, 1539, 3574, 3584, 4032], 'exhibits': [749, 1201], 'high': [751, 1702, 2853], 'proportion': [752, 1703, 2101], 'negative': [754, 778, 787, 800, 1404, 1455, 1705, 1729, 1754, 1793, 1818, 2224, 3281, 3635, 3677, 3703, 3707, 3713, 3920, 3996, 4086], 'frequent': [756, 1707, 3907], 'positive': [757, 776, 1402, 1708, 1743, 1752, 1816, 2222, 3286, 3711, 3790, 3816, 3841, 3918, 4088, 4102], 'Ecological': [759, 921, 1521], 'responsive': [762, 1715, 3875], 'recipient': [763, 3787], 'species': [764, 808, 846, 885, 1083, 1713, 1758, 1907, 1965, 2203, 2514, 2757, 2779, 2831, 2837, 2894, 2901, 2904, 2940, 2953, 2968, 3055, 3058, 3061, 3143, 3184, 3197, 3200, 3204, 3207, 3578, 3616, 3693, 3716, 3725, 4154, 4171], 'were': [765, 1682, 1720, 1777, 1790, 1800, 2065, 2092, 2122, 2161, 2193, 2395, 2431, 2670, 2695, 2824, 2912, 2914, 2928, 3022, 3050, 3328, 3452, 3634, 3699, 3978, 4052], 'discovered': [766], 'network.': [769, 892, 1724], 'Our': [770, 1698, 1765, 2628, 3967], 'model': [771, 903, 1631, 1663, 1689, 1699, 1763, 1766, 1885, 2541, 2629, 3125, 3233, 3272, 3340, 3367, 3400, 3493, 3500, 3518, 3554, 3732, 3826, 3937], 'demonstrated': [772, 3073], 'prevalent': [775, 1747, 1904], 'interaction': [779, 3267, 3290, 3304, 3320, 3421, 3563, 3592, 3625, 3817, 4089, 4113], 'topology': [780], 'enables': [781], 'robust': [782, 1757], 'coexistence': [783, 916, 1281, 1759, 2743, 2950, 3908], 'implementing': [785], 'feedback': [788], 'loop': [789], 'balances': [791], 'disparities': [792], 'monospecies': [794, 826, 1099, 1678, 1799, 1867, 2190, 2664, 2715, 2785, 3106, 3309, 3749, 3942, 3959], 'fitness': [795, 2796, 2819, 3795], 'levels.': [796], 'could': [802, 1092, 1541], 'generate': [803, 1401], 'history-dependent': [804, 1772, 3004], 'initial': [807, 2100, 2676, 2893, 2967, 3030, 3054], 'proportions': [809, 2895, 2941, 2969, 3056], 'frequently': [811], 'do': [812], 'not': [813, 1093, 1291, 2825, 2982, 3329, 3520, 3609, 4142], 'originate': [814, 1461, 3659], 'bistability.': [816], 'Measurements': [817], 'extracellular': [819], 'metabolites': [820, 1486, 1812], 'illuminated': [821, 848], 'metabolic': [823, 1796], 'capabilities': [824, 1797], 'potential': [828, 2654], 'molecular': [829, 1276, 1349], 'basis': [830], 'In': [834, 2184, 2592, 3138, 4065], 'sum,': [835], 'these': [836, 1788, 1806, 1834, 2822, 2910, 3071, 3629, 3891, 4071, 4148], 'methods': [837], 'defined': [838, 1302], 'roles': [841, 922], 'human-associated': [844, 1905], 'intestinal': [845, 1906], 'design': [849, 2011, 2087, 3046], 'principles': [850, 913, 1563], 'communities.': [853, 1566, 3121], 'Synopsis': [854], 'Analysis': [855], 'shows': [866], 'dynamics.': [877], 'study': [879, 932, 2206], 'reveals': [880], 'drivers,': [882], 'metabolite': [883, 924, 1822, 3661], 'hub': [884], 'ecologically': [887, 3874], 'sensitive': [888], 'organisms': [889, 1240, 1716, 1829, 2823, 3049, 3886, 3911], 'A': [893, 1746, 2413, 2992, 3344, 3468], 'data-driven': [894], 'pipeline': [895, 1657], 'is': [896, 980, 1155, 1310, 1327, 1378, 1555, 1626, 2543, 2599, 3733, 3798, 3878], 'used': [897, 1574, 1593, 1609, 1683, 2204, 2640, 3380], 'construct': [899, 1659], 'predictive': [901, 1661, 3456], 'dynamic': [902, 1687, 1859, 2740, 2876, 3338, 3384, 3524], 'anaerobic': [907, 2402], 'Design': [912], 'stable': [915, 1280, 2949, 3085], 'history-dependence': [918], 'elucidated.': [920], 'profiles': [925, 1823], 'analyzed': [927], 'each': [929, 2513, 2525, 2756, 2798, 3139, 3724, 3771, 3814], 'organism.': [930], 'highlights': [933], 'challenges': [934], 'using': [936, 1802, 2046, 2067, 2094, 2113, 2136, 2146, 2180, 2404, 2569, 2672, 2697, 2916, 2965, 3042, 3052, 3565], 'phylogenetic': [937, 1952, 4145], 'exo-metabolomic': [939], '"signals"': [940], 'functions.': [947], 'Introduction': [948], 'Microbes': [949], 'have': [950, 1183, 1247, 1417, 1966], 'evolved': [951], 'occupy': [957], 'nearly': [958], 'every': [959, 2118, 2566], 'environment': [960], 'Earth,': [962], 'spanning': [963, 1888, 2028], 'extreme': [964], 'environments': [965, 1445], 'such': [966, 1063, 1213, 1446, 1850, 2476, 2577, 3393], 'acid': [968], 'mine': [969], 'drains': [970], 'hot': [972], 'springs': [973], 'multicellular': [975], 'organisms.': [976, 2871], 'dense': [982], 'collection': [983], 'microorganisms': [985], 'inhabits': [987], 'gastrointestinal': [990], 'tract': [991], '(Lozupone': [992], 'al,': [994, 998, 1002, 1018, 1031, 1035, 1141, 1145, 1150, 1175, 1207, 1252, 1345, 1478, 1519, 1550, 1962, 1984, 1988, 1992, 1996, 2000, 2004, 2060, 2239, 2245, 2255, 2266, 2277, 2286, 2296, 2304, 2312, 2323, 2334, 2351, 2362, 2369, 2376, 2386, 2551, 2555, 2590, 2626], '2012;': [995], 'Earle': [996, 1143], '2015;': [999, 1142, 1146], 'Tropini': [1000], '2017)': [1003], 'performs': [1005], 'numerous': [1006, 1742], 'functions': [1007, 1073], 'impact': [1009, 1528, 1730, 3678], 'physiology,': [1011], 'nutrition,': [1012], 'behavior,': [1013], 'development': [1015, 1366], '(Ley': [1016, 1173], '2005;': [1019], 'Fischbach': [1020], 'Sonnenburg,': [1022, 1296], '2011;': [1023, 1993, 2623], 'Foster': [1024], 'McVey': [1026], 'Neufeld,': [1027], '2013;': [1028, 1997, 2001, 2005], 'Louis': [1029], '2014;': [1032, 1036], 'Sharon': [1033], 'Rooks': [1037], 'Garrett,': [1039], '2016).': [1040, 1520, 1551, 2591], 'Functions': [1041], 'partitioned': [1047], 'among': [1048], 'genetically': [1049], 'distinct': [1050, 1124, 2966], 'populations': [1051], 'interact': [1053], 'perform': [1055], 'complex': [1056], 'chemical': [1057], 'transformations': [1058, 2358], 'exhibit': [1060, 1525], 'emergent': [1061], 'properties': [1062, 1613, 3392], 'colonization': [1065], 'resistance': [1066], 'at': [1067, 1127, 1569, 2106, 2434, 2504, 2571, 2891, 2942, 3028, 3176, 3195, 3247, 3864], 'level.': [1070], 'Such': [1071], 'collective': [1072], 'realized': [1075], 'combined': [1078, 2093, 3837], 'operating': [1084, 1223], 'multiple': [1086, 1330, 1979, 3885], 'time': [1087, 1204, 2482, 3040, 3117, 3141, 3956], 'spatial': [1089, 1104], 'scales': [1090], 'be': [1094, 1503, 1542, 1573, 1592, 1608, 1644, 3379, 3923], 'achieved': [1095], 'single': [1098, 3855], 'population.': [1100], 'degree': [1102, 3488], 'structuring': [1105], 'varies': [1110], 'across': [1111, 1245, 2758, 3903], 'length': [1112], 'scales:': [1113], 'At': [1114], 'macroscale': [1116], 'hundreds': [1118, 1158], 'micrometers,': [1120, 1131], 'bacteria': [1121], 'cluster': [1122], 'into': [1123, 2110, 2177, 2764, 2930], 'habitats,': [1125], 'whereas': [1126, 1734, 3682], 'scale': [1129, 2071], 'intermixing': [1132], 'members': [1135, 1736, 4117], 'has': [1136, 1362], 'been': [1137, 1184, 1248, 1418, 1967], 'observed': [1138], '(Donaldson': [1139], 'Mark': [1147], 'Welch': [1148], '2017).': [1151, 1346, 2627], 'composed': [1156, 1750, 3827], 'bacterial': [1160], 'species,': [1161, 1523, 3415], 'majority': [1163, 1770, 3506], 'which': [1165, 1524, 4024], 'span': [1166], 'Firmicutes,': [1168, 1286, 1893, 2039], 'Bacteroidetes,': [1169, 1892, 2038], 'Actinobacteria': [1171, 1289, 1738, 4121], 'phyla': [1172, 1285, 1891, 2031], '2006).': [1176], 'Constituent': [1177], 'strains': [1178, 2439], 'shown': [1185, 1419, 1968], 'persist': [1187], 'an': [1189, 1230, 1627, 1727, 2095, 2151, 2172, 2401, 2405, 2673, 2956, 3029, 3581, 3873, 3926], 'individual': [1190], 'over': [1191, 1203, 2459, 3955], 'long': [1192, 2441], 'periods': [1193], 'time,': [1195], 'demonstrating': [1196, 2860, 4096], '(Faith': [1205], '2013).': [1208], 'Perturbations': [1209], 'system': [1212, 1612, 1957, 3391], 'dietary': [1215], 'shifts': [1216], 'or': [1217, 1466, 1470, 1494, 2098, 2219, 2223, 2975, 3202, 3650, 3663, 3919, 3928, 4120, 4164], 'antibiotic': [1218], 'administration': [1219], 'can': [1220, 1460, 1482, 1502, 1572, 1591, 1607, 1643, 1842, 1853, 2466, 2584, 3378, 3643, 3658, 3922, 4104, 4155, 4172], 'shift': [1221], 'point': [1224, 3041], 'alternative': [1231], 'state': [1232, 1785, 2454, 3308, 3615], '(Relman,': [1233], '2012).': [1234, 1431, 1587, 3947], 'While': [1235], 'identities': [1237], 'co-occurrence': [1243], 'relationships': [1244], 'individuals': [1246], 'elucidated': [1249, 1801], '(Faust': [1250, 1584], '2012),': [1253], 'we': [1254, 1650, 3821], 'lack': [1255], 'quantitative': [1257, 2937], 'understanding': [1258, 1560], 'how': [1260], 'shape': [1263, 2583], 'assembly,': [1265], 'stability,': [1266], 'response': [1268, 1394], 'perturbations.': [1270], 'For': [1271], 'example,': [1272], 'enable': [1279], 'dominant': [1284], 'Bacteroidetes': [1287, 1725], 'well': [1292], 'understood': [1293], '(Fischbach': [1294], '2011).': [1297], 'resilience': [1299, 1357], 'microbiomes,': [1301], 'capacity': [1305], 'recover': [1307], 'perturbations,': [1309], 'strongly': [1311], 'linked': [1312], 'diversity.': [1315], 'Indeed,': [1316], 'reduction': [1318, 3929], 'diversity': [1321, 1953], 'associated': [1328], 'with': [1329, 1636, 2150, 2209, 2440, 3157, 3255, 3322, 3602, 3909, 3992, 4027, 4057], 'diseases,': [1331], 'suggesting': [1332, 3792], 'high-dimensional': [1335], 'functionally': [1337], 'heterogeneous': [1338], 'ecosystem': [1339], 'promotes': [1340], 'health': [1342, 1974], '(Sommer': [1343], 'Understanding': [1347], 'factors': [1352], 'influencing': [1353, 1878], 'implications': [1363], 'targeted': [1368], 'interventions': [1369], 'modulate': [1371], 'states.': [1373], 'Central': [1374], 'problem': [1377], 'inferring': [1379], 'unknown': [1380], 'developing': [1384], 'tools': [1385, 1602], 'temporal': [1388, 1596, 1864, 2470, 2499, 3510], 'changes': [1389, 1597, 2792, 3182], 'behaviors': [1392, 1516, 1580, 1865, 2741, 2927, 3015, 3385, 3525], 'environmental': [1396], 'stimuli.': [1397], 'Cooperation': [1398], 'competition': [1400, 1436, 1463], 'feedbacks': [1405], 'influence': [1410, 1514, 2585], 'functional': [1411, 1950], 'activities': [1412], 'stability.': [1414], 'Negative': [1415, 3641], 'dominate': [1421], 'inter-relationships': [1423], 'aquatic': [1426], 'microcosms': [1427], '(Foster': [1428, 3944], 'Bell,': [1430, 3946], 'However,': [1432, 1820, 3516, 4136], 'prevalence': [1434, 3994], 'cooperation': [1438], 'occupying': [1442], 'other': [1443, 2977, 3000, 3910], 'remains': [1452], 'elusive.': [1453], 'Direct': [1454], 'resources': [1465], 'space,': [1467], 'biomolecular': [1468, 3648], 'warfare,': [1469, 3649], 'production': [1471, 3651], 'toxic': [1473, 3653], 'waste': [1474, 3654], 'products': [1475], '(Hibbing': [1476], '2010).': [1479, 1622, 1963], 'Positive': [1480, 3656], 'stem': [1483], 'secreted': [1485], 'utilized': [1489], 'member': [1493], 'detoxification': [1495, 3664], 'environment.': [1498, 3667], 'Pairwise': [1499, 2733, 3697], 'modified': [1504, 2827], 'third': [1507], 'organism,': [1508], 'leading': [1509], 'effects': [1512], '(Bairey': [1517], 'driver': [1522, 1712], 'large': [1527, 3690], 'structure': [1531, 2503, 3027], 'function,': [1533], 'represent': [1534, 1843, 3169, 3229, 3240, 3298, 3411, 3522], 'key': [1535, 1557], 'nodes': [1536], 'manipulated': [1543], 'control': [1545], 'states': [1547], '(Gibson': [1548], 'Predicting': [1552], 'dynamics': [1554, 1667], 'step': [1558], 'toward': [1559], 'organizational': [1562], 'Computational': [1567], 'models': [1568, 1590], 'different': [1570, 2505, 2892, 2972, 3053], 'resolutions': [1571], 'analyze': [1576, 1611, 3390], 'Raes,': [1586], 'Dynamic': [1588], 'computational': [1589, 1662, 1688, 3339], 'investigate': [1595], 'structure,': [1600], 'dynamical': [1604], 'systems': [1605], 'theory': [1606], 'parameter': [1617, 3397, 3432, 3443], 'sensitivity': [1618], '(Astrom': [1619], 'Murray,': [1621], 'Generalized': [1623], 'Lotka–Volterra': [1624, 3100, 3365], '(gLV)': [1625, 3101, 3366], 'ordinary': [1628, 3740], 'differential': [1629, 3741], 'equation': [1630], 'represents': [1633, 2073, 3368, 3872], 'limited': [1638], 'number': [1639, 2075, 2531, 3413, 3691], 'parameters': [1641, 3352], 'deduced': [1645], 'time-series': [1647, 3354], 'data.': [1648, 3556], 'Here,': [1649], 'develop': [1651], 'systematic': [1653], 'modeling': [1654, 3346], 'experimental': [1656, 2086, 2918, 3045, 3230], 'interrogate': [1669], 'mediating': [1672], 'assembly.': [1674, 1832], 'Time-resolved': [1675], 'assemblages': [1681, 1870, 2394, 3109, 3193], 'train': [1685], 'revealed': [1700], 'Specific': [1710], 'context': [1719], 'identified': [1721], 'exhibited': [1726, 1756, 2735, 3580, 3897, 4014, 4094, 4122], 'overall': [1728], 'community,': [1733], 'specific': [1735, 1827, 2870], 'Firmicutes': [1740, 4138], 'displayed': [1741, 2716, 2809, 2838, 3002, 3083, 3147, 3674, 4084], 'outgoing': [1744, 3755, 4126], 'sub-network': [1749], 'variations': [1761, 2500, 3009], 'parameters.': [1764], 'showed': [1767, 3969, 4115], 'due': [1778], 'slow': [1780], 'convergence': [1781], 'steady': [1784, 2453, 3307, 3614], 'composition': [1786, 2455, 2694, 3802], 'networks': [1789, 3698], 'enriched': [1791, 3700], 'exo-metabolomics': [1803], 'profiling,': [1804], 'data': [1807, 3133, 4149], 'pinpointed': [1808], 'set': [1810, 2882, 3190, 3528, 3737, 3838], 'predicted': [1813], 'mediate': [1815], 'failed': [1824], 'forecast': [1826], 'influential': [1828], 'modulating': [1830], 'Together,': [1833, 3070, 4147], 'results': [1835, 3072, 3968], 'combinations': [1838], 'couplings': [1852, 3717], 'realize': [1854], 'repertoire': [1857], 'behaviors.': [1860], 'Results': [1861], 'Probing': [1862], 'aimed': [1872], 'dissect': [1874], 'reduced': [1883], 'complexity': [1884], 'Actinobacteria,': [1894, 2037], 'Proteobacteria.': [1896, 2041], 'To': [1897, 2656, 2872, 3315, 3424, 3809], 'end,': [1899], 'ecology': [1902, 2027], 'encompassing': [1903], 'Bacteroides': [1908, 1911, 1914, 1917, 2247, 2257, 2268, 2279, 2806, 3668, 3998, 4119], 'thetaiotaomicron': [1909, 2280], '(BT),': [1910], 'ovatus': [1912, 2269], '(BO),': [1913], 'uniformis': [1915, 2258], '(BU),': [1916], 'vulgatus': [1918, 2248], '(BV),': [1919], 'Blautia': [1920, 2314], 'hydrogenotrophica': [1921, 2315], '(BH),': [1922], 'Collinsella': [1923, 2336], 'aerofaciens': [1924, 2337], '(CA),': [1925], 'Clostridium': [1926, 2388], 'hiranonis': [1927, 2389], '(CH),': [1928], 'Desulfovibrio': [1929, 2378], 'piger': [1930, 2379], '(DP),': [1931], 'Eggerthella': [1932, 2353], 'lenta': [1933, 2354], '(EL),': [1934], 'Eubacterium': [1935, 2325], 'rectale': [1936, 2326], '(ER),': [1937], 'Faecalibacterium': [1938, 2288], 'prausnitzii': [1939, 2289], '(FP),': [1940], 'Prevotella': [1942, 2229], 'copri': [1943, 2230], '(PC)': [1944, 2231], 'designed': [1946], 'mirror': [1948], 'natural': [1956], '(Fig': [1958, 2483, 2886, 3512, 3639, 4034], '1A;': [1959], 'Qin': [1960], 'These': [1964], 'contribute': [1970], 'significantly': [1971, 2826, 2864, 3879, 4015, 4053], 'implicated': [1977], 'diseases': [1981, 2211], '(Watterlot': [1982, 2294], '2008;': [1985], 'Larsen': [1986], '2010;': [1989], 'Thota': [1990], 'Fujimoto': [1994], 'Haiser': [1998], 'Scher': [2002], 'Table': [2006, 2199, 2201], '1).': [2007], 'Figure': [2008, 3094], '1.': [2009, 2200], 'Experimental': [2010, 3122], 'high-throughput': [2013], 'characterization': [2014], 'Phylogenetic': [2021, 2042], 'tree': [2022], '12-member': [2025], 'analysis': [2043, 3779], 'performed': [2045, 2162, 2491, 2671], 'concatenated': [2048], 'alignment': [2049], 'single-copy': [2051], 'marker': [2052], 'genes': [2053], 'obtained': [2054], 'via': [2055], 'PhyloSift': [2056], '(preprint:': [2057], 'Darling': [2058], '2014).': [2061], 'Maximum': [2062], 'likelihood': [2063], 'trees': [2064], 'generated': [2066], 'default': [2068], 'options.': [2069], 'bar': [2072, 2155], 'substitutions': [2077], 'per': [2078, 2534], 'site': [2079], 'alignment.': [2082], 'Schematic': [2083], 'study.': [2090], 'Species': [2091, 2227, 3110], 'approximately': [2096, 2164, 2493, 2565, 2674, 3075], '1:1': [2097, 2675], '19:1': [2099], 'based': [2102, 2212, 2645, 2679, 2896, 2934, 3024, 3127, 3209, 3454, 3543, 3618, 3986, 4060], 'absorbance': [2104, 2570], '600': [2107, 2572], 'nm': [2108, 2573], '(OD600)': [2109, 3954], 'microtiter': [2111, 2398], 'plates': [2112, 2399], 'liquid-handling': [2114, 2407], 'robotic': [2115], 'manipulation.': [2116], 'Approximately': [2117], '12': [2119], 'h,': [2120], 'samples': [2121], 'collected': [2123], 'multiplexed': [2125, 2137, 2704], '16S': [2126, 2138, 2486, 2705], 'rRNA': [2127, 2139, 2487, 2706], 'gene': [2128, 2140, 2488, 2707], 'sequencing': [2129, 2141, 2489], '(black': [2130], 'circles).': [2131], 'Relative': [2132], 'abundance': [2133, 2511, 2547, 2634, 2644, 2677, 2754, 2780, 2957, 2987, 3112, 3145, 3186, 3216, 3310, 3358, 3617, 3849, 3863, 3902], 'measured': [2135, 2696], 'V3–V4': [2144], 'region': [2145], 'dual-indexed': [2147], 'primers': [2148], 'compatible': [2149], 'Illumina': [2152], 'platform': [2153], '(stacked': [2154], 'plot,': [2156], 'bottom': [2157], 'right).': [2158], 'Serial': [2159], 'transfers': [2160, 2465], '24': [2165], 'intervals': [2166, 2436, 2495], '(purple': [2167], 'bars,': [2168], 'top)': [2169], 'transferring': [2171], 'aliquot': [2173], 'fresh': [2178], 'media': [2179, 2415], '1:20': [2182], 'dilution.': [2183], 'parallel,': [2185], 'OD600': [2187, 2586, 2637, 2647, 2681, 2698, 2787, 2898, 3211], 'performed.': [2194], 'Download': [2195, 2197, 3331, 3333], 'figure': [2196, 3332], 'PowerPoint': [2198, 3334], 'associations': [2208], 'previous': [2214], 'literature.': [2215], 'Arrows': [2216], 'pointing': [2217], 'up': [2218], 'down': [2220], 'denote': [2221, 3155, 3253, 3280], 'associations,': [2225], 'respectively': [2226, 2709, 3090, 3638], 'Association(s)': [2228], 'Inflammatory': [2232], 'autoimmune': [2234], 'disease': [2235, 2292, 2300, 2307, 2365], '(↑)': [2236, 2252, 2274, 2320, 2331, 2348, 2359, 2366, 2373, 2383], '(Scher': [2237], '2013),': [2240, 2363], 'autism': [2241, 2382], '(↓)': [2242, 2262, 2293, 2301, 2308, 2341], '(Kang': [2243], '2013)': [2246], '(BV)': [2249], 'Ulcerative': [2250, 2282], 'colitis': [2251, 2283], '(Bamba': [2253], '1995)': [2256], '(BU)': [2259], 'Metabolic/immunological': [2260], 'dysfunction': [2261], '(Gauffin': [2263], 'Cano': [2264], '2012)': [2267, 2324, 2387], '(BO)': [2270], 'Type': [2271, 2328], 'I': [2272], 'diabetes': [2273, 2330], '(Giongo': [2275], '2011)': [2278, 2287], '(BT)': [2281], '(↑)(Bloom': [2284], '(FP)': [2290], "Crohn's": [2291, 2364], '2008),': [2297], 'inflammatory': [2298], 'bowel': [2299], '(Segain': [2302], '2000),': [2305], 'Celiac': [2306], '(De': [2309], 'Palma': [2310], '2010)': [2313, 2335], '(BH)': [2316], 'Healthy': [2317], 'colon': [2319], '(Nava': [2321], '(ER)': [2327], 'II': [2329], '(Larsen': [2332], '(CA)': [2338], 'Colon': [2339], 'cancer': [2340], '(Moore': [2342], 'Moore,': [2344], '1995),': [2345], 'rheumatoid': [2346, 2371], 'arthritis': [2347, 2372], '(Chen': [2349, 2374], '2016)': [2352, 2377], '(EL)': [2355], 'Cardiac': [2356], 'drug': [2357], '(Haiser': [2360], '(Thota': [2367], '2011),': [2370], '(DP)': [2380], 'Regressive': [2381], '(Finegold': [2384], '(CH)': [2390], 'None': [2391], 'reported': [2392], 'Synthetic': [2393], 'arrayed': [2396], 'chamber': [2403], 'automated': [2406], 'procedure': [2408], '(see': [2409, 2416, 2536, 2710, 3445, 3760], 'Materials': [2410, 2417, 2537, 2711, 3446, 3761], 'Methods).': [2412, 2539, 2713, 3448, 3763], 'rich': [2414], 'Methods)': [2419], 'selected': [2421, 3189], 'support': [2423], 'growth': [2425, 2507, 2606, 2614, 2691, 2721, 2737, 2767, 2862, 3416, 3622, 3750], 'all': [2427, 2663, 3119], 'monospecies.': [2428], 'serially': [2432], 'transferred': [2433], '24-h': [2435], 'prevent': [2438], 'lag': [2442, 2726], 'phases': [2443, 2727], 'being': [2445], 'eliminated': [2446], 'allow': [2448], 'approach': [2451], 'monitoring': [2457], 'many': [2460], 'cell': [2461, 2579, 2602], 'generations.': [2462], 'Further,': [2463], 'serial': [2464], 'also': [2467], 'reflect': [2468, 4143], 'recurrent': [2469], 'perturbations': [2471], 'diet': [2478], 'colonic': [2480], 'transit': [2481], '1B).': [2484], 'Multiplexed': [2485], '12-h': [2494], 'elucidate': [2497], 'stages.': [2508], 'relative': [2510, 2791, 2986, 3111, 3144, 3185, 3215, 3357], 'computed': [2516, 3949], 'sum': [2519, 3159, 3257, 3940], 'read': [2522], 'counts': [2523], 'organism': [2526, 2774, 2799, 3772, 3876], 'divided': [2527], 'total': [2530, 2558, 2701, 3360], 'reads': [2533], 'condition': [2535], 'Since': [2540], 'construction': [2542], 'aided': [2544], 'absolute': [2546, 2633, 2643, 2753, 3901], 'information': [2548], '(Bucci': [2549], '2016;': [2552], 'Widder': [2553], '2016),': [2556], 'biomass': [2559, 2702, 3361, 3953], 'monitored': [2564], '30': [2567], 'min': [2568], '(OD600).': [2574, 3362], 'Cellular': [2575], 'traits': [2576], 'adhesion,': [2580, 2603], 'size,': [2581], '(Stevenson': [2588], 'addition,': [2593], 'counting': [2594], 'colony-forming': [2596], 'units': [2597], '(CFU)': [2598], 'biased': [2600], 'dormant': [2604], 'sub-populations,': [2605], 'selection': [2607], 'solid': [2609], 'vs.': [2610], 'liquid': [2611], 'media,': [2612], 'stage': [2615], '(Jansson': [2616], 'Prosser,': [2618], '1997;': [2619], 'Volkmer': [2620], 'Heinemann,': [2622], 'Ou': [2624], 'trained': [2631, 3273, 3501], 'estimated': [2635], 'thus': [2649], 'automatically': [2650], 'accounts': [2651], 'any': [2653], 'biases.': [2655], 'infer': [2657, 3351], 'interactions,': [2659, 3318, 3372, 3630, 3753, 3791], '(66': [2668], 'combinations)': [2669], 'ratio': [2678], 'values': [2682, 2899, 3444, 3473], '(PW1': [2683], 'dataset,': [2684, 2729, 2921], 'Appendix': [2685, 2730, 2922, 3067], 'Fig': [2686, 2731, 2748, 2776, 2833, 2923, 3068, 3092, 3495, 3695, 3719, 3807, 3868, 3965, 4132], 'S1,': [2687], 'Dataset': [2688, 2888], 'EV1).': [2689], 'Monospecies': [2690], 'sequencing,': [2708], 'broad': [2718], 'range': [2719, 3469], 'rates,': [2722, 3417, 3751], 'carrying': [2723], 'capacities': [2724], '(M': [2728], 'S2).': [2732], 'single-species': [2745, 2946], 'dominance': [2746], '(Appendix': [2747, 2775, 2832, 3091, 3494, 3694, 3718, 3806, 3867, 3912, 3964, 4131], 'S1).': [2749], 'distribution': [2751, 2848], 'PW1': [2761, 3904], 'provided': [2762], 'insight': [2763], 'variability': [2765, 3899], 'presence': [2770, 2802, 2868, 3883], 'second': [2773, 2804, 2830, 2908], 'S3A).': [2777], 'Absolute': [2778], 'normalized': [2782], 'maximum': [2786], 'value': [2788, 3567], 'evaluate': [2790, 3958], 'baseline': [2795], 'species.': [2805], 'CH': [2808, 3686], 'lowest': [2811], 'coefficient': [2812, 3305, 3472, 3593, 3626], 'variation': [2814], '(CV),': [2815], 'indicating': [2816], 'levels': [2820], 'S3B).': [2834], 'remaining': [2836, 3018], 'bimodal': [2840], '(FP,': [2841], 'DP,': [2842], 'PC,': [2843, 3534, 3541], 'BH,': [2844, 2856, 3532, 3684, 3830], 'CA),': [2846], 'long-tail': [2847], '(ER': [2849], 'EL),': [2851], 'and/or': [2852], 'CV': [2854], '(ER,': [2855], 'PC),': [2859], 'altered': [2865], 'further': [2873], 'probe': [2874], 'consortia,': [2880], '15': [2884], '2B,': [2887], 'EV2)': [2889], 'inoculated': [2890, 2964, 3051, 3194], '(95%': [2900, 3057], 'A,': [2902, 3059, 3198, 3205], '5%': [2903, 3060, 3196, 3206], 'B,': [2905, 3062], 'wherein': [2909, 2951, 3047], 'percentages': [2911], 'reversed)': [2913], 'characterized': [2915], 'our': [2917], 'workflow': [2919], '(PW2': [2920], 'S4).': [2924], 'classified': [2929, 2997, 3023], 'following': [2932], 'categories': [2933], 'threshold': [2938, 3546], '72': [2943, 3038, 3865], 'h:': [2944], '(i)': [2945], 'dominance;': [2947], '(ii)': [2948], 'both': [2952, 4098], 'persisted': [2954], 'above': [2955], 'threshold;': [2958], '(iii)': [2959], 'history': [2960, 3088], 'dependence': [2961], 'whereby': [2962, 3575], 'mapped': [2970], 'structures;': [2974], '(iv)': [2976], 'did': [2981, 3519, 4141], 'quantitatively': [2983], 'satisfy': [2984], 'thresholds': [2988, 3594], 'cases': [2990], '1–3.': [2991], 'subset': [2993], 'category': [3001], 'weak': [3003], 'potentially': [3006], 'attributed': [3007], 'biological': [3011, 3179, 3250], 'replicates.': [3012, 3180, 3251], 'qualitative': [3014], '51': [3019], '(t': [3031, 3036], '=': [3032, 3037, 3312], '0)': [3033, 3284, 3289], 'final': [3035], 'h)': [3039], 'PW2': [3044], 'reciprocal': [3065], 'percentages,': [3066], 'S5A).': [3069], '50,': [3076], '24,': [3077], '12%': [3079], 'dominance,': [3084], 'coexistence,': [3086], 'dependence,': [3089], 'S5B).': [3093, 3916], '2.': [3095], 'Model': [3096], 'training': [3097, 3450, 3485], 'generalized': [3099, 3364], 'function': [3115, 3746], 'fits': [3126, 3234], 'T3': [3129, 3503], 'represented': [3131, 3218], 'points': [3134, 3226], 'lines,': [3136], 'respectively.': [3137, 3153, 3224, 3237, 3314, 3423], 'subplot,': [3140], 'x-': [3150, 3221], 'y-axis,': [3152, 3223], 'Stars': [3154, 3252], 'datasets': [3156, 3254], 'mean': [3161, 3174, 3245, 3259, 3549], 'squared': [3162, 3260, 3550], 'errors': [3163, 3261], 'greater': [3164, 3262], 'than': [3165, 3263, 3326, 3606, 3852, 3980], '0.15.': [3166, 3264], 'Error': [3167, 3238], 'bars': [3168, 3239], '1': [3170, 3241], 's.d.': [3171, 3242], 'least': [3177, 3248], 'three': [3178, 3249], 'Temporal': [3181], '95%': [3199, 3203], 'B': [3201, 3208], 'values.': [3212, 3627], 'Time': [3213], 'Data': [3225], 'lines': [3228], 'T3,': [3236], 'Inferred': [3265], 'inter-species': [3266, 3303, 3319, 3375, 3420, 3562, 3758, 3842, 3858], 'coefficients': [3268, 3321, 3564, 3601, 4114], 'gLV': [3271, 3499, 3782, 3825, 4112], 'T3.': [3275], 'Gray': [3276], 'green': [3278], 'edges': [3279], '(αij': [3282, 3287], '<': [3283], '>': [3288], 'coefficients.': [3291], 'edge': [3293], 'width': [3294], 'node': [3296], 'size': [3297], 'magnitude': [3300, 3324, 3440, 3559, 3604], '(xe': [3311], '−μiαii−1),': [3313], 'highlight': [3316], 'significant': [3317, 3898], 'less': [3325, 3605, 3979], '1e-5': [3327, 3569], 'displayed.': [3330], 'Construction': [3335], 'growth,': [3370], 'intra-species': [3371, 3752], 'sensitivity.': [3398], 'equations': [3401, 3742], 'given': [3403], 'by:': [3404], 'where': [3405], 'n,': [3406], 'μ,': [3407], 'αii,': [3408], 'αij': [3410], 'intra-species,': [3418], 'coefficients,': [3422], 'minimize': [3425], 'overfitting': [3426], 'data,': [3429], 'regularized': [3431], 'estimation': [3433], 'implemented': [3436], 'penalized': [3438], 'Three': [3449], 'sets': [3451, 3486], 'evaluated': [3453], 'capability:': [3457], '(T1)': [3458], 'M;': [3459], '(T2)': [3460], 'M,': [3461, 3465], 'PW1;': [3462], '(T3)': [3464], 'PW1,': [3466], 'PW2.': [3467], 'regularization': [3471], '(λ)': [3474], 'scanned': [3476], 'balance': [3478], 'goodness': [3480], 'fit': [3482], 'sparsity': [3490], 'S6).': [3496], 'parameterized': [3498], 'captured': [3504], '2A': [3513], 'B).': [3515, 4135], 'accurately': [3521], 'EL;': [3533], 'CA;': [3535], 'BO,': [3536], 'CH;': [3537], 'ER,': [3538], 'BH;': [3539, 4040], 'BH': [3542, 4093, 4161], 'error': [3551], 'between': [3552, 3587], 'Thresholding': [3557], 'yielded': [3570], 'densely': [3572], 'connected': [3573], '77%': [3576], 'pairs': [3579], 'interaction.': [3582], 'connectivity': [3585], 'varied': [3586], '75': [3588], '79%': [3590], 'ranging': [3595], '1e-6': [3597], '1e-3.': [3599], 'Interaction': [3600], '1e-3': [3607], 'expected': [3610], 'change': [3612], 'rate': [3623], 'Of': [3628], '56': [3631], '21%': [3633], 'positive,': [3637], '2C).': [3640, 4035], 'arise': [3644], 'resource': [3646], 'competition,': [3647], 'by-products.': [3655], 'secretion': [3662], '(BO,': [3669], 'BV,': [3670, 3832, 4001, 4003], 'BU,': [3671, 3831, 4007], 'BT)': [3673], 'net': [3676], 'network,': [3681, 4068], 'EL,': [3683, 4039, 4041, 4043, 4045, 4047, 4075, 4077, 4079, 4092], 'positively': [3687], 'stimulated': [3688], 'S7A).': [3696, 3808], 'unidirectional': [3702, 4099], '(−/0,': [3704], '36%),': [3705], 'bidirectional': [3706, 4101], '(−/−,': [3708], '32%),': [3709], '(+/−,': [3714], '26%)': [3715], 'S7B).': [3720], 'contribution': [3722, 3812], 'full': [3727], 'dictated': [3734], 'coupled': [3739, 3799, 4085], 'incoming': [3757, 3815, 4128], 'Therefore,': [3764, 3870], 'prediction': [3766], 'about': [3767], 'role': [3769], 'requires': [3776], 'simulation': [3777], 'model.': [3783, 4064], 'FP': [3784, 3797, 3819, 3848, 3862, 3871, 3896], 'five': [3789, 3840, 4069], 'determine': [3810], 'abundance,': [3820], 'examined': [3822], '6-member': [3824], 'FP,': [3829], 'CH,': [3833, 4050, 4082], 'DP.': [3835], 'required': [3845], 'alter': [3847], 'twofold,': [3853], 'dual': [3857], 'moderately': [3860], 'increased': [3861], 'h': [3866], 'S7C).': [3869], 'enhanced': [3880, 4054], 'conditions.': [3892], 'Corroborating': [3893], 'notion,': [3895], 'Figs': [3913], 'S3': [3914], 'Strong': [3917], 'deciphered': [3924], 'enhancement': [3927], 'productivity': [3932], 'compared': [3933, 3982, 4019], 'null': [3936, 3989, 4022, 4063], 'representing': [3938], 'productivities': [3943, 3963, 3972, 4018, 4037], 'integral': [3951], 'S8).': [3966], '38%': [3974], 'twofold': [3981], 'predictions': [3985, 4059], 'models,': [3990], 'consistent': [3991, 4026], 'BU;': [4002, 4006, 4042, 4074], 'BO;': [4004, 4008, 4046, 4078], 'BT,': [4005, 4009, 4012], 'BV;': [4010, 4048, 4080], 'BO': [4013], 'lower': [4016], 'model,': [4023], 'mutual': [4030], 'inhibitory': [4031], 'topologies': [4033, 4090], 'BT;': [4044, 4076], 'ER': [4051], 'comparison': [4056], '(EL,': [4073], 'ER)': [4083], 'mutualism,': [4095], 'augment': [4105], 'productivity.': [4107], 'Hierarchical': [4108], 'clustering': [4109, 4139], 'similar': [4123, 4157], 'patterns': [4124], 'S9A': [4133], 'pattern': [4140], 'relationships.': [4146], 'distantly': [4152], 'related': [4153, 4170], 'display': [4156], '(e.g.,': [4160], 'DP': [4163], 'PC': [4165], 'CA)': [4167], 'closely': [4169], 'exhi': [4173]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2773368689', 'counts_by_year': [{'year': 2024, 'cited_by_count': 64}, {'year': 2023, 'cited_by_count': 73}, {'year': 2022, 'cited_by_count': 74}, {'year': 2021, 'cited_by_count': 83}, {'year': 2020, 'cited_by_count': 51}, {'year': 2019, 'cited_by_count': 55}, {'year': 2018, 'cited_by_count': 17}, {'year': 2017, 'cited_by_count': 2}], 'updated_date': '2024-12-18T20:09:55.826784', 'created_date': '2017-12-22'}
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